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31 results on '"Jiang, Huaiyang"'

1. Gene variants identified by whole-exome sequencing in 33 French women with premature ovarian insufficiency.

Author: Yang, Xiang, Yang, Xiang, Touraine, Philippe, Desai, Swapna, Humphreys, Gregory, Jiang, Huaiyang, Yatsenko, Alexander, Rajkovic, Aleksandar, Yang, Xiang, Yang, Xiang, Touraine, Philippe, Desai, Swapna, Humphreys, Gregory, Jiang, Huaiyang, Yatsenko, Alexander, and Rajkovic, Aleksandar
Abstract: PurposeTo investigate the potential genetic etiology of premature ovarian insufficiency (POI).MethodsWhole-exome sequencing (WES) was done on DNA samples from women diagnosed with POI. Mutations identified were analyzed by in silico tools and were annotated according to the guidelines of the American College of Medical Genetics and Genomics. Plausible variants were confirmed by Sanger sequencing.ResultsFour of the 33 individuals (12%) carried pathogenic or likely pathogenic variants, and 6 individuals carried variants of unknown significance. The genes identified with pathogenic or likely pathogenic variants included PMM2, MCM9, and PSMC3IP.ConclusionsWES is an efficient tool for identifying gene variants in POI women; however, interpretation of variants is hampered by few exome studies involving ovarian disorders and the need for trio sequencing to determine inheritance and to detect de novo variants.
Published: 2019

2. X-linked ADGRG2 mutation and obstructive azoospermia in a large Pakistani family.

Author: Khan, Muhammad Jaseem, Khan, Muhammad Jaseem, Pollock, Nijole, Jiang, Huaiyang, Castro, Carlos, Nazli, Rubina, Ahmed, Jawad, Basit, Sulman, Rajkovic, Aleksandar, Yatsenko, Alexander N, Khan, Muhammad Jaseem, Khan, Muhammad Jaseem, Pollock, Nijole, Jiang, Huaiyang, Castro, Carlos, Nazli, Rubina, Ahmed, Jawad, Basit, Sulman, Rajkovic, Aleksandar, and Yatsenko, Alexander N
Abstract: We performed whole exome sequencing to identify an unknown genetic cause of azoospermia and male infertility in a large Pakistani family. Three infertile males were subjected to semen analysis, hormone testing, testicular histology, ultrasonography, karyotyping, Y-chromosome microdeletion and CFTR testing. The clinical testing suggested a diagnosis of obstructive azoospermia (OA). To identify the cause, we performed whole exome sequencing (WES) for 2 infertile brothers and 2 fertile family members. For segregation analysis and variant confirmation, we performed Sanger sequencing. WES data analysis of the family revealed segregated variants in 3 candidate genes. We considered novel nonsense variant c.2440C > T(p.Arg814*) in X-linked gene ADGRG2 as biologically most plausible. It is predicted to truncate the protein by 204 amino acids (aa) at a key transmembrane domain. Adgrg2-knockout male mice show sperm loss due to obstructive fluid stasis, while ADGRG2 mutations cause OA in the infertile male patients. Our analysis of testicular histology reveals secondary severe reduction of spermatogenesis, consistent with human and knockout mouse phenotypes. The ADGRG2 nonsense mutation is absent in the largest population databases, ExAC and gnomAD. Analysis of the novel nonsense mutation in extended family members confirmed co-segregation of the mutation with OA in all affected males. The likely pathogenic nature of the mutation is supported by its truncation effect on the transmembrane domain and distinctive ultrasound results. The study demonstrates effectiveness of WES in discovering a genetic cause of azoospermia.
Published: 2018

3. Functional study of a novel missense single-nucleotide variant of NUP107 in two daughters of Mexican origin with premature ovarian insufficiency.

Author: Ren, Yu, Ren, Yu, Diao, Feiyang, Katari, Sunita, Yatsenko, Svetlana, Jiang, Huaiyang, Wood-Trageser, Michelle A, Rajkovic, Aleksandar, Ren, Yu, Ren, Yu, Diao, Feiyang, Katari, Sunita, Yatsenko, Svetlana, Jiang, Huaiyang, Wood-Trageser, Michelle A, and Rajkovic, Aleksandar
Abstract: BackgroundHypergonadotropic hypogonadism (HH) is a genetically heterogeneous disorder that usually presents with amenorrhea, atrophic ovaries, and low estrogen. Most cases of HH are idiopathic and nonsyndromic. Nucleoporin 107 (NUP107), a protein involved in transport between cytoplasm and nucleus with putative roles in meiosis/mitosis progression, was recently implicated as a cause of HH. We identified a NUP107 genetic variant in a nonconsanguineous family with two sisters affected with primary amenorrhea and HH, and generated a mouse model that carried the human variant.MethodsWe performed a high-resolution X-chromosome microarray and whole exome sequencing on parents and two sisters with HH to identify pathogenic variants. We generated a mouse model of candidate NUP107 variant using CRISPR/Cas9.ResultsWhole exome sequencing identified a novel and rare missense variant in the NUP107 gene (c.1063C>T, p.R355C) in both sisters with HH. In order to determine functional significance of this variant, we used CRISPR/Cas9 to introduce the human variant into the mouse genome. Mice with the homolog of the R355C variant, as well as the nine base pairs deletion in Nup107 had female subfertility.ConclusionsOur findings indicate that NUP107 R355C variant falls in the category of variant of unknown significance as the cause of HH and infertility.
Published: 2018

4. Functional study of a novel missense single-nucleotide variant of NUP107 in two daughters of Mexican origin with premature ovarian insufficiency.

Author: Ren, Yu, Ren, Yu, Diao, Feiyang, Katari, Sunita, Yatsenko, Svetlana, Jiang, Huaiyang, Wood-Trageser, Michelle A, Rajkovic, Aleksandar, Ren, Yu, Ren, Yu, Diao, Feiyang, Katari, Sunita, Yatsenko, Svetlana, Jiang, Huaiyang, Wood-Trageser, Michelle A, and Rajkovic, Aleksandar
Abstract: BackgroundHypergonadotropic hypogonadism (HH) is a genetically heterogeneous disorder that usually presents with amenorrhea, atrophic ovaries, and low estrogen. Most cases of HH are idiopathic and nonsyndromic. Nucleoporin 107 (NUP107), a protein involved in transport between cytoplasm and nucleus with putative roles in meiosis/mitosis progression, was recently implicated as a cause of HH. We identified a NUP107 genetic variant in a nonconsanguineous family with two sisters affected with primary amenorrhea and HH, and generated a mouse model that carried the human variant.MethodsWe performed a high-resolution X-chromosome microarray and whole exome sequencing on parents and two sisters with HH to identify pathogenic variants. We generated a mouse model of candidate NUP107 variant using CRISPR/Cas9.ResultsWhole exome sequencing identified a novel and rare missense variant in the NUP107 gene (c.1063C>T, p.R355C) in both sisters with HH. In order to determine functional significance of this variant, we used CRISPR/Cas9 to introduce the human variant into the mouse genome. Mice with the homolog of the R355C variant, as well as the nine base pairs deletion in Nup107 had female subfertility.ConclusionsOur findings indicate that NUP107 R355C variant falls in the category of variant of unknown significance as the cause of HH and infertility.
Published: 2018

5. X-linked ADGRG2 mutation and obstructive azoospermia in a large Pakistani family.

Author: Khan, Muhammad Jaseem, Khan, Muhammad Jaseem, Pollock, Nijole, Jiang, Huaiyang, Castro, Carlos, Nazli, Rubina, Ahmed, Jawad, Basit, Sulman, Rajkovic, Aleksandar, Yatsenko, Alexander N, Khan, Muhammad Jaseem, Khan, Muhammad Jaseem, Pollock, Nijole, Jiang, Huaiyang, Castro, Carlos, Nazli, Rubina, Ahmed, Jawad, Basit, Sulman, Rajkovic, Aleksandar, and Yatsenko, Alexander N
Abstract: We performed whole exome sequencing to identify an unknown genetic cause of azoospermia and male infertility in a large Pakistani family. Three infertile males were subjected to semen analysis, hormone testing, testicular histology, ultrasonography, karyotyping, Y-chromosome microdeletion and CFTR testing. The clinical testing suggested a diagnosis of obstructive azoospermia (OA). To identify the cause, we performed whole exome sequencing (WES) for 2 infertile brothers and 2 fertile family members. For segregation analysis and variant confirmation, we performed Sanger sequencing. WES data analysis of the family revealed segregated variants in 3 candidate genes. We considered novel nonsense variant c.2440C > T(p.Arg814*) in X-linked gene ADGRG2 as biologically most plausible. It is predicted to truncate the protein by 204 amino acids (aa) at a key transmembrane domain. Adgrg2-knockout male mice show sperm loss due to obstructive fluid stasis, while ADGRG2 mutations cause OA in the infertile male patients. Our analysis of testicular histology reveals secondary severe reduction of spermatogenesis, consistent with human and knockout mouse phenotypes. The ADGRG2 nonsense mutation is absent in the largest population databases, ExAC and gnomAD. Analysis of the novel nonsense mutation in extended family members confirmed co-segregation of the mutation with OA in all affected males. The likely pathogenic nature of the mutation is supported by its truncation effect on the transmembrane domain and distinctive ultrasound results. The study demonstrates effectiveness of WES in discovering a genetic cause of azoospermia.
Published: 2018

6. Exome sequencing reveals MCM8 mutation underlies ovarian failure and chromosomal instability.

Author: AlAsiri, Saleh, AlAsiri, Saleh, Basit, Sulman, Wood-Trageser, Michelle A, Yatsenko, Svetlana A, Jeffries, Elizabeth P, Surti, Urvashi, Ketterer, Deborah M, Afzal, Sibtain, Ramzan, Khushnooda, Faiyaz-Ul Haque, Muhammad, Jiang, Huaiyang, Trakselis, Michael A, Rajkovic, Aleksandar, AlAsiri, Saleh, AlAsiri, Saleh, Basit, Sulman, Wood-Trageser, Michelle A, Yatsenko, Svetlana A, Jeffries, Elizabeth P, Surti, Urvashi, Ketterer, Deborah M, Afzal, Sibtain, Ramzan, Khushnooda, Faiyaz-Ul Haque, Muhammad, Jiang, Huaiyang, Trakselis, Michael A, and Rajkovic, Aleksandar
Abstract: Premature ovarian failure (POF) is a genetically and phenotypically heterogeneous disorder that includes individuals with manifestations ranging from primary amenorrhea to loss of menstrual function prior to age 40. POF presents as hypergonadotropic hypogonadism and can be part of a syndrome or occur in isolation. Here, we studied 3 sisters with primary amenorrhea, hypothyroidism, and hypergonadotropic hypogonadism. The sisters were born to parents who are first cousins. SNP analysis and whole-exome sequencing revealed the presence of a pathogenic variant of the minichromosome maintenance 8 gene (MCM8, c.446C>G; p.P149R) located within a region of homozygosity that was present in the affected daughters but not in their unaffected sisters. Because MCM8 participates in homologous recombination and dsDNA break repair, we tested fibroblasts from the affected sisters for hypersensitivity to chromosomal breaks. Compared with fibroblasts from unaffected daughters, chromosomal break repair was deficient in fibroblasts from the affected individuals, likely due to inhibited recruitment of MCM8 p.P149R to sites of DNA damage. Our study identifies an autosomal recessive disorder caused by an MCM8 mutation that manifests with endocrine dysfunction and genomic instability.
Published: 2015

7. Finding the missing honey bee genes: Lessons learned from a genome upgrade

Author: Elsik, Christine G, Worley, Kim C, Bennett, Anna K, Beye, Martin, Camara, Francisco, Childers, Christopher P, de Graaf, Dirk C, Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D, Foster, Leonard J, Graur, Dan, Guigo, Roderic, Hoff, Katharina Jasmin, Holder, Michael E, Hudson, Matthew E, Hunt, Greg J, Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L, Ma, Jian, Maleszka, Ryszard, Moritz, Robin F A, Munoz-Torres, Monica C, Murphy, Terence D, Muzny, Donna M, Newsham, Irene F, Reese, Justin T, Robertson, Hugh M, Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M, Vaerenbergh, Matthias Van, Waterhouse, Robert M, Weaver, Daniel B, Whitfield, Charles W, Wu, Yuanqing, Zdobnov, Evgeny M, Zhang, Lan, Zhu, Dianhui, Gibbs, Richard A, Elsik, Christine G, Worley, Kim C, Bennett, Anna K, Beye, Martin, Camara, Francisco, Childers, Christopher P, de Graaf, Dirk C, Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D, Foster, Leonard J, Graur, Dan, Guigo, Roderic, Hoff, Katharina Jasmin, Holder, Michael E, Hudson, Matthew E, Hunt, Greg J, Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L, Ma, Jian, Maleszka, Ryszard, Moritz, Robin F A, Munoz-Torres, Monica C, Murphy, Terence D, Muzny, Donna M, Newsham, Irene F, Reese, Justin T, Robertson, Hugh M, Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M, Vaerenbergh, Matthias Van, Waterhouse, Robert M, Weaver, Daniel B, Whitfield, Charles W, Wu, Yuanqing, Zdobnov, Evgeny M, Zhang, Lan, Zhu, Dianhui, and Gibbs, Richard A
Abstract: Background: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Results: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Conclusions: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination. 2014 Elsik et al.; licensee BioMed Central Ltd.
Published: 2014

8. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

Author: Chipman, Ariel D, Ferrier, David E K, Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S T, Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis J P, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, Richards, Stephen, Chipman, Ariel D, Ferrier, David E K, Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S T, Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis J P, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, and Richards, Stephen
Abstract: Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific l
Published: 2014

9. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Author: Chipman, Ariel D, Tyler-Smith, Chris1, Chipman, Ariel D, Ferrier, David EK, Brena, Carlo, Qu, Jiaxin, Hughes, Daniel ST, Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer CJ, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis JP, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome HL, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Chipman, Ariel D, Tyler-Smith, Chris1, Chipman, Ariel D, Ferrier, David EK, Brena, Carlo, Qu, Jiaxin, Hughes, Daniel ST, Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer CJ, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis JP, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome HL, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, and Zou, Xiaoyan
Abstract: Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life
Published: 2014

10. Finding the missing honey bee genes: lessons learned from a genome upgrade

Author: Elsik, Christine G., Worley, Kim C., Bennett, Anna K., Beye, Martin, Camara, Francisco, Childers, Christopher P., de Graaf, Dirk C., Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D., Foster, Leonard J., Graur, Dan, Guigo, Roderic, Hoff, Katharina J., Holder, Michael E., Hudson, Matthew E., Hunt, Greg J., Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L., Ma, Jian, Maleszka, Ryszard, Moritz, Robin F. A., Munoz-Torres, Monica C., Murphy, Terence D., Muzny, Donna M., Newsham, Irene F., Reese, Justin T., Robertson, Hugh M., Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M., Vaerenbergh, Matthias V., Waterhouse, Robert M., Weaver, Daniel B., Whitfield, Charles W., Wu, Yuanqing, Zdobnov, Evgeny M., Zhang, Lan, Zhu, Dianhui, Gibbs, Richard A., Elsik, Christine G., Worley, Kim C., Bennett, Anna K., Beye, Martin, Camara, Francisco, Childers, Christopher P., de Graaf, Dirk C., Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D., Foster, Leonard J., Graur, Dan, Guigo, Roderic, Hoff, Katharina J., Holder, Michael E., Hudson, Matthew E., Hunt, Greg J., Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L., Ma, Jian, Maleszka, Ryszard, Moritz, Robin F. A., Munoz-Torres, Monica C., Murphy, Terence D., Muzny, Donna M., Newsham, Irene F., Reese, Justin T., Robertson, Hugh M., Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M., Vaerenbergh, Matthias V., Waterhouse, Robert M., Weaver, Daniel B., Whitfield, Charles W., Wu, Yuanqing, Zdobnov, Evgeny M., Zhang, Lan, Zhu, Dianhui, and Gibbs, Richard A.
Abstract: BACKGROUND: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. RESULTS: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. CONCLUSIONS: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.
Published: 2014

11. Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

Author: Chen, Zhen-Xia, Chen, Zhen-Xia, Sturgill, David, Qu, Jiaxin, Jiang, Huaiyang, Park, Soo, Boley, Nathan, Suzuki, Ana Maria, Fletcher, Anthony R, Plachetzki, David C, FitzGerald, Peter C, Artieri, Carlo G, Atallah, Joel, Barmina, Olga, Brown, James B, Blankenburg, Kerstin P, Clough, Emily, Dasgupta, Abhijit, Gubbala, Sai, Han, Yi, Jayaseelan, Joy C, Kalra, Divya, Kim, Yoo-Ah, Kovar, Christie L, Lee, Sandra L, Li, Mingmei, Malley, James D, Malone, John H, Mathew, Tittu, Mattiuzzo, Nicolas R, Munidasa, Mala, Muzny, Donna M, Ongeri, Fiona, Perales, Lora, Przytycka, Teresa M, Pu, Ling-Ling, Robinson, Garrett, Thornton, Rebecca L, Saada, Nehad, Scherer, Steven E, Smith, Harold E, Vinson, Charles, Warner, Crystal B, Worley, Kim C, Wu, Yuan-Qing, Zou, Xiaoyan, Cherbas, Peter, Kellis, Manolis, Eisen, Michael B, Piano, Fabio, Kionte, Karin, Fitch, David H, Sternberg, Paul W, Cutter, Asher D, Duff, Michael O, Hoskins, Roger A, Graveley, Brenton R, Gibbs, Richard A, Bickel, Peter J, Kopp, Artyom, Carninci, Piero, Celniker, Susan E, Oliver, Brian, Richards, Stephen, Chen, Zhen-Xia, Chen, Zhen-Xia, Sturgill, David, Qu, Jiaxin, Jiang, Huaiyang, Park, Soo, Boley, Nathan, Suzuki, Ana Maria, Fletcher, Anthony R, Plachetzki, David C, FitzGerald, Peter C, Artieri, Carlo G, Atallah, Joel, Barmina, Olga, Brown, James B, Blankenburg, Kerstin P, Clough, Emily, Dasgupta, Abhijit, Gubbala, Sai, Han, Yi, Jayaseelan, Joy C, Kalra, Divya, Kim, Yoo-Ah, Kovar, Christie L, Lee, Sandra L, Li, Mingmei, Malley, James D, Malone, John H, Mathew, Tittu, Mattiuzzo, Nicolas R, Munidasa, Mala, Muzny, Donna M, Ongeri, Fiona, Perales, Lora, Przytycka, Teresa M, Pu, Ling-Ling, Robinson, Garrett, Thornton, Rebecca L, Saada, Nehad, Scherer, Steven E, Smith, Harold E, Vinson, Charles, Warner, Crystal B, Worley, Kim C, Wu, Yuan-Qing, Zou, Xiaoyan, Cherbas, Peter, Kellis, Manolis, Eisen, Michael B, Piano, Fabio, Kionte, Karin, Fitch, David H, Sternberg, Paul W, Cutter, Asher D, Duff, Michael O, Hoskins, Roger A, Graveley, Brenton R, Gibbs, Richard A, Bickel, Peter J, Kopp, Artyom, Carninci, Piero, Celniker, Susan E, Oliver, Brian, and Richards, Stephen
Abstract: Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.
Published: 2014

12. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Author: Chipman, Ariel D, Tyler-Smith, Chris1, Chipman, Ariel D, Ferrier, David EK, Brena, Carlo, Qu, Jiaxin, Hughes, Daniel ST, Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer CJ, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis JP, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome HL, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Chipman, Ariel D, Tyler-Smith, Chris1, Chipman, Ariel D, Ferrier, David EK, Brena, Carlo, Qu, Jiaxin, Hughes, Daniel ST, Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer CJ, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis JP, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome HL, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, and Zou, Xiaoyan
Abstract: Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life
Published: 2014

13. MCM9 mutations are associated with ovarian failure, short stature, and chromosomal instability.

Author: Wood-Trageser, Michelle A, Wood-Trageser, Michelle A, Gurbuz, Fatih, Yatsenko, Svetlana A, Jeffries, Elizabeth P, Kotan, L Damla, Surti, Urvashi, Ketterer, Deborah M, Matic, Jelena, Chipkin, Jacqueline, Jiang, Huaiyang, Trakselis, Michael A, Topaloglu, A Kemal, Rajkovic, Aleksandar, Wood-Trageser, Michelle A, Wood-Trageser, Michelle A, Gurbuz, Fatih, Yatsenko, Svetlana A, Jeffries, Elizabeth P, Kotan, L Damla, Surti, Urvashi, Ketterer, Deborah M, Matic, Jelena, Chipkin, Jacqueline, Jiang, Huaiyang, Trakselis, Michael A, Topaloglu, A Kemal, and Rajkovic, Aleksandar
Abstract: Premature ovarian failure (POF) is genetically heterogeneous and manifests as hypergonadotropic hypogonadism either as part of a syndrome or in isolation. We studied two unrelated consanguineous families with daughters exhibiting primary amenorrhea, short stature, and a 46,XX karyotype. A combination of SNP arrays, comparative genomic hybridization arrays, and whole-exome sequencing analyses identified homozygous pathogenic variants in MCM9, a gene implicated in homologous recombination and repair of double-stranded DNA breaks. In one family, the MCM9 c.1732+2T>C variant alters a splice donor site, resulting in abnormal alternative splicing and truncated forms of MCM9 that are unable to be recruited to sites of DNA damage. In the second family, MCM9 c.394C>T (p.Arg132(∗)) results in a predicted loss of functional MCM9. Repair of chromosome breaks was impaired in lymphocytes from affected, but not unaffected, females in both families, consistent with MCM9 function in homologous recombination. Autosomal-recessive variants in MCM9 cause a genomic-instability syndrome associated with hypergonadotropic hypogonadism and short stature. Preferential sensitivity of germline meiosis to MCM9 functional deficiency and compromised DNA repair in the somatic component most likely account for the ovarian failure and short stature.
Published: 2014

14. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

Author: Chipman, Ariel D, Ferrier, David E K, Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S T, Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis J P, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, Richards, Stephen, Chipman, Ariel D, Ferrier, David E K, Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S T, Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis J P, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, and Richards, Stephen
Abstract: Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific l
Published: 2014

15. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

Author: Chipman, Ariel D., Ferrier, David E.K., Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S.T., Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, Richards, Stephen, Chipman, Ariel D., Ferrier, David E.K., Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S.T., Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, and Richards, Stephen
Abstract: Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific l
Published: 2014

16. Finding the Missing Honey Bee Genes: Lessons Learned From a Genome Upgrade.

Author: Elsik, Christine G, Worley, Kim C, Bennett, Anna K, Beye, Martin, Camara, Francisco, Childers, Christopher P, de Graaf, Dirk C, Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D, Foster, Leonard J, Graur, Dan, Guigo, Roderic, HGSC production teams, Hoff, Katharina Jasmin, Holder, Michael E, Hudson, Matthew E, Hunt, Greg, Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L, Ma, Jian, Maleszka, Ryszard, Moritz, Robin FA, Munoz-Torres, Monica C, Murphy, Terence D, Muzny, Donna M, Newsham, Irene F, Reese, Justin T, Robertson, Hugh M, Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M, Van Vaerenbergh, Matthias, Waterhouse, Robert M, Weaver, Daniel B, Whitfield, Charles W, Wu, Yuanqing, Zdobnov, Evgeny M, Zhang, Lan, Zhu, Dianhui, Gibbs, Richard A, Elsik, Christine G, Worley, Kim C, Bennett, Anna K, Beye, Martin, Camara, Francisco, Childers, Christopher P, de Graaf, Dirk C, Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D, Foster, Leonard J, Graur, Dan, Guigo, Roderic, HGSC production teams, Hoff, Katharina Jasmin, Holder, Michael E, Hudson, Matthew E, Hunt, Greg, Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L, Ma, Jian, Maleszka, Ryszard, Moritz, Robin FA, Munoz-Torres, Monica C, Murphy, Terence D, Muzny, Donna M, Newsham, Irene F, Reese, Justin T, Robertson, Hugh M, Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M, Van Vaerenbergh, Matthias, Waterhouse, Robert M, Weaver, Daniel B, Whitfield, Charles W, Wu, Yuanqing, Zdobnov, Evgeny M, Zhang, Lan, Zhu, Dianhui, and Gibbs, Richard A
Abstract: Background The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Results Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Conclusions Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.
Published: 2014

17. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

Author: Chipman, Ariel D., Ferrier, David E.K., Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S.T., Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, Richards, Stephen, Chipman, Ariel D., Ferrier, David E.K., Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S.T., Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, and Richards, Stephen
Abstract: Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific l
Published: 2014

18. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

Author: Chipman, Ariel D., Ferrier, David E.K., Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S.T., Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, Richards, Stephen, Chipman, Ariel D., Ferrier, David E.K., Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S.T., Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, and Richards, Stephen
Abstract: Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific l
Published: 2014

19. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

Author: Chipman, Ariel D., Ferrier, David E.K., Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S.T., Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, Richards, Stephen, Chipman, Ariel D., Ferrier, David E.K., Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S.T., Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, and Richards, Stephen
Abstract: Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific l
Published: 2014

20. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Author: Bradnam, Keith R, Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, Inanç, Boisvert, Sébastien, Chapman, Jarrod A, Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A, Ganapathy, Ganeshkumar, Gibbs, Richard A, Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B, Ho, Isaac Y, Howard, Jason, Hunt, Martin, Jackman, Shaun D, Jaffe, David B, Jarvis, Erich D, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J, Kitzman, Jacob O, Knight, James R, Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Naquin, Delphine, Ning, Zemin, Otto, Thomas D, Paten, Benedict, Paulo, Octávio S, Phillippy, Adam M, Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S, Ruby, J, Scalabrin, Simone, Schatz, Michael C, Schwartz, David C, Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I, Shendure, Jay, Shi, Yujian, Simpson, Jared T, Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Vieira, Bruno M, Wang, Jun, Worley, Kim C, Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, Korf, Ian F, Bradnam, Keith R, Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, Inanç, Boisvert, Sébastien, Chapman, Jarrod A, Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A, Ganapathy, Ganeshkumar, Gibbs, Richard A, Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B, Ho, Isaac Y, Howard, Jason, Hunt, Martin, Jackman, Shaun D, Jaffe, David B, Jarvis, Erich D, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J, Kitzman, Jacob O, Knight, James R, Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Naquin, Delphine, Ning, Zemin, Otto, Thomas D, Paten, Benedict, Paulo, Octávio S, Phillippy, Adam M, Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S, Ruby, J, Scalabrin, Simone, Schatz, Michael C, Schwartz, David C, Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I, Shendure, Jay, Shi, Yujian, Simpson, Jared T, Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Vieira, Bruno M, Wang, Jun, Worley, Kim C, Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, and Korf, Ian F
Abstract: Background The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
Published: 2013

21. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Author: Bradnam, Keith R, Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, Inanç, Boisvert, Sébastien, Chapman, Jarrod A, Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A, Ganapathy, Ganeshkumar, Gibbs, Richard A, Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B, Ho, Isaac Y, Howard, Jason, Hunt, Martin, Jackman, Shaun D, Jaffe, David B, Jarvis, Erich D, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J, Kitzman, Jacob O, Knight, James R, Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Naquin, Delphine, Ning, Zemin, Otto, Thomas D, Paten, Benedict, Paulo, Octávio S, Phillippy, Adam M, Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S, Ruby, J, Scalabrin, Simone, Schatz, Michael C, Schwartz, David C, Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I, Shendure, Jay, Shi, Yujian, Simpson, Jared T, Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Vieira, Bruno M, Wang, Jun, Worley, Kim C, Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, Korf, Ian F, Bradnam, Keith R, Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, Inanç, Boisvert, Sébastien, Chapman, Jarrod A, Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A, Ganapathy, Ganeshkumar, Gibbs, Richard A, Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B, Ho, Isaac Y, Howard, Jason, Hunt, Martin, Jackman, Shaun D, Jaffe, David B, Jarvis, Erich D, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J, Kitzman, Jacob O, Knight, James R, Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Naquin, Delphine, Ning, Zemin, Otto, Thomas D, Paten, Benedict, Paulo, Octávio S, Phillippy, Adam M, Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S, Ruby, J, Scalabrin, Simone, Schatz, Michael C, Schwartz, David C, Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I, Shendure, Jay, Shi, Yujian, Simpson, Jared T, Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Vieira, Bruno M, Wang, Jun, Worley, Kim C, Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, and Korf, Ian F
Abstract: Background The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
Published: 2013

22. Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Author: Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., Hunter, Wayne, Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., and Hunter, Wayne
Abstract: Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
Published: 2010
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23. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

Author: Werren, John H, Richards, Stephen, Desjardins, Christopher A, Niehuis, Oliver, Gadau, Jürgen, Colbourne, John K, Beukeboom, Leo W, Desplan, Claude, Elsik, Christine G, Grimmelikhuijzen, Cornelis J P, Kitts, Paul, Lynch, Jeremy A, Murphy, Terence, Oliveira, Deodoro C S G, Smith, Christopher D, van de Zande, Louis, Worley, Kim C, Zdobnov, Evgeny M, Aerts, Maarten, Albert, Stefan, Anaya, Victor H, Anzola, Juan M, Barchuk, Angel R, Behura, Susanta K, Bera, Agata N, Berenbaum, May R, Bertossa, Rinaldo C, Bitondi, Márcia M G, Bordenstein, Seth R, Bork, Peer, Bornberg-Bauer, Erich, Brunain, Marleen, Cazzamali, Giuseppe, Chaboub, Lesley, Chacko, Joseph, Chavez, Dean, Childers, Christopher P, Choi, Jeong-Hyeon, Clark, Michael E, Claudianos, Charles, Clinton, Rochelle A, Cree, Andrew G, Cristino, Alexandre S, Dang, Phat M, Darby, Alistair C, de Graaf, Dirk C, Devreese, Bart, Dinh, Huyen H, Edwards, Rachel, Elango, Navin, Elhaik, Eran, Ermolaeva, Olga, Evans, Jay D, Foret, Sylvain, Fowler, Gerald R, Gerlach, Daniel, Gibson, Joshua D, Gilbert, Donald G, Graur, Dan, Gründer, Stefan, Hagen, Darren E, Han, Yi, Hauser, Frank, Hultmark, Dan, Hunter, Henry C, Hurst, Gregory D D, Jhangian, Shalini N, Jiang, Huaiyang, Johnson, Reed M, Jones, Andrew K, Junier, Thomas, Kadowaki, Tatsuhiko, Kamping, Albert, Kapustin, Yuri, Kechavarzi, Bobak, Kim, Jaebum, Kim, Jay, Kiryutin, Boris, Koevoets, Tosca, Kovar, Christie L, Kriventseva, Evgenia V, Kucharski, Robert, Lee, Heewook, Lee, Sandra L, Lees, Kristin, Lewis, Lora R, Loehlin, David W, Logsdon, John M, Lopez, Jacqueline A, Lozado, Ryan J, Maglott, Donna, Maleszka, Ryszard, Mayampurath, Anoop, Mazur, Danielle J, McClure, Marcella A, Moore, Andrew D, Morgan, Margaret B, Muller, Jean, Munoz-Torres, Monica C, Muzny, Donna M, Nazareth, Lynne V, Neupert, Susanne, Nguyen, Ngoc B, Nunes, Francis M F, Oakeshott, John G, Okwuonu, Geoffrey O, Pannebakker, Bart A, Pejaver, Vikas R, Peng, Zuogang, Pratt, Stephen C, Predel, Reinhard, Pu, Ling-Ling, Ranson, Hilary, Raychoudhury, Rhitoban, Rechtsteiner, Andreas, Reese, Justin T, Reid, Jeffrey G, Riddle, Megan, Robertson, Hugh M, Romero-Severson, Jeanne, Rosenberg, Miriam, Sackton, Timothy B, Sattelle, David B, Schlüns, Helge, Schmitt, Thomas, Schneider, Martina, Schüler, Andreas, Schurko, Andrew M, Shuker, David M, Simões, Zilá L P, Sinha, Saurabh, Smith, Zachary, Solovyev, Victor, Souvorov, Alexandre, Springauf, Andreas, Stafflinger, Elisabeth, Stage, Deborah E, Stanke, Mario, Tanaka, Yoshiaki, Telschow, Arndt, Trent, Carol, Vattathil, Selina, Verhulst, Eveline C, Viljakainen, Lumi, Wanner, Kevin W, Waterhouse, Robert M, Whitfield, James B, Wilkes, Timothy E, Williamson, Michael, Willis, Judith H, Wolschin, Florian, Wyder, Stefan, Yamada, Takuji, Yi, Soojin V, Zecher, Courtney N, Zhang, Lan, Gibbs, Richard A, Werren, John H, Richards, Stephen, Desjardins, Christopher A, Niehuis, Oliver, Gadau, Jürgen, Colbourne, John K, Beukeboom, Leo W, Desplan, Claude, Elsik, Christine G, Grimmelikhuijzen, Cornelis J P, Kitts, Paul, Lynch, Jeremy A, Murphy, Terence, Oliveira, Deodoro C S G, Smith, Christopher D, van de Zande, Louis, Worley, Kim C, Zdobnov, Evgeny M, Aerts, Maarten, Albert, Stefan, Anaya, Victor H, Anzola, Juan M, Barchuk, Angel R, Behura, Susanta K, Bera, Agata N, Berenbaum, May R, Bertossa, Rinaldo C, Bitondi, Márcia M G, Bordenstein, Seth R, Bork, Peer, Bornberg-Bauer, Erich, Brunain, Marleen, Cazzamali, Giuseppe, Chaboub, Lesley, Chacko, Joseph, Chavez, Dean, Childers, Christopher P, Choi, Jeong-Hyeon, Clark, Michael E, Claudianos, Charles, Clinton, Rochelle A, Cree, Andrew G, Cristino, Alexandre S, Dang, Phat M, Darby, Alistair C, de Graaf, Dirk C, Devreese, Bart, Dinh, Huyen H, Edwards, Rachel, Elango, Navin, Elhaik, Eran, Ermolaeva, Olga, Evans, Jay D, Foret, Sylvain, Fowler, Gerald R, Gerlach, Daniel, Gibson, Joshua D, Gilbert, Donald G, Graur, Dan, Gründer, Stefan, Hagen, Darren E, Han, Yi, Hauser, Frank, Hultmark, Dan, Hunter, Henry C, Hurst, Gregory D D, Jhangian, Shalini N, Jiang, Huaiyang, Johnson, Reed M, Jones, Andrew K, Junier, Thomas, Kadowaki, Tatsuhiko, Kamping, Albert, Kapustin, Yuri, Kechavarzi, Bobak, Kim, Jaebum, Kim, Jay, Kiryutin, Boris, Koevoets, Tosca, Kovar, Christie L, Kriventseva, Evgenia V, Kucharski, Robert, Lee, Heewook, Lee, Sandra L, Lees, Kristin, Lewis, Lora R, Loehlin, David W, Logsdon, John M, Lopez, Jacqueline A, Lozado, Ryan J, Maglott, Donna, Maleszka, Ryszard, Mayampurath, Anoop, Mazur, Danielle J, McClure, Marcella A, Moore, Andrew D, Morgan, Margaret B, Muller, Jean, Munoz-Torres, Monica C, Muzny, Donna M, Nazareth, Lynne V, Neupert, Susanne, Nguyen, Ngoc B, Nunes, Francis M F, Oakeshott, John G, Okwuonu, Geoffrey O, Pannebakker, Bart A, Pejaver, Vikas R, Peng, Zuogang, Pratt, Stephen C, Predel, Reinhard, Pu, Ling-Ling, Ranson, Hilary, Raychoudhury, Rhitoban, Rechtsteiner, Andreas, Reese, Justin T, Reid, Jeffrey G, Riddle, Megan, Robertson, Hugh M, Romero-Severson, Jeanne, Rosenberg, Miriam, Sackton, Timothy B, Sattelle, David B, Schlüns, Helge, Schmitt, Thomas, Schneider, Martina, Schüler, Andreas, Schurko, Andrew M, Shuker, David M, Simões, Zilá L P, Sinha, Saurabh, Smith, Zachary, Solovyev, Victor, Souvorov, Alexandre, Springauf, Andreas, Stafflinger, Elisabeth, Stage, Deborah E, Stanke, Mario, Tanaka, Yoshiaki, Telschow, Arndt, Trent, Carol, Vattathil, Selina, Verhulst, Eveline C, Viljakainen, Lumi, Wanner, Kevin W, Waterhouse, Robert M, Whitfield, James B, Wilkes, Timothy E, Williamson, Michael, Willis, Judith H, Wolschin, Florian, Wyder, Stefan, Yamada, Takuji, Yi, Soojin V, Zecher, Courtney N, Zhang, Lan, and Gibbs, Richard A
Abstract: We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.
Published: 2010
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24. Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Author: Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., Hunter, Wayne, Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., and Hunter, Wayne
Abstract: Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
Published: 2010
Full Text: View/download PDF

25. Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Author: Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., Hunter, Wayne, Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., and Hunter, Wayne
Abstract: Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
Published: 2010
Full Text: View/download PDF

26. Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Author: Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., Hunter, Wayne, Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., and Hunter, Wayne
Abstract: Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
Published: 2010
Full Text: View/download PDF

27. Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Author: Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., Hunter, Wayne, Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., and Hunter, Wayne
Abstract: Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
Published: 2010
Full Text: View/download PDF

28. The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution

Author: Elsik, Christine G., Tellam, Ross L., Worley, Kim C., Gibbs, Richard A., Abatepaulo, Antonio R. R., Abbey, Colette A., Adelson, David L., Aerts, Jan, Ahola, Virpi, Alexander, Lee, Alioto, Tyler, Almeida, Iassudara G., Amadio, Ariel F., Anatriello, Elen, Antonarakis, Stylianos E., Anzola, Juan M., Astashyn, Alex, Bahadue, Suria M., Baldwin, Cynthia L., Barris, Wes, Baxter, Rebecca, Bell, Stephanie Nicole, Bennett, Anna K., Bennett, Gary L., Biase, Fernando H., Boldt, Clayton R., Bradley, Daniel G., Brinkman, Fiona S. L., Brinkmeyer-Langford, Candice L., Brown, Wendy C., Brownstein, Michael J., Buhay, Christian, Caetano, Alexandre R., Camara, Francisco, Carroll, Jeffrey A., Carvalho, Wanessa A., Casey, Theresa, Cervelatti, Elaine P., Chack, Joseph, Chacko, Elsa, Chandrabose, Mimi M., Chapin, Jennifer E., Chapple, Charles E., Chen, Hsiu-Chuan, Chen, Lin, Cheng, Ye, Cheng, Ze, Childers, Christopher P., Chitko-McKown, Carol G., Chiu, Readman, Choi, Jungwoo, Chrast, Jacqueline, Colley, Adam J., Connelley, Tomothy, Cree, Andy, Curry, Stacey, Dalrymple, Brian, Diep Dao, Marvin, Davis, Clay, de Oliveira, Carlo J. F., de Miranda Santos, Isabel K. F., de Campos, Tatiana A., Deobald, Heather, Devinoy, Eve, Dickins, C. Michael, Yan, Ding, Dinh, Huyen H., De Donato, Marcos, Donohue, Kaitlin E., Donthu, Ravikiran, Dovc, Peter, Dugan-Rocha, Shannon, Durbin, K. James, Eberlein, Annett, Edgar, Robert C., Egan, Amy, Eggen, Andre, Eichler, Evan E., Elhaik, Eran, Ellis, Shirley A., Elnitski, Laura, Ermolaeva, Olga, Eyras, Eduardo, Fitzsimmons, Carolyn J., Fowler, Gerald R., Franzin, Alessandra M., Fritz, Krista, Gabisi, Ramatu Ayiesha, Garcia, Gustavo R., Garcia, Jose Fernando, Genini, Sem, Gerlach, Daniel, German, J. Bruce, Gilbert, James G. R., Gill, Clare A., Gladney, Cody J., Glass, Elizabeth J., Goodell, Jason, Grant, Jason R., Graur, Dan, Greaser, Marion L., Green, Jonathan A., Green, Ronnie D., Guan, Leluo, Guigo, Roderic, Hadsell, Darryl L., Hagen, Darren E., Hakimov, Hatam A., Halgren, Rob, Hamernik, Debora L., Hamilton, Cerissa, Harhay, Gregory P., Harrow, Jennifer L., Hart, Elizabeth A., Hastings, Nicola, Havlak, Paul, Henrichsen, Charlotte N., Hernandez, Judith, Hernandez, Marta, Herzig, Carolyn T. A., Hiendleder, Stefan G., Hines, Sandra, Hitchens, Matthew Edward, Hlavina, Wratko, Hobbs, Matthew, Holder, Michael, Holt, Robert A., Hu, Zhi-Liang, Hume, Jennifer, Iivanainen, Antti, Ingham, Aaron, Iso-Touru, Terhi, Jamis, Catherine, Jann, Oliver, Jensen, Kirsty, Jhangiani, Shalini N., Jiang, Huaiyang, Johnson, Angela Jolivet, Jones, Steven J. M., Joshi, Vandita, Junier, Thomas, Kapetis, Dimos, Kappes, Steve M., Kapustin, Yuri, Keele, John W., Kent, Matthew P., Kerr, Tovah, Khalil, Sari S., Khatib, Hasan, Kiryutin, Boris, Kitts, Paul, Kokocinski, Felix, Kolbehdari, Davood, Kovar, Christie L., Kriventseva, Evgenia V., Kumar, Charu G., Kumar, Dinesh, Lahmers, Kevin K., Landrum, Melissa, Larkin, Denis M., Lau, Lilian P. L., Leach, Richard, Lee, Justin C. M., Lee, Sandra, Lemay, Danielle G., Lewin, Harris A., Lewis, Lora R., Li, Changxi, Lien, Sigbjorn, Liu, George E., Liu, Yih-shin, Liu, Yue, Logan, Krystin M., Lopez, John, Lozado, Ryan J., Lutzow, Ylva Strandberg, Lynn, David J., MacNeil, Michael D., Maglott, Donna, Malinverni, Roberto, Maqbool, Nauman J., Marques, Elisa, Marra, Marco A., Martin, William F., Martins, Natalia F., Maruyama, Sandra R., Matukumalli, Lakshmi K., Mazza, Raffaele, McEwan, John C., McKay, Stephanie D., McLean, Kim L., McWilliam, Sean, Medrano, Juan F., Memili, Erdogan, Moen, Charles, Molenaar, Adrian J., Moore, Stephen S., Moore, Richard, More, Daniela D., Moreno, Barbara T., Morgan, Margaret B., Muntean, Carl T., Muzny, Donna M., Nandakumar, Hari P., Nazareth, Lynne V., Nguyen, Ngoc Bich, Nicholas, Frank W., Nogueira, Marcelo F. G., Okwuonu, Geoffrey O., Olsaker, Ingrid, Pant, Sameer D., Panzitta, Francesca, Pastor, Rosemeire C. P., Patel, Bella Mayurkumar, Payne, Gemma M., Plass, Mireya, Poli, Mario A., Poslusny, Nathan, Pruitt, Kim, Pu, Ling-Ling, Qin, Xiang, Rachagani, Satyanarayana, Raison, Joy M., Ranganathan, Shoba, Ratnakumar, Abhirami, Razpet, Andrej, Reecy, James, Reese, Justin T., Ren, Yanru, Reymond, Alexandre, Riggs, Penny K., Rijnkels, Monique, Rincon, Gonzalo, Roberts, Andy, Rodriguez-Osorio, Nelida, Rodriguez-Zas, Sandra L., Romero, Natasha E., Rosenwald, Anne, Ruiz, San Juana, Sabo, Aniko, Salih, Hanni, Sando, Lillian, Santibanez, Jireh, Sapojnikov, Victor, Schein, Jacqueline E., Schmutz, Sheila M., Schnabel, Robert D., Schook, Lawrence, Searle, Stephen M., Seo, Seongwon, Shen, Yufeng, Shen, Libing, Sherman, Laura, Skow, Loren C., Smith, Timothy, Snelling, Warren M., Sodergren, Erica, Solovyev, Victor, Song, Henry, Song, Jiuzhou, Sonstegard, Tad S., Southey, Bruce R., Souvorov, Alexandre, Spurlock, Diane, Steffen, David, Stone, Roger T., Stothard, Paul, Sugimoto, Yoshikazu, Sweedler, Jonathan V., Takasuga, Akiko, Tammen, Imke, Taniguchi, Masaaki, Taylor, Jeremy F., Telugu, Bhanu Prakash V. L., Ucla, Catherine, Urbanski, Jennifer M., Utsunomiya, Yuri T., Van, Curtis P., Vattathil, Selina, Verschoor, Chris P., Waardenberg, Ashley J., Walker, Angela, Wang, Zhiquan, Ward, Robert, Warren, James T., Waterman, Richard C., Weikard, Rosemarie, Weinstock, George M., Welsh, Thomas H., Jr., Wheeler, David A., Wheeler, Thomas T., White, Stephen N., Whiteside, Matthew D., Wilczek-Boney, Katarzyna, Williams, John L., Williams, Rex Lee, Jr., Wilming, Laurens G., Womack, James, Wright, Rita A., Wunderlich, Kris R., Wyss, Carine, Yang, Mary Q., Yang, Jianqi, Zdobnov, Evgeny M., Zhang, Jingkun, Zhao, Feng-Qi, Zhu, Bin, Elsik, Christine G., Tellam, Ross L., Worley, Kim C., Gibbs, Richard A., Abatepaulo, Antonio R. R., Abbey, Colette A., Adelson, David L., Aerts, Jan, Ahola, Virpi, Alexander, Lee, Alioto, Tyler, Almeida, Iassudara G., Amadio, Ariel F., Anatriello, Elen, Antonarakis, Stylianos E., Anzola, Juan M., Astashyn, Alex, Bahadue, Suria M., Baldwin, Cynthia L., Barris, Wes, Baxter, Rebecca, Bell, Stephanie Nicole, Bennett, Anna K., Bennett, Gary L., Biase, Fernando H., Boldt, Clayton R., Bradley, Daniel G., Brinkman, Fiona S. L., Brinkmeyer-Langford, Candice L., Brown, Wendy C., Brownstein, Michael J., Buhay, Christian, Caetano, Alexandre R., Camara, Francisco, Carroll, Jeffrey A., Carvalho, Wanessa A., Casey, Theresa, Cervelatti, Elaine P., Chack, Joseph, Chacko, Elsa, Chandrabose, Mimi M., Chapin, Jennifer E., Chapple, Charles E., Chen, Hsiu-Chuan, Chen, Lin, Cheng, Ye, Cheng, Ze, Childers, Christopher P., Chitko-McKown, Carol G., Chiu, Readman, Choi, Jungwoo, Chrast, Jacqueline, Colley, Adam J., Connelley, Tomothy, Cree, Andy, Curry, Stacey, Dalrymple, Brian, Diep Dao, Marvin, Davis, Clay, de Oliveira, Carlo J. F., de Miranda Santos, Isabel K. F., de Campos, Tatiana A., Deobald, Heather, Devinoy, Eve, Dickins, C. Michael, Yan, Ding, Dinh, Huyen H., De Donato, Marcos, Donohue, Kaitlin E., Donthu, Ravikiran, Dovc, Peter, Dugan-Rocha, Shannon, Durbin, K. James, Eberlein, Annett, Edgar, Robert C., Egan, Amy, Eggen, Andre, Eichler, Evan E., Elhaik, Eran, Ellis, Shirley A., Elnitski, Laura, Ermolaeva, Olga, Eyras, Eduardo, Fitzsimmons, Carolyn J., Fowler, Gerald R., Franzin, Alessandra M., Fritz, Krista, Gabisi, Ramatu Ayiesha, Garcia, Gustavo R., Garcia, Jose Fernando, Genini, Sem, Gerlach, Daniel, German, J. Bruce, Gilbert, James G. R., Gill, Clare A., Gladney, Cody J., Glass, Elizabeth J., Goodell, Jason, Grant, Jason R., Graur, Dan, Greaser, Marion L., Green, Jonathan A., Green, Ronnie D., Guan, Leluo, Guigo, Roderic, Hadsell, Darryl L., Hagen, Darren E., Hakimov, Hatam A., Halgren, Rob, Hamernik, Debora L., Hamilton, Cerissa, Harhay, Gregory P., Harrow, Jennifer L., Hart, Elizabeth A., Hastings, Nicola, Havlak, Paul, Henrichsen, Charlotte N., Hernandez, Judith, Hernandez, Marta, Herzig, Carolyn T. A., Hiendleder, Stefan G., Hines, Sandra, Hitchens, Matthew Edward, Hlavina, Wratko, Hobbs, Matthew, Holder, Michael, Holt, Robert A., Hu, Zhi-Liang, Hume, Jennifer, Iivanainen, Antti, Ingham, Aaron, Iso-Touru, Terhi, Jamis, Catherine, Jann, Oliver, Jensen, Kirsty, Jhangiani, Shalini N., Jiang, Huaiyang, Johnson, Angela Jolivet, Jones, Steven J. M., Joshi, Vandita, Junier, Thomas, Kapetis, Dimos, Kappes, Steve M., Kapustin, Yuri, Keele, John W., Kent, Matthew P., Kerr, Tovah, Khalil, Sari S., Khatib, Hasan, Kiryutin, Boris, Kitts, Paul, Kokocinski, Felix, Kolbehdari, Davood, Kovar, Christie L., Kriventseva, Evgenia V., Kumar, Charu G., Kumar, Dinesh, Lahmers, Kevin K., Landrum, Melissa, Larkin, Denis M., Lau, Lilian P. L., Leach, Richard, Lee, Justin C. M., Lee, Sandra, Lemay, Danielle G., Lewin, Harris A., Lewis, Lora R., Li, Changxi, Lien, Sigbjorn, Liu, George E., Liu, Yih-shin, Liu, Yue, Logan, Krystin M., Lopez, John, Lozado, Ryan J., Lutzow, Ylva Strandberg, Lynn, David J., MacNeil, Michael D., Maglott, Donna, Malinverni, Roberto, Maqbool, Nauman J., Marques, Elisa, Marra, Marco A., Martin, William F., Martins, Natalia F., Maruyama, Sandra R., Matukumalli, Lakshmi K., Mazza, Raffaele, McEwan, John C., McKay, Stephanie D., McLean, Kim L., McWilliam, Sean, Medrano, Juan F., Memili, Erdogan, Moen, Charles, Molenaar, Adrian J., Moore, Stephen S., Moore, Richard, More, Daniela D., Moreno, Barbara T., Morgan, Margaret B., Muntean, Carl T., Muzny, Donna M., Nandakumar, Hari P., Nazareth, Lynne V., Nguyen, Ngoc Bich, Nicholas, Frank W., Nogueira, Marcelo F. G., Okwuonu, Geoffrey O., Olsaker, Ingrid, Pant, Sameer D., Panzitta, Francesca, Pastor, Rosemeire C. P., Patel, Bella Mayurkumar, Payne, Gemma M., Plass, Mireya, Poli, Mario A., Poslusny, Nathan, Pruitt, Kim, Pu, Ling-Ling, Qin, Xiang, Rachagani, Satyanarayana, Raison, Joy M., Ranganathan, Shoba, Ratnakumar, Abhirami, Razpet, Andrej, Reecy, James, Reese, Justin T., Ren, Yanru, Reymond, Alexandre, Riggs, Penny K., Rijnkels, Monique, Rincon, Gonzalo, Roberts, Andy, Rodriguez-Osorio, Nelida, Rodriguez-Zas, Sandra L., Romero, Natasha E., Rosenwald, Anne, Ruiz, San Juana, Sabo, Aniko, Salih, Hanni, Sando, Lillian, Santibanez, Jireh, Sapojnikov, Victor, Schein, Jacqueline E., Schmutz, Sheila M., Schnabel, Robert D., Schook, Lawrence, Searle, Stephen M., Seo, Seongwon, Shen, Yufeng, Shen, Libing, Sherman, Laura, Skow, Loren C., Smith, Timothy, Snelling, Warren M., Sodergren, Erica, Solovyev, Victor, Song, Henry, Song, Jiuzhou, Sonstegard, Tad S., Southey, Bruce R., Souvorov, Alexandre, Spurlock, Diane, Steffen, David, Stone, Roger T., Stothard, Paul, Sugimoto, Yoshikazu, Sweedler, Jonathan V., Takasuga, Akiko, Tammen, Imke, Taniguchi, Masaaki, Taylor, Jeremy F., Telugu, Bhanu Prakash V. L., Ucla, Catherine, Urbanski, Jennifer M., Utsunomiya, Yuri T., Van, Curtis P., Vattathil, Selina, Verschoor, Chris P., Waardenberg, Ashley J., Walker, Angela, Wang, Zhiquan, Ward, Robert, Warren, James T., Waterman, Richard C., Weikard, Rosemarie, Weinstock, George M., Welsh, Thomas H., Jr., Wheeler, David A., Wheeler, Thomas T., White, Stephen N., Whiteside, Matthew D., Wilczek-Boney, Katarzyna, Williams, John L., Williams, Rex Lee, Jr., Wilming, Laurens G., Womack, James, Wright, Rita A., Wunderlich, Kris R., Wyss, Carine, Yang, Mary Q., Yang, Jianqi, Zdobnov, Evgeny M., Zhang, Jingkun, Zhao, Feng-Qi, and Zhu, Bin
Abstract: To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
Published: 2009
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29. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

Author: Margulies, Elliott H, Cooper, Gregory M, Asimenos, George, Thomas, Daryl J, Dewey, Colin N, Siepel, Adam, Birney, Ewan, Keefe, Damian, Schwartz, Ariel S, Hou, Minmei, Taylor, James, Nikolaev, Sergey, Montoya-Burgos, Juan I, Löytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Brown, James B, Bickel, Peter, Holmes, Ian, Mullikin, James C, Ureta-Vidal, Abel, Paten, Benedict, Stone, Eric A, Rosenbloom, Kate R, Kent, W James, Bouffard, Gerard G, Guan, Xiaobin, Hansen, Nancy F, Idol, Jacquelyn R, Maduro, Valerie V B, Maskeri, Baishali, McDowell, Jennifer C, Park, Morgan, Thomas, Pamela J, Young, Alice C, Blakesley, Robert W, Muzny, Donna M, Sodergren, Erica, Wheeler, David A, Worley, Kim C, Jiang, Huaiyang, Weinstock, George M, Gibbs, Richard A, Graves, Tina, Fulton, Robert, Mardis, Elaine R, Wilson, Richard K, Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B, Chang, Jean L, Lindblad-Toh, Kerstin, Lander, Eric S, Hinrichs, Angie, Trumbower, Heather, Clawson, Hiram, Zweig, Ann, Kuhn, Robert M, Barber, Galt, Harte, Rachel, Karolchik, Donna, Field, Matthew A, Moore, Richard A, Matthewson, Carrie A, Schein, Jacqueline E, Marra, Marco A, Antonarakis, Stylianos E, Batzoglou, Serafim, Goldman, Nick, Hardison, Ross, Haussler, David, Miller, Webb, Pachter, Lior, Green, Eric D, Sidow, Arend, Margulies, Elliott H, Cooper, Gregory M, Asimenos, George, Thomas, Daryl J, Dewey, Colin N, Siepel, Adam, Birney, Ewan, Keefe, Damian, Schwartz, Ariel S, Hou, Minmei, Taylor, James, Nikolaev, Sergey, Montoya-Burgos, Juan I, Löytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Brown, James B, Bickel, Peter, Holmes, Ian, Mullikin, James C, Ureta-Vidal, Abel, Paten, Benedict, Stone, Eric A, Rosenbloom, Kate R, Kent, W James, Bouffard, Gerard G, Guan, Xiaobin, Hansen, Nancy F, Idol, Jacquelyn R, Maduro, Valerie V B, Maskeri, Baishali, McDowell, Jennifer C, Park, Morgan, Thomas, Pamela J, Young, Alice C, Blakesley, Robert W, Muzny, Donna M, Sodergren, Erica, Wheeler, David A, Worley, Kim C, Jiang, Huaiyang, Weinstock, George M, Gibbs, Richard A, Graves, Tina, Fulton, Robert, Mardis, Elaine R, Wilson, Richard K, Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B, Chang, Jean L, Lindblad-Toh, Kerstin, Lander, Eric S, Hinrichs, Angie, Trumbower, Heather, Clawson, Hiram, Zweig, Ann, Kuhn, Robert M, Barber, Galt, Harte, Rachel, Karolchik, Donna, Field, Matthew A, Moore, Richard A, Matthewson, Carrie A, Schein, Jacqueline E, Marra, Marco A, Antonarakis, Stylianos E, Batzoglou, Serafim, Goldman, Nick, Hardison, Ross, Haussler, David, Miller, Webb, Pachter, Lior, Green, Eric D, and Sidow, Arend
Abstract: A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization.
Published: 2007
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30. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Author: Birney, Ewan, Stamatoyannopoulos, John A., Dutta, Anindya, Guigó, Roderic, Gingeras, Thomas R., Margulies, Elliott H., Weng, Zhiping, Snyder, Michael, Dermitzakis, Emmanouil T., Thurman, Robert E., Kuehn, Michael S., Taylor, Christopher M., Neph, Shane, Koch, Christoph M., Asthana, Saurabh, Malhotra, Ankit, Adzhubei, Ivan, Greenbaum, Jason A., Andrews, Robert M., Flicek, Paul, Boyle, Patrick J., Cao, Hua, Carter, Nigel P., Clelland, Gayle K., Davis, Sean, Day, Nathan, Dhami, Pawandeep, Dillon, Shane C., Dorschner, Michael O., Fiegler, Heike, Giresi, Paul G., Goldy, Jeff, Hawrylycz, Michael, Haydock, Andrew, Humbert, Richard, James, Keith D., Johnson, Brett E., Johnson, Ericka M., Frum, Tristan T., Rosenzweig, Elizabeth R., Karnani, Neerja, Lee, Kirsten, Lefebvre, Gregory C., Navas, Patrick A., Neri, Fidencio, Parker, Stephen C., Sabo, Peter J., Sandstrom, Richard, Shafer, Anthony, Vetrie, David, Weaver, Molly, Wilcox, Sarah, Yu, Man, Collins, Francis S., Dekker, Job, Lieb, Jason D., Tullius, Thomas D., Crawford, Gregory E., Sunyaev, Shamil, Noble, William S., Dunham, Ian, Denoeud, France, Reymond, Alexandre, Kapranov, Philipp, Rozowsky, Joel, Zheng, Deyou, Castelo, Robert, Frankish, Adam, Harrow, Jennifer, Ghosh, Srinka, Sandelin, Albin, Hofacker, Ivo L., Baertsch, Robert, Keefe, Damian, Dike, Sujit, Cheng, Jill, Hirsch, Heather A., Sekinger, Edward A., Lagarde, Julien, Abril, Josep F., Shahab, Atif, Flamm, Christoph, Fried, Claudia, Hackermüller, Jörg, Hertel, Jana, Lindemeyer, Manja, Missal, Kristin, Tanzer, Andrea, Washietl, Stefan, Korbel, Jan, Emanuelsson, Olof, Pedersen, Jakob S., Holroyd, Nancy, Taylor, Ruth, Swarbreck, David, Matthews, Nicholas, Dickson, Mark C., Thomas, Daryl J., Weirauch, Matthew T., Gilbert, James, Drenkow, Jorg, Bell, Ian, Zhao, XiaoDong, Srinivasan, K. G., Sung, Wing-Kin, Ooi, Hong Sain, Chiu, Kuo Ping, Foissac, Sylvain, Alioto, Tyler, Brent, Michael, Pachter, Lior, Tress, Michael L., Valencia, Alfonso, Choo, Siew Woh, Choo, Chiou Yu, Ucla, Catherine, Manzano, Caroline, Wyss, Carine, Cheung, Evelyn, Clark, Taane G., Brown, James B., Ganesh, Madhavan, Patel, Sandeep, Tammana, Hari, Chrast, Jacqueline, Henrichsen, Charlotte N., Kai, Chikatoshi, Kawai, Jun, Nagalakshmi, Ugrappa, Wu, Jiaqian, Lian, Zheng, Lian, Jin, Newburger, Peter, Zhang, Xueqing, Bickel, Peter, Mattick, John S., Carninci, Piero, Hayashizaki, Yoshihide, Weissman, Sherman, Hubbard, Tim, Myers, Richard M., Rogers, Jane, Stadler, Peter F., Lowe, Todd M., Wei, Chia-Lin, Ruan, Yijun, Struhl, Kevin, Gerstein, Mark, Antonarakis, Stylianos E., Fu, Yutao, Green, Eric D., Karaöz, U., Siepel, Adam, Taylor, James, Liefer, Laura A, Wetterstrand, Kris A., Good, Peter J., Feingold, Elise A., Guyer, Mark S., Cooper, Gregory M., Asimenos, George, Dewey, Colin N., Hou, Minmei, Nikolaev, Sergey, Montoya-Burgos, Juan I., Löytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Huang, Haiyan, Zhang, Nancy R., Holmes, Ian, Mullikin, James C., Ureta-Vidal, Abel, Paten, Benedict, Seringhaus, Michael, Church, Deanna, Rosenbloom, Kate, Kent, W. James, Stone, Eric A., Batzoglou, Serafim, Goldman, Nick, Hardison, Ross C., Haussler, David, Miller, Webb, Sidow, Arend, Trinklein, Nathan D., Zhang, Zhengdong D., Barrera, Leah, Stuart, Rhona, King, David C., Ameur, Adam, Enroth, Stefan, Bieda, Mark C., Kim, Jonghwan, Bhinge, Akshay A., Jiang, Nan, Liu, Jun, Yao, Fei, Vega, Vinsensius B., Lee, Charlie W., Ng, Patrick, Yang, Annie, Moqtaderi, Zarmik, Zhu, Zhou, Xu, Xiaoqin, Squazzo, Sharon, Oberley, Matthew J., Inman, David, Singer, Michael A., Richmond, Todd A., Munn, Kyle J., Rada-Iglesias, Alvaro, Wallerman, Ola, Komorowski, Jan, Fowler, Joanna C., Couttet, Phillippe, Bruce, Alexander W., Dovey, Oliver M., Ellis, Peter D., Langford, Cordelia F., Nix, David A., Euskirchen, Ghia, Hartman, Stephen, Urban, Alexander E., Kraus, Peter, Van Calcar, Sara, Heintzman, Nate, Kim, Tae Hoon, Wang, Kun, Qu, Chunxu, Hon, Gary, Luna, Rosa, Glass, Christopher K., Rosenfeld, M. Geoff, Aldred, Shelley Force, Cooper, Sara J., Halees, Anason, Lin, Jane M., Shulha, Hennady P., Zhang, Xiaoling, Xu, Mousheng, Haidar, Jaafar N., Yu, Yong, Iyer, Vishwanath R., Green, Roland D., Wadelius, Claes, Farnham, Peggy J., Ren, Bing, Harte, Rachel A., Hinrichs, Angie S., Trumbower, Heather, Clawson, Hiram, Hillman-Jackson, Jennifer, Zweig, Ann S., Smith, Kayla, Thakkapallayil, Archana, Barber, Galt, Kuhn, Robert M., Karolchik, Donna, Armengol, Lluis, Bird, Christine P., de Bakker, Paul I., Kern, Andrew D., Lopez-Bigas, Nuria, Martin, Joel D., Stranger, Barbara E., Woodroffe, Abigail, Davydov, Eugene, Dimas, Antigone, Eyras, Eduardo, Hallgrímsdóttir, Ingileif B., Huppert, Julian, Zody, Michael C., Abecasis, G. R., Estivill, Xavier, Bouffard, Gerard G., Guan, Xiaobin, Hansen, Nancy F., Idol, Jacquelyn R., Maduro, Valerie V., Maskeri, Baishali, McDowell, Jennifer C., Park, Morgan, Thomas, Pamela J., Young, Alice C., Blakesley, Robert W., Muzny, Donna M., Sodergren, Erica, Wheeler, David A., Worley, Kim C., Jiang, Huaiyang, Weinstock, George M., Gibbs, Richard A., Graves, Tina, Fulton, Robert, Mardis, Elaine R., Wilson, Richard K., Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B., Chang, Jean L., Lindblad-Toh, Kerstin, Lander, Eric S., Koriabine, Maxim, Nefedov, Mikhail, Osoegawa, Kazutoyo, Yoshinaga, Yuko, Zhu, Baoli, de Jong, Pieter J., Birney, Ewan, Stamatoyannopoulos, John A., Dutta, Anindya, Guigó, Roderic, Gingeras, Thomas R., Margulies, Elliott H., Weng, Zhiping, Snyder, Michael, Dermitzakis, Emmanouil T., Thurman, Robert E., Kuehn, Michael S., Taylor, Christopher M., Neph, Shane, Koch, Christoph M., Asthana, Saurabh, Malhotra, Ankit, Adzhubei, Ivan, Greenbaum, Jason A., Andrews, Robert M., Flicek, Paul, Boyle, Patrick J., Cao, Hua, Carter, Nigel P., Clelland, Gayle K., Davis, Sean, Day, Nathan, Dhami, Pawandeep, Dillon, Shane C., Dorschner, Michael O., Fiegler, Heike, Giresi, Paul G., Goldy, Jeff, Hawrylycz, Michael, Haydock, Andrew, Humbert, Richard, James, Keith D., Johnson, Brett E., Johnson, Ericka M., Frum, Tristan T., Rosenzweig, Elizabeth R., Karnani, Neerja, Lee, Kirsten, Lefebvre, Gregory C., Navas, Patrick A., Neri, Fidencio, Parker, Stephen C., Sabo, Peter J., Sandstrom, Richard, Shafer, Anthony, Vetrie, David, Weaver, Molly, Wilcox, Sarah, Yu, Man, Collins, Francis S., Dekker, Job, Lieb, Jason D., Tullius, Thomas D., Crawford, Gregory E., Sunyaev, Shamil, Noble, William S., Dunham, Ian, Denoeud, France, Reymond, Alexandre, Kapranov, Philipp, Rozowsky, Joel, Zheng, Deyou, Castelo, Robert, Frankish, Adam, Harrow, Jennifer, Ghosh, Srinka, Sandelin, Albin, Hofacker, Ivo L., Baertsch, Robert, Keefe, Damian, Dike, Sujit, Cheng, Jill, Hirsch, Heather A., Sekinger, Edward A., Lagarde, Julien, Abril, Josep F., Shahab, Atif, Flamm, Christoph, Fried, Claudia, Hackermüller, Jörg, Hertel, Jana, Lindemeyer, Manja, Missal, Kristin, Tanzer, Andrea, Washietl, Stefan, Korbel, Jan, Emanuelsson, Olof, Pedersen, Jakob S., Holroyd, Nancy, Taylor, Ruth, Swarbreck, David, Matthews, Nicholas, Dickson, Mark C., Thomas, Daryl J., Weirauch, Matthew T., Gilbert, James, Drenkow, Jorg, Bell, Ian, Zhao, XiaoDong, Srinivasan, K. G., Sung, Wing-Kin, Ooi, Hong Sain, Chiu, Kuo Ping, Foissac, Sylvain, Alioto, Tyler, Brent, Michael, Pachter, Lior, Tress, Michael L., Valencia, Alfonso, Choo, Siew Woh, Choo, Chiou Yu, Ucla, Catherine, Manzano, Caroline, Wyss, Carine, Cheung, Evelyn, Clark, Taane G., Brown, James B., Ganesh, Madhavan, Patel, Sandeep, Tammana, Hari, Chrast, Jacqueline, Henrichsen, Charlotte N., Kai, Chikatoshi, Kawai, Jun, Nagalakshmi, Ugrappa, Wu, Jiaqian, Lian, Zheng, Lian, Jin, Newburger, Peter, Zhang, Xueqing, Bickel, Peter, Mattick, John S., Carninci, Piero, Hayashizaki, Yoshihide, Weissman, Sherman, Hubbard, Tim, Myers, Richard M., Rogers, Jane, Stadler, Peter F., Lowe, Todd M., Wei, Chia-Lin, Ruan, Yijun, Struhl, Kevin, Gerstein, Mark, Antonarakis, Stylianos E., Fu, Yutao, Green, Eric D., Karaöz, U., Siepel, Adam, Taylor, James, Liefer, Laura A, Wetterstrand, Kris A., Good, Peter J., Feingold, Elise A., Guyer, Mark S., Cooper, Gregory M., Asimenos, George, Dewey, Colin N., Hou, Minmei, Nikolaev, Sergey, Montoya-Burgos, Juan I., Löytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Huang, Haiyan, Zhang, Nancy R., Holmes, Ian, Mullikin, James C., Ureta-Vidal, Abel, Paten, Benedict, Seringhaus, Michael, Church, Deanna, Rosenbloom, Kate, Kent, W. James, Stone, Eric A., Batzoglou, Serafim, Goldman, Nick, Hardison, Ross C., Haussler, David, Miller, Webb, Sidow, Arend, Trinklein, Nathan D., Zhang, Zhengdong D., Barrera, Leah, Stuart, Rhona, King, David C., Ameur, Adam, Enroth, Stefan, Bieda, Mark C., Kim, Jonghwan, Bhinge, Akshay A., Jiang, Nan, Liu, Jun, Yao, Fei, Vega, Vinsensius B., Lee, Charlie W., Ng, Patrick, Yang, Annie, Moqtaderi, Zarmik, Zhu, Zhou, Xu, Xiaoqin, Squazzo, Sharon, Oberley, Matthew J., Inman, David, Singer, Michael A., Richmond, Todd A., Munn, Kyle J., Rada-Iglesias, Alvaro, Wallerman, Ola, Komorowski, Jan, Fowler, Joanna C., Couttet, Phillippe, Bruce, Alexander W., Dovey, Oliver M., Ellis, Peter D., Langford, Cordelia F., Nix, David A., Euskirchen, Ghia, Hartman, Stephen, Urban, Alexander E., Kraus, Peter, Van Calcar, Sara, Heintzman, Nate, Kim, Tae Hoon, Wang, Kun, Qu, Chunxu, Hon, Gary, Luna, Rosa, Glass, Christopher K., Rosenfeld, M. Geoff, Aldred, Shelley Force, Cooper, Sara J., Halees, Anason, Lin, Jane M., Shulha, Hennady P., Zhang, Xiaoling, Xu, Mousheng, Haidar, Jaafar N., Yu, Yong, Iyer, Vishwanath R., Green, Roland D., Wadelius, Claes, Farnham, Peggy J., Ren, Bing, Harte, Rachel A., Hinrichs, Angie S., Trumbower, Heather, Clawson, Hiram, Hillman-Jackson, Jennifer, Zweig, Ann S., Smith, Kayla, Thakkapallayil, Archana, Barber, Galt, Kuhn, Robert M., Karolchik, Donna, Armengol, Lluis, Bird, Christine P., de Bakker, Paul I., Kern, Andrew D., Lopez-Bigas, Nuria, Martin, Joel D., Stranger, Barbara E., Woodroffe, Abigail, Davydov, Eugene, Dimas, Antigone, Eyras, Eduardo, Hallgrímsdóttir, Ingileif B., Huppert, Julian, Zody, Michael C., Abecasis, G. R., Estivill, Xavier, Bouffard, Gerard G., Guan, Xiaobin, Hansen, Nancy F., Idol, Jacquelyn R., Maduro, Valerie V., Maskeri, Baishali, McDowell, Jennifer C., Park, Morgan, Thomas, Pamela J., Young, Alice C., Blakesley, Robert W., Muzny, Donna M., Sodergren, Erica, Wheeler, David A., Worley, Kim C., Jiang, Huaiyang, Weinstock, George M., Gibbs, Richard A., Graves, Tina, Fulton, Robert, Mardis, Elaine R., Wilson, Richard K., Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B., Chang, Jean L., Lindblad-Toh, Kerstin, Lander, Eric S., Koriabine, Maxim, Nefedov, Mikhail, Osoegawa, Kazutoyo, Yoshinaga, Yuko, Zhu, Baoli, and de Jong, Pieter J.
Abstract: We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
Published: 2007
Full Text: View/download PDF

31. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Author: Birney, Ewan, Stamatoyannopoulos, John A, Dutta, Anindya, Guigó, Roderic, Gingeras, Thomas R, Margulies, Elliott H, Weng, Zhiping, Snyder, Michael, Dermitzakis, Emmanouil T, Thurman, Robert E, Kuehn, Michael S, Taylor, Christopher M, Neph, Shane, Koch, Christoph M, Asthana, Saurabh, Malhotra, Ankit, Adzhubei, Ivan, Greenbaum, Jason A, Andrews, Robert M, Flicek, Paul, Boyle, Patrick J, Cao, Hua, Carter, Nigel P, Clelland, Gayle K, Davis, Sean, Day, Nathan, Dhami, Pawandeep, Dillon, Shane C, Dorschner, Michael O, Fiegler, Heike, Giresi, Paul G, Goldy, Jeff, Hawrylycz, Michael, Haydock, Andrew, Humbert, Richard, James, Keith D, Johnson, Brett E, Johnson, Ericka M, Frum, Tristan T, Rosenzweig, Elizabeth R, Karnani, Neerja, Lee, Kirsten, Lefebvre, Gregory C, Navas, Patrick A, Neri, Fidencio, Parker, Stephen C J, Sabo, Peter J, Sandstrom, Richard, Shafer, Anthony, Vetrie, David, Weaver, Molly, Wilcox, Sarah, Yu, Man, Collins, Francis S, Dekker, Job, Lieb, Jason D, Tullius, Thomas D, Crawford, Gregory E, Sunyaev, Shamil, Noble, William S, Dunham, Ian, Denoeud, France, Reymond, Alexandre, Kapranov, Philipp, Rozowsky, Joel, Zheng, Deyou, Castelo, Robert, Frankish, Adam, Harrow, Jennifer, Ghosh, Srinka, Sandelin, Albin, Hofacker, Ivo L, Baertsch, Robert, Keefe, Damian, Dike, Sujit, Cheng, Jill, Hirsch, Heather A, Sekinger, Edward A, Lagarde, Julien, Abril, Josep F, Shahab, Atif, Flamm, Christoph, Fried, Claudia, Hackermüller, Jörg, Hertel, Jana, Lindemeyer, Manja, Missal, Kristin, Tanzer, Andrea, Washietl, Stefan, Korbel, Jan, Emanuelsson, Olof, Pedersen, Jakob S, Holroyd, Nancy, Taylor, Ruth, Swarbreck, David, Matthews, Nicholas, Dickson, Mark C, Thomas, Daryl J, Weirauch, Matthew T, Gilbert, James, Drenkow, Jorg, Bell, Ian, Zhao, XiaoDong, Srinivasan, K G, Sung, Wing-Kin, Ooi, Hong Sain, Chiu, Kuo Ping, Foissac, Sylvain, Alioto, Tyler, Brent, Michael, Pachter, Lior, Tress, Michael L, Valencia, Alfonso, Choo, Siew Woh, Choo, Chiou Yu, Ucla, Catherine, Manzano, Caroline, Wyss, Carine, Cheung, Evelyn, Clark, Taane G, Brown, James B, Ganesh, Madhavan, Patel, Sandeep, Tammana, Hari, Chrast, Jacqueline, Henrichsen, Charlotte N, Kai, Chikatoshi, Kawai, Jun, Nagalakshmi, Ugrappa, Wu, Jiaqian, Lian, Zheng, Lian, Jin, Newburger, Peter, Zhang, Xueqing, Bickel, Peter, Mattick, John S, Carninci, Piero, Hayashizaki, Yoshihide, Weissman, Sherman, Hubbard, Tim, Myers, Richard M, Rogers, Jane, Stadler, Peter F, Lowe, Todd M, Wei, Chia-Lin, Ruan, Yijun, Struhl, Kevin, Gerstein, Mark, Antonarakis, Stylianos E, Fu, Yutao, Green, Eric D, Karaöz, Ulaş, Siepel, Adam, Taylor, James, Liefer, Laura A, Wetterstrand, Kris A, Good, Peter J, Feingold, Elise A, Guyer, Mark S, Cooper, Gregory M, Asimenos, George, Dewey, Colin N, Hou, Minmei, Nikolaev, Sergey, Montoya-Burgos, Juan I, Löytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Huang, Haiyan, Zhang, Nancy R, Holmes, Ian, Mullikin, James C, Ureta-Vidal, Abel, Paten, Benedict, Seringhaus, Michael, Church, Deanna, Rosenbloom, Kate, Kent, W James, Stone, Eric A, Batzoglou, Serafim, Goldman, Nick, Hardison, Ross C, Haussler, David, Miller, Webb, Sidow, Arend, Trinklein, Nathan D, Zhang, Zhengdong D, Barrera, Leah, Stuart, Rhona, King, David C, Ameur, Adam, Enroth, Stefan, Bieda, Mark C, Kim, Jonghwan, Bhinge, Akshay A, Jiang, Nan, Liu, Jun, Yao, Fei, Vega, Vinsensius B, Lee, Charlie W H, Ng, Patrick, Yang, Annie, Moqtaderi, Zarmik, Zhu, Zhou, Xu, Xiaoqin, Squazzo, Sharon, Oberley, Matthew J, Inman, David, Singer, Michael A, Richmond, Todd A, Munn, Kyle J, Rada-Iglesias, Alvaro, Wallerman, Ola, Komorowski, Jan, Fowler, Joanna C, Couttet, Phillippe, Bruce, Alexander W, Dovey, Oliver M, Ellis, Peter D, Langford, Cordelia F, Nix, David A, Euskirchen, Ghia, Hartman, Stephen, Urban, Alexander E, Kraus, Peter, Van Calcar, Sara, Heintzman, Nate, Kim, Tae Hoon, Wang, Kun, Qu, Chunxu, Hon, Gary, Luna, Rosa, Glass, Christopher K, Rosenfeld, M Geoff, Aldred, Shelley Force, Cooper, Sara J, Halees, Anason, Lin, Jane M, Shulha, Hennady P, Zhang, Xiaoling, Xu, Mousheng, Haidar, Jaafar N S, Yu, Yong, Iyer, Vishwanath R, Green, Roland D, Wadelius, Claes, Farnham, Peggy J, Ren, Bing, Harte, Rachel A, Hinrichs, Angie S, Trumbower, Heather, Clawson, Hiram, Hillman-Jackson, Jennifer, Zweig, Ann S, Smith, Kayla, Thakkapallayil, Archana, Barber, Galt, Kuhn, Robert M, Karolchik, Donna, Armengol, Lluis, Bird, Christine P, de Bakker, Paul I W, Kern, Andrew D, Lopez-Bigas, Nuria, Martin, Joel D, Stranger, Barbara E, Woodroffe, Abigail, Davydov, Eugene, Dimas, Antigone, Eyras, Eduardo, Hallgrímsdóttir, Ingileif B, Huppert, Julian, Zody, Michael C, Abecasis, Gonçalo R, Estivill, Xavier, Bouffard, Gerard G, Guan, Xiaobin, Hansen, Nancy F, Idol, Jacquelyn R, Maduro, Valerie V B, Maskeri, Baishali, McDowell, Jennifer C, Park, Morgan, Thomas, Pamela J, Young, Alice C, Blakesley, Robert W, Muzny, Donna M, Sodergren, Erica, Wheeler, David A, Worley, Kim C, Jiang, Huaiyang, Weinstock, George M, Gibbs, Richard A, Graves, Tina, Fulton, Robert, Mardis, Elaine R, Wilson, Richard K, Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B, Chang, Jean L, Lindblad-Toh, Kerstin, Lander, Eric S, Koriabine, Maxim, Nefedov, Mikhail, Osoegawa, Kazutoyo, Yoshinaga, Yuko, Zhu, Baoli, de Jong, Pieter J, Birney, Ewan, Stamatoyannopoulos, John A, Dutta, Anindya, Guigó, Roderic, Gingeras, Thomas R, Margulies, Elliott H, Weng, Zhiping, Snyder, Michael, Dermitzakis, Emmanouil T, Thurman, Robert E, Kuehn, Michael S, Taylor, Christopher M, Neph, Shane, Koch, Christoph M, Asthana, Saurabh, Malhotra, Ankit, Adzhubei, Ivan, Greenbaum, Jason A, Andrews, Robert M, Flicek, Paul, Boyle, Patrick J, Cao, Hua, Carter, Nigel P, Clelland, Gayle K, Davis, Sean, Day, Nathan, Dhami, Pawandeep, Dillon, Shane C, Dorschner, Michael O, Fiegler, Heike, Giresi, Paul G, Goldy, Jeff, Hawrylycz, Michael, Haydock, Andrew, Humbert, Richard, James, Keith D, Johnson, Brett E, Johnson, Ericka M, Frum, Tristan T, Rosenzweig, Elizabeth R, Karnani, Neerja, Lee, Kirsten, Lefebvre, Gregory C, Navas, Patrick A, Neri, Fidencio, Parker, Stephen C J, Sabo, Peter J, Sandstrom, Richard, Shafer, Anthony, Vetrie, David, Weaver, Molly, Wilcox, Sarah, Yu, Man, Collins, Francis S, Dekker, Job, Lieb, Jason D, Tullius, Thomas D, Crawford, Gregory E, Sunyaev, Shamil, Noble, William S, Dunham, Ian, Denoeud, France, Reymond, Alexandre, Kapranov, Philipp, Rozowsky, Joel, Zheng, Deyou, Castelo, Robert, Frankish, Adam, Harrow, Jennifer, Ghosh, Srinka, Sandelin, Albin, Hofacker, Ivo L, Baertsch, Robert, Keefe, Damian, Dike, Sujit, Cheng, Jill, Hirsch, Heather A, Sekinger, Edward A, Lagarde, Julien, Abril, Josep F, Shahab, Atif, Flamm, Christoph, Fried, Claudia, Hackermüller, Jörg, Hertel, Jana, Lindemeyer, Manja, Missal, Kristin, Tanzer, Andrea, Washietl, Stefan, Korbel, Jan, Emanuelsson, Olof, Pedersen, Jakob S, Holroyd, Nancy, Taylor, Ruth, Swarbreck, David, Matthews, Nicholas, Dickson, Mark C, Thomas, Daryl J, Weirauch, Matthew T, Gilbert, James, Drenkow, Jorg, Bell, Ian, Zhao, XiaoDong, Srinivasan, K G, Sung, Wing-Kin, Ooi, Hong Sain, Chiu, Kuo Ping, Foissac, Sylvain, Alioto, Tyler, Brent, Michael, Pachter, Lior, Tress, Michael L, Valencia, Alfonso, Choo, Siew Woh, Choo, Chiou Yu, Ucla, Catherine, Manzano, Caroline, Wyss, Carine, Cheung, Evelyn, Clark, Taane G, Brown, James B, Ganesh, Madhavan, Patel, Sandeep, Tammana, Hari, Chrast, Jacqueline, Henrichsen, Charlotte N, Kai, Chikatoshi, Kawai, Jun, Nagalakshmi, Ugrappa, Wu, Jiaqian, Lian, Zheng, Lian, Jin, Newburger, Peter, Zhang, Xueqing, Bickel, Peter, Mattick, John S, Carninci, Piero, Hayashizaki, Yoshihide, Weissman, Sherman, Hubbard, Tim, Myers, Richard M, Rogers, Jane, Stadler, Peter F, Lowe, Todd M, Wei, Chia-Lin, Ruan, Yijun, Struhl, Kevin, Gerstein, Mark, Antonarakis, Stylianos E, Fu, Yutao, Green, Eric D, Karaöz, Ulaş, Siepel, Adam, Taylor, James, Liefer, Laura A, Wetterstrand, Kris A, Good, Peter J, Feingold, Elise A, Guyer, Mark S, Cooper, Gregory M, Asimenos, George, Dewey, Colin N, Hou, Minmei, Nikolaev, Sergey, Montoya-Burgos, Juan I, Löytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Huang, Haiyan, Zhang, Nancy R, Holmes, Ian, Mullikin, James C, Ureta-Vidal, Abel, Paten, Benedict, Seringhaus, Michael, Church, Deanna, Rosenbloom, Kate, Kent, W James, Stone, Eric A, Batzoglou, Serafim, Goldman, Nick, Hardison, Ross C, Haussler, David, Miller, Webb, Sidow, Arend, Trinklein, Nathan D, Zhang, Zhengdong D, Barrera, Leah, Stuart, Rhona, King, David C, Ameur, Adam, Enroth, Stefan, Bieda, Mark C, Kim, Jonghwan, Bhinge, Akshay A, Jiang, Nan, Liu, Jun, Yao, Fei, Vega, Vinsensius B, Lee, Charlie W H, Ng, Patrick, Yang, Annie, Moqtaderi, Zarmik, Zhu, Zhou, Xu, Xiaoqin, Squazzo, Sharon, Oberley, Matthew J, Inman, David, Singer, Michael A, Richmond, Todd A, Munn, Kyle J, Rada-Iglesias, Alvaro, Wallerman, Ola, Komorowski, Jan, Fowler, Joanna C, Couttet, Phillippe, Bruce, Alexander W, Dovey, Oliver M, Ellis, Peter D, Langford, Cordelia F, Nix, David A, Euskirchen, Ghia, Hartman, Stephen, Urban, Alexander E, Kraus, Peter, Van Calcar, Sara, Heintzman, Nate, Kim, Tae Hoon, Wang, Kun, Qu, Chunxu, Hon, Gary, Luna, Rosa, Glass, Christopher K, Rosenfeld, M Geoff, Aldred, Shelley Force, Cooper, Sara J, Halees, Anason, Lin, Jane M, Shulha, Hennady P, Zhang, Xiaoling, Xu, Mousheng, Haidar, Jaafar N S, Yu, Yong, Iyer, Vishwanath R, Green, Roland D, Wadelius, Claes, Farnham, Peggy J, Ren, Bing, Harte, Rachel A, Hinrichs, Angie S, Trumbower, Heather, Clawson, Hiram, Hillman-Jackson, Jennifer, Zweig, Ann S, Smith, Kayla, Thakkapallayil, Archana, Barber, Galt, Kuhn, Robert M, Karolchik, Donna, Armengol, Lluis, Bird, Christine P, de Bakker, Paul I W, Kern, Andrew D, Lopez-Bigas, Nuria, Martin, Joel D, Stranger, Barbara E, Woodroffe, Abigail, Davydov, Eugene, Dimas, Antigone, Eyras, Eduardo, Hallgrímsdóttir, Ingileif B, Huppert, Julian, Zody, Michael C, Abecasis, Gonçalo R, Estivill, Xavier, Bouffard, Gerard G, Guan, Xiaobin, Hansen, Nancy F, Idol, Jacquelyn R, Maduro, Valerie V B, Maskeri, Baishali, McDowell, Jennifer C, Park, Morgan, Thomas, Pamela J, Young, Alice C, Blakesley, Robert W, Muzny, Donna M, Sodergren, Erica, Wheeler, David A, Worley, Kim C, Jiang, Huaiyang, Weinstock, George M, Gibbs, Richard A, Graves, Tina, Fulton, Robert, Mardis, Elaine R, Wilson, Richard K, Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B, Chang, Jean L, Lindblad-Toh, Kerstin, Lander, Eric S, Koriabine, Maxim, Nefedov, Mikhail, Osoegawa, Kazutoyo, Yoshinaga, Yuko, Zhu, Baoli, and de Jong, Pieter J
Abstract: We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function., QC 20111222
Published: 2007
Full Text: View/download PDF

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31 results on '"Jiang, Huaiyang"'

1. Gene variants identified by whole-exome sequencing in 33 French women with premature ovarian insufficiency.

2. X-linked ADGRG2 mutation and obstructive azoospermia in a large Pakistani family.

3. Functional study of a novel missense single-nucleotide variant of NUP107 in two daughters of Mexican origin with premature ovarian insufficiency.

4. Functional study of a novel missense single-nucleotide variant of NUP107 in two daughters of Mexican origin with premature ovarian insufficiency.

5. X-linked ADGRG2 mutation and obstructive azoospermia in a large Pakistani family.

6. Exome sequencing reveals MCM8 mutation underlies ovarian failure and chromosomal instability.

7. Finding the missing honey bee genes: Lessons learned from a genome upgrade

8. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

9. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

10. Finding the missing honey bee genes: lessons learned from a genome upgrade

11. Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

12. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

13. MCM9 mutations are associated with ovarian failure, short stature, and chromosomal instability.

14. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

15. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

16. Finding the Missing Honey Bee Genes: Lessons Learned From a Genome Upgrade.

17. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

18. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

19. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

20. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

21. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

22. Genome Sequence of the Pea Aphid Acyrthosiphon pisum

23. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

24. Genome Sequence of the Pea Aphid Acyrthosiphon pisum

25. Genome Sequence of the Pea Aphid Acyrthosiphon pisum

26. Genome Sequence of the Pea Aphid Acyrthosiphon pisum

27. Genome Sequence of the Pea Aphid Acyrthosiphon pisum

28. The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution

29. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

30. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

31. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

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31 results on '"Jiang, Huaiyang"'

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