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1. Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus

Author

Hawes Alicia C, Dinh Huyen H, Buhay Christian J, Blyth Peter R, Dugan Shannon, Ding Yan, Hemphill Lisa, Muzny Donna M, Cardenas Ana, Fox George E, Uzman Akif, Tirumalai Madhan, Petrosino Joseph, Igboeli Okezie, Liu Yamei, Fortunov Régine M, Williams Tiffany M, Shang Yue, Mason Edward O, Yerrapragada Shailaja, Jiang Huaiyang, Qin Xiang, Hultén Kristina G, Highlander Sarah K, Holder Michael, Kovar Christie L, Lee Sandra L, Liu Wen, Nazareth Lynne V, Wang Qiaoyan, Zhou Jianling, Kaplan Sheldon L, and Weinstock George M

Subjects
Microbiology, QR1-502
Abstract

Abstract Background Community acquired (CA) methicillin-resistant Staphylococcus aureus (MRSA) increasingly causes disease worldwide. USA300 has emerged as the predominant clone causing superficial and invasive infections in children and adults in the USA. Epidemiological studies suggest that USA300 is more virulent than other CA-MRSA. The genetic determinants that render virulence and dominance to USA300 remain unclear. Results We sequenced the genomes of two pediatric USA300 isolates: one CA-MRSA and one CA-methicillin susceptible (MSSA), isolated at Texas Children's Hospital in Houston. DNA sequencing was performed by Sanger dideoxy whole genome shotgun (WGS) and 454 Life Sciences pyrosequencing strategies. The sequence of the USA300 MRSA strain was rigorously annotated. In USA300-MRSA 2658 chromosomal open reading frames were predicted and 3.1 and 27 kilobase (kb) plasmids were identified. USA300-MSSA contained a 20 kb plasmid with some homology to the 27 kb plasmid found in USA300-MRSA. Two regions found in US300-MRSA were absent in USA300-MSSA. One of these carried the arginine deiminase operon that appears to have been acquired from S. epidermidis. The USA300 sequence was aligned with other sequenced S. aureus genomes and regions unique to USA300 MRSA were identified. Conclusion USA300-MRSA is highly similar to other MRSA strains based on whole genome alignments and gene content, indicating that the differences in pathogenesis are due to subtle changes rather than to large-scale acquisition of virulence factor genes. The USA300 Houston isolate differs from another sequenced USA300 strain isolate, derived from a patient in San Francisco, in plasmid content and a number of sequence polymorphisms. Such differences will provide new insights into the evolution of pathogens.

Published
2007
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2. Implementation of preemptive DNA sequence–based pharmacogenomics testing across a large academic medical center: The Mayo-Baylor RIGHT 10K Study

Author

Wang, Liewei, Scherer, Steven E., Bielinski, Suzette J., Muzny, Donna M., Jones, Leila A., Black, John Logan, III, Moyer, Ann M., Giri, Jyothsna, Sharp, Richard R., Matey, Eric T., Wright, Jessica A., Oyen, Lance J., Nicholson, Wayne T., Wiepert, Mathieu, Sullard, Terri, Curry, Timothy B., Rohrer Vitek, Carolyn R., McAllister, Tammy M., St. Sauver, Jennifer L., Caraballo, Pedro J., Lazaridis, Konstantinos N., Venner, Eric, Qin, Xiang, Hu, Jianhong, Kovar, Christie L., Korchina, Viktoriya, Walker, Kimberly, Doddapaneni, HarshaVardhan, Wu, Tsung-Jung, Raj, Ritika, Denson, Shawn, Liu, Wen, Chandanavelli, Gauthami, Zhang, Lan, Wang, Qiaoyan, Kalra, Divya, Karow, Mary Beth, Harris, Kimberley J., Sicotte, Hugues, Peterson, Sandra E., Barthel, Amy E., Moore, Brenda E., Skierka, Jennifer M., Kluge, Michelle L., Kotzer, Katrina E., Kloke, Karen, Vander Pol, Jessica M., Marker, Heather, Sutton, Joseph A., Kekic, Adrijana, Ebenhoh, Ashley, Bierle, Dennis M., Schuh, Michael J., Grilli, Christopher, Erickson, Sara, Umbreit, Audrey, Ward, Leah, Crosby, Sheena, Nelson, Eric A., Levey, Sharon, Elliott, Michelle, Peters, Steve G., Pereira, Naveen, Frye, Mark, Shamoun, Fadi, Goetz, Matthew P., Kullo, Iftikhar J., Wermers, Robert, Anderson, Jan A., Formea, Christine M., El Melik, Razan M., Zeuli, John D., Herges, Joseph R., Krieger, Carrie A., Hoel, Robert W., Taraba, Jodi L., St. Thomas, Scott R., Absah, Imad, Bernard, Matthew E., Fink, Stephanie R., Gossard, Andrea, Grubbs, Pamela L., Jacobson, Therese M., Takahashi, Paul, Zehe, Sharon C., Buckles, Susan, Bumgardner, Michelle, Gallagher, Colette, Fee-Schroeder, Kelliann, Nicholas, Nichole R., Powers, Melody L., Ragab, Ahmed K., Richardson, Darcy M., Stai, Anthony, Wilson, Jaymi, Pacyna, Joel E., Olson, Janet E., Sutton, Erica J., Beck, Annika T., Horrow, Caroline, Kalari, Krishna R., Larson, Nicholas B., Liu, Hongfang, Wang, Liwei, Lopes, Guilherme S., Borah, Bijan J., Freimuth, Robert R., Zhu, Ye, Jacobson, Debra J., Hathcock, Matthew A., Armasu, Sebastian M., McGree, Michaela E., Jiang, Ruoxiang, Koep, Tyler H., Ross, Jason L., Hilden, Matthew G., Bosse, Kathleen, Ramey, Bronwyn, Searcy, Isabelle, Boerwinkle, Eric, Gibbs, Richard A., and Weinshilboum, Richard M.

Published
2022
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3. Hemichordate genomes and deuterostome origins.

Author

Simakov, Oleg, Kawashima, Takeshi, Marlétaz, Ferdinand, Jenkins, Jerry, Koyanagi, Ryo, Mitros, Therese, Hisata, Kanako, Bredeson, Jessen, Shoguchi, Eiichi, Gyoja, Fuki, Yue, Jia-Xing, Chen, Yi-Chih, Freeman, Robert M, Sasaki, Akane, Hikosaka-Katayama, Tomoe, Sato, Atsuko, Fujie, Manabu, Baughman, Kenneth W, Levine, Judith, Gonzalez, Paul, Cameron, Christopher, Fritzenwanker, Jens H, Pani, Ariel M, Goto, Hiroki, Kanda, Miyuki, Arakaki, Nana, Yamasaki, Shinichi, Qu, Jiaxin, Cree, Andrew, Ding, Yan, Dinh, Huyen H, Dugan, Shannon, Holder, Michael, Jhangiani, Shalini N, Kovar, Christie L, Lee, Sandra L, Lewis, Lora R, Morton, Donna, Nazareth, Lynne V, Okwuonu, Geoffrey, Santibanez, Jireh, Chen, Rui, Richards, Stephen, Muzny, Donna M, Gillis, Andrew, Peshkin, Leonid, Wu, Michael, Humphreys, Tom, Su, Yi-Hsien, Putnam, Nicholas H, Schmutz, Jeremy, Fujiyama, Asao, Yu, Jr-Kai, Tagawa, Kunifumi, Worley, Kim C, Gibbs, Richard A, Kirschner, Marc W, Lowe, Christopher J, Satoh, Noriyuki, Rokhsar, Daniel S, and Gerhart, John

Subjects
Animals, Chordata, Nonvertebrate, Echinodermata, Transforming Growth Factor beta, Evolution, Molecular, Phylogeny, Signal Transduction, Conserved Sequence, Synteny, Multigene Family, Genome, Chordata, Nonvertebrate, Evolution, Molecular, General Science & Technology
Abstract

Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal 'gill' slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.

Published
2015

4. Author Correction: Comparative and demographic analysis of orang-utan genomes

Author

Locke, Devin P., Hillier, LaDeana W., Warren, Wesley C., Worley, Kim C., Nazareth, Lynne V., Muzny, Donna M., Yang, Shiaw-Pyng, Wang, Zhengyuan, Chinwalla, Asif T., Minx, Pat, Mitreva, Makedonka, Cook, Lisa, Delehaunty, Kim D., Fronick, Catrina, Schmidt, Heather, Fulton, Lucinda A., Fulton, Robert S., Nelson, Joanne O., Magrini, Vincent, Pohl, Craig, Graves, Tina A., Markovic, Chris, Cree, Andy, Dinh, Huyen H., Hume, Jennifer, Kovar, Christie L., Fowler, Gerald R., Lunter, Gerton, Meader, Stephen, Heger, Andreas, Ponting, Chris P., Marques-Bonet, Tomas, Alkan, Can, Chen, Lin, Cheng, Ze, Kidd, Jeffrey M., Eichler, Evan E., White, Simon, Searle, Stephen, Vilella, Albert J., Chen, Yuan, Flicek, Paul, Ma, Jian, Raney, Brian, Suh, Bernard, Burhans, Richard, Herrero, Javier, Haussler, David, Faria, Rui, Fernando, Olga, Darré, Fleur, Farré, Domènec, Gazave, Elodie, Oliva, Meritxell, Navarro, Arcadi, Roberto, Roberta, Capozzi, Oronzo, Archidiacono, Nicoletta, Della Valle, Giuliano, Purgato, Stefania, Rocchi, Mariano, Konkel, Miriam K., Walker, Jerilyn A., Ullmer, Brygg, Batzer, Mark A., Smit, Arian F. A., Hubley, Robert, Casola, Claudio, Schrider, Daniel R., Hahn, Matthew W., Quesada, Victor, Puente, Xose S., Ordoñez, Gonzalo R., López-Otín, Carlos, Vinar, Tomas, Brejova, Brona, Ratan, Aakrosh, Harris, Robert S., Miller, Webb, Kosiol, Carolin, Lawson, Heather A., Taliwal, Vikas, Martins, André L., Siepel, Adam, RoyChoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos D., Gutenkunst, Ryan N., Mailund, Thomas, Dutheil, Julien Y., Hobolth, Asger, Schierup, Mikkel H., Ryder, Oliver A., Yoshinaga, Yuko, de Jong, Pieter J., Weinstock, George M., Rogers, Jeffrey, Mardis, Elaine R., Gibbs, Richard A., and Wilson, Richard K.

Published
2022
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5. Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Author

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

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Animals, Cluster Analysis, Computational Biology, Drosophila melanogaster, Evolution, Molecular, Exons, Female, Gene Expression Profiling, Genome, Insect, Humans, Male, Molecular Sequence Annotation, Nucleotide Motifs, Phylogeny, Position-Specific Scoring Matrices, Promoter Regions, Genetic, RNA Editing, RNA Splice Sites, RNA Splicing, Reproducibility of Results, Transcription Initiation Site, Transcriptome, Medical and Health Sciences, Bioinformatics
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

6. Targeted sequencing in candidate genes for atrial fibrillation: The Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Targeted Sequencing Study

Author

Lin, Honghuang, Sinner, Moritz F, Brody, Jennifer A, Arking, Dan E, Lunetta, Kathryn L, Rienstra, Michiel, Lubitz, Steven A, Magnani, Jared W, Sotoodehnia, Nona, McKnight, Barbara, McManus, David D, Boerwinkle, Eric, Psaty, Bruce M, Rotter, Jerome I, Bis, Joshua C, Gibbs, Richard A, Muzny, Donna, Kovar, Christie L, Morrison, Alanna C, Gupta, Mayetri, Folsom, Aaron R, Kääb, Stefan, Heckbert, Susan R, Alonso, Alvaro, Ellinor, Patrick T, Benjamin, Emelia J, and Group, on behalf of the CHARGE Atrial Fibrillation Working

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Human Genome, Cardiovascular, Biotechnology, Aging, Genetics, Heart Disease, Aetiology, 2.1 Biological and endogenous factors, Aged, Atrial Fibrillation, Female, Genetic Predisposition to Disease, Genetic Variation, Genome-Wide Association Study, Homeodomain Proteins, Humans, Linkage Disequilibrium, Male, Middle Aged, Polymorphism, Single Nucleotide, Receptors, Interleukin-6, Arrhythmia, Atrial fibrillation, Epidemiology, CHARGE Atrial Fibrillation Working Group, Biomedical Engineering, Cardiorespiratory Medicine and Haematology, Cardiovascular System & Hematology, Cardiovascular medicine and haematology
Abstract

BackgroundGenome-wide association studies (GWAS) have identified common genetic variants that predispose to atrial fibrillation (AF). It is unclear whether rare and low-frequency variants in genes implicated by such GWAS confer additional risk of AF.ObjectiveTo study the association of genetic variants with AF at GWAS top loci.MethodsIn the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Targeted Sequencing Study, we selected and sequenced 77 target gene regions from GWAS loci of complex diseases or traits, including 4 genes hypothesized to be related to AF (PRRX1, CAV1, CAV2, and ZFHX3). Sequencing was performed in participants with (n = 948) and without (n = 3330) AF from the Atherosclerosis Risk in Communities Study, the Cardiovascular Health Study, the Framingham Heart Study, and the Massachusetts General Hospital.ResultsOne common variant (rs11265611; P = 1.70 × 10(-6)) intronic to IL6R (interleukin-6 receptor gene) was significantly associated with AF after Bonferroni correction (odds ratio 0.70; 95% confidence interval 0.58-0.85). The variant was not genotyped or imputed by prior GWAS, but it is in linkage disequilibrium (r(2) = .69) with the single-nucleotide polymorphism, with the strongest association with AF so far at this locus (rs4845625). In the rare variant joint analysis, damaging variants within the PRRX1 region showed significant association with AF after Bonferroni correction (P = .01).ConclusionsWe identified 1 common single-nucleotide polymorphism and 1 gene region that were significantly associated with AF. Future sequencing efforts with larger sample sizes and more comprehensive genome coverage are anticipated to identify additional AF-related variants.

Published
2014

7. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

Author

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

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Prevention, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Arthropods, Circadian Rhythm Signaling Peptides and Proteins, DNA Methylation, Evolution, Molecular, Female, Genome, Genome, Mitochondrial, Hormones, Male, Multigene Family, Phylogeny, Polymorphism, Genetic, Protein Kinases, RNA, Untranslated, Receptors, Odorant, Selenoproteins, Sex Chromosomes, Synteny, Transcription Factors, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
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 history.

Published
2014

8. A high-resolution map of human evolutionary constraint using 29 mammals.

Author

Lindblad-Toh, Kerstin, Garber, Manuel, Zuk, Or, Lin, Michael F, Parker, Brian J, Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Jordan, Gregory, Mauceli, Evan, Ward, Lucas D, Lowe, Craig B, Holloway, Alisha K, Clamp, Michele, Gnerre, Sante, Alföldi, Jessica, Beal, Kathryn, Chang, Jean, Clawson, Hiram, Cuff, James, Di Palma, Federica, Fitzgerald, Stephen, Flicek, Paul, Guttman, Mitchell, Hubisz, Melissa J, Jaffe, David B, Jungreis, Irwin, Kent, W James, Kostka, Dennis, Lara, Marcia, Martins, Andre L, Massingham, Tim, Moltke, Ida, Raney, Brian J, Rasmussen, Matthew D, Robinson, Jim, Stark, Alexander, Vilella, Albert J, Wen, Jiayu, Xie, Xiaohui, Zody, Michael C, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin, Jen, Bloom, Toby, Chin, Chee Whye, Heiman, Dave, Nicol, Robert, Nusbaum, Chad, Young, Sarah, Wilkinson, Jane, Worley, Kim C, Kovar, Christie L, Muzny, Donna M, Gibbs, Richard A, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree, Andrew, Dihn, Huyen H, Fowler, Gerald, Jhangiani, Shalili, Joshi, Vandita, Lee, Sandra, Lewis, Lora R, Nazareth, Lynne V, Okwuonu, Geoffrey, Santibanez, Jireh, Warren, Wesley C, Mardis, Elaine R, Weinstock, George M, Wilson, Richard K, Genome Institute at Washington University, Delehaunty, Kim, Dooling, David, Fronik, Catrina, Fulton, Lucinda, Fulton, Bob, Graves, Tina, Minx, Patrick, Sodergren, Erica, Birney, Ewan, Margulies, Elliott H, Herrero, Javier, Green, Eric D, Haussler, David, Siepel, Adam, Goldman, Nick, Pollard, Katherine S, Pedersen, Jakob S, Lander, Eric S, and Kellis, Manolis

Subjects
Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Animals, Mammals, Humans, Disease, RNA, Sequence Alignment, Sequence Analysis, DNA, Genomics, Evolution, Molecular, Phylogeny, Genome, Genome, Human, Exons, Health, Selection, Genetic, Molecular Sequence Annotation, Sequence Analysis, DNA, Evolution, Molecular, Human, Selection, Genetic, General Science & Technology
Abstract

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.

Published
2011

9. The sheep genome illuminates biology of the rumen and lipid metabolism

Author

Jiang, Yu, Xie, Min, Chen, Wenbin, Talbot, Richard, Maddox, Jillian F., Faraut, Thomas, Wu, Chunhua, Muzny, Donna M., Li, Yuxiang, Zhang, Wenguang, Stanton, Jo-Ann, Brauning, Rudiger, Barris, Wesley C., Hourlier, Thibaut, Aken, Bronwen L., Searle, Stephen M. J., Adelson, David L., Bian, Chao, Cam, Graham R., Chen, Yulin, Cheng, Shifeng, DeSilva, Udaya, Dixen, Karen, Dong, Yang, Fan, Guangyi, Franklin, Ian R., Fu, Shaoyin, Fuentes-Utrilla, Pablo, Guan, Rui, Highland, Margaret A., Holder, Michael E., Huang, Guodong, Ingham, Aaron B., Jhangiani, Shalini N., Kalra, Divya, Kovar, Christie L., Lee, Sandra L., Liu, Weiqing, Liu, Xin, Lu, Changxin, Lv, Tian, Mathew, Tittu, McWilliam, Sean, Menzies, Moira, Pan, Shengkai, Robelin, David, Servin, Bertrand, Townley, David, Wang, Wenliang, Wei, Bin, White, Stephen N., Yang, Xinhua, Ye, Chen, Yue, Yaojing, Zeng, Peng, Zhou, Qing, Hansen, Jacob B., Kristiansen, Karsten, Gibbs, Richard A., Flicek, Paul, Warkup, Christopher C., Jones, Huw E., Oddy, V. Hutton, Nicholas, Frank W., McEwan, John C., Kijas, James W., Wang, Jun, Worley, Kim C., Archibald, Alan L., Cockett, Noelle, Xu, Xun, Wang, Wen, and Dalrymple, Brian P.

Published
2014

10. Whole-exome sequencing of 14 389 individuals from the ESP and CHARGE consortia identifies novel rare variation associated with hemostatic factors

Author

Pankratz, Nathan, primary, Wei, Peng, additional, Brody, Jennifer A, additional, Chen, Ming-Huei, additional, de Vries, Paul S, additional, Huffman, Jennifer E, additional, Stimson, Mary Rachel, additional, Auer, Paul L, additional, Boerwinkle, Eric, additional, Cushman, Mary, additional, de Maat, Moniek P M, additional, Folsom, Aaron R, additional, Franco, Oscar H, additional, Gibbs, Richard A, additional, Haagenson, Kelly K, additional, Hofman, Albert, additional, Johnsen, Jill M, additional, Kovar, Christie L, additional, Kraaij, Robert, additional, McKnight, Barbara, additional, Metcalf, Ginger A, additional, Muzny, Donna, additional, Psaty, Bruce M, additional, Tang, Weihong, additional, Uitterlinden, André G, additional, van Rooij, Jeroen G J, additional, Dehghan, Abbas, additional, O'Donnell, Christopher J, additional, Reiner, Alex P, additional, Morrison, Alanna C, additional, and Smith, Nicholas L, additional

Published
2022
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11. Whole-exome sequencing of 14 389 individuals from the ESP and CHARGE consortia identifies novel rare variation associated with hemostatic factors

Author

Pankratz, Nathan, Wei, Peng, Brody, Jennifer A., Chen, Ming Huei, de Vries, Paul S., Huffman, Jennifer E., Stimson, Mary Rachel, Auer, Paul L., Boerwinkle, Eric, Cushman, Mary, de Maat, Moniek P.M., Folsom, Aaron R., Franco, Oscar H., Gibbs, Richard A., Haagenson, Kelly K., Hofman, Albert, Johnsen, Jill M., Kovar, Christie L., Kraaij, Robert, McKnight, Barbara, Metcalf, Ginger A., Muzny, Donna, Psaty, Bruce M., Tang, Weihong, Uitterlinden, André G., van Rooij, Jeroen G.J., Dehghan, Abbas, O'Donnell, Christopher J., Reiner, Alex P., Morrison, Alanna C., Smith, Nicholas L., Pankratz, Nathan, Wei, Peng, Brody, Jennifer A., Chen, Ming Huei, de Vries, Paul S., Huffman, Jennifer E., Stimson, Mary Rachel, Auer, Paul L., Boerwinkle, Eric, Cushman, Mary, de Maat, Moniek P.M., Folsom, Aaron R., Franco, Oscar H., Gibbs, Richard A., Haagenson, Kelly K., Hofman, Albert, Johnsen, Jill M., Kovar, Christie L., Kraaij, Robert, McKnight, Barbara, Metcalf, Ginger A., Muzny, Donna, Psaty, Bruce M., Tang, Weihong, Uitterlinden, André G., van Rooij, Jeroen G.J., Dehghan, Abbas, O'Donnell, Christopher J., Reiner, Alex P., Morrison, Alanna C., and Smith, Nicholas L.

Abstract

Plasma levels of fibrinogen, coagulation factors VII and VIII and von Willebrand factor (vWF) are four intermediate phenotypes that are heritable and have been associated with the risk of clinical thrombotic events. To identify rare and low-frequency variants associated with these hemostatic factors, we conducted whole-exome sequencing in 10 860 individuals of European ancestry (EA) and 3529 African Americans (AAs) from the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium and the National Heart, Lung and Blood Institute's Exome Sequencing Project. Gene-based tests demonstrated significant associations with rare variation (minor allele frequency < 5%) in fibrinogen gamma chain (FGG) (with fibrinogen, P = 9.1 × 10-13), coagulation factor VII (F7) (with factor VII, P = 1.3 × 10-72; seven novel variants) and VWF (with factor VIII and vWF; P = 3.2 × 10-14; one novel variant). These eight novel rare variant associations were independent of the known common variants at these loci and tended to have much larger effect sizes. In addition, one of the rare novel variants in F7 was significantly associated with an increased risk of venous thromboembolism in AAs (Ile200Ser; rs141219108; P = 4.2 × 10-5). After restricting gene-based analyses to only loss-of-function variants, a novel significant association was detected and replicated between factor VIII levels and a stop-gain mutation exclusive to AAs (rs3211938) in CD36 molecule (CD36). This variant has previously been linked to dyslipidemia but not with the levels of a hemostatic factor. These efforts represent the largest integration of whole-exome sequence data from two national projects to identify genetic variation associated with plasma hemostatic factors.

Published
2022

12. Genetic testing in ambulatory cardiology clinics reveals high rate of findings with clinical management implications

Author

Murdock, David R., primary, Venner, Eric, additional, Muzny, Donna M., additional, Metcalf, Ginger A., additional, Murugan, Mullai, additional, Hadley, Trevor D., additional, Chander, Varuna, additional, de Vries, Paul S., additional, Jia, Xiaoming, additional, Hussain, Aliza, additional, Agha, Ali M., additional, Sabo, Aniko, additional, Li, Shoudong, additional, Meng, Qingchang, additional, Hu, Jianhong, additional, Tian, Xia, additional, Cohen, Michelle, additional, Yi, Victoria, additional, Kovar, Christie L., additional, Gingras, Marie-Claude, additional, Korchina, Viktoriya, additional, Howard, Chad, additional, Riconda, Daniel L., additional, Pereira, Stacey, additional, Smith, Hadley S., additional, Huda, Zohra A., additional, Buentello, Alexandria, additional, Marino, Patricia R., additional, Leiber, Lee, additional, Balasubramanyam, Ashok, additional, Amos, Christopher I., additional, Civitello, Andrew B., additional, Chelu, Mihail G., additional, Maag, Ronald, additional, McGuire, Amy L., additional, Boerwinkle, Eric, additional, Wehrens, Xander H.T., additional, Ballantyne, Christie M., additional, and Gibbs, Richard A., additional

Published
2021
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13. Comprehensive molecular characterization of human colon and rectal cancer

Author

Muzny, Donna M., Bainbridge, Matthew N., Chang, Kyle, Dinh, Huyen H., Drummond, Jennifer A., Fowler, Gerald, and Kovar, Christie L.

Subjects
Nucleotide sequencing -- Usage, Oncology, Experimental, DNA sequencing -- Usage, Colorectal cancer -- Diagnosis -- Genetic aspects, Cancer -- Genetic aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. A subset of these samples (97) underwent low-depth-of-coverage whole-genome sequencing. In total, 16% of colorectal carcinomas were found to be hypermutated: three-quarters of these had the expected high microsatellite instability, usually with hypermethylation and MLH1 silencing, and one-quarter had somatic mismatch-repair gene and polymerase [epsilon] (POLE) mutations. Excluding the hypermutated cancers, colon and rectum cancers were found to have considerably similar patterns of genomic alteration. Twenty-four genes were significantly mutated, and in addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9 and FAM123B. Recurrent copy-number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include the fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive colorectal carcinoma and an important role for MYC-directed transcriptional activation and repression. The Cancer Genome Atlas consortium reports on their genome-wide characterization of somatic alterations in colorectal cancer; in addition to revealing a remarkably consistent pattern of genomic alteration, with 24 genes being significantly mutated, the study identifies new targets for therapeutic intervention and suggests an important role for MYC-directed transcriptional activation and repression. Mutations associated with colorectal cancer The Cancer Genome Atlas consortium reports on their genome-wide characterization of somatic alterations in colorectal carcinoma. Combined analysis of exome sequence data, DNA copy number, promoter methylation, messenger RNA and microRNA expression, as well as low-coverage whole-genome sequencing reveal that 16% of these carcinomas have hypermutation. Of these, three-quarters have the expected high microsatellite instability, but the rest have somatic mismatch repair gene mutations. The data reveal a remarkably consistent pattern of genomic alteration, with 24 genes being significantly mutated. As well as identifying new biomarkers for aggressive colorectal carcinoma, the data imply an important role for MYC-directed transcriptional activation and repression., Author(s): Donna M. Muzny [sup.2] , Matthew N. Bainbridge [sup.2] , Kyle Chang [sup.2] , Huyen H. Dinh [sup.2] , Jennifer A. Drummond [sup.2] , Gerald Fowler [sup.2] , Christie [...]

Published
2012
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14. Comparative and demographic analysis of orang-utan genomes

Author

Locke, Devin P., Hillier, LaDeana W., Warren, Wesley C., Worley, Kim C., Nazareth, Lynne V., Muzny, Donna M., Yang, Shiaw-Pyng, Wang, Zhengyuan, Chinwalla, Asif T., Minx, Pat, Mitreva, Makedonka, Cook, Lisa, Delehaunty, Kim D., Fronick, Catrina, Schmidt, Heather, Fulton, Lucinda A., Fulton, Robert S., Nelson, Joanne O., Magrini, Vincent, Pohl, Craig, Graves, Tina A., Markovic, Chris, Cree, Andy, Dinh, Huyen H., Hume, Jennifer, Kovar, Christie L., Fowler, Gerald R., Lunter, Gerton, Meader, Stephen, Heger, Andreas, Ponting, Chris P., Marques-Bonet, Tomas, Alkan, Can, Chen, Lin, Cheng, Ze, Kidd, Jeffrey M., Eichler, Evan E., White, Simon, Searle, Stephen, Vilella, Albert J., Chen, Yuan, Flicek, Paul, Ma, Jian, Raney, Brian, Suh, Bernard, Burhans, Richard, Herrero, Javier, Haussler, David, Faria, Rui, Fernando, Olga, Darré, Fleur, Farré, Domènec, Gazave, Elodie, Oliva, Meritxell, Navarro, Arcadi, Roberto, Roberta, Capozzi, Oronzo, Archidiacono, Nicoletta, Valle, Giuliano Della, Purgato, Stefania, Rocchi, Mariano, Konkel, Miriam K., Walker, Jerilyn A., Ullmer, Brygg, Batzer, Mark A., Smit, Arian F. A., Hubley, Robert, Casola, Claudio, Schrider, Daniel R., Hahn, Matthew W., Quesada, Victor, Puente, Xose S., Ordoñez, Gonzalo R., López-Otín, Carlos, Vinar, Tomas, Brejova, Brona, Ratan, Aakrosh, Harris, Robert S., Miller, Webb, Kosiol, Carolin, Lawson, Heather A., Taliwal, Vikas, Martins, André L., Siepel, Adam, RoyChoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos D., Gutenkunst, Ryan N., Mailund, Thomas, Dutheil, Julien Y., Hobolth, Asger, Schierup, Mikkel H., Ryder, Oliver A., Yoshinaga, Yuko, de Jong, Pieter J., Weinstock, George M., Rogers, Jeffrey, Mardis, Elaine R., Gibbs, Richard A., and Wilson, Richard K.

Published
2011
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15. A collagen-binding adhesin, Acb, and ten other putative MSCRAMM and pilus family proteins of streptococcus gallolyticus subsp, gallolyticus (Streptococcus boris group, biotype I)

Author

Sillanpaa, Jouko, Nallapareddy, Sreedhar R., Qin, Xiang, Singh, Kavindra V., Muzny, Donna M., Kovar, Christie L., Nazareth, Lynne V., Gibbs, Richard A., Ferraro, Mary J., Steckelberg, James M., Weinstock, George M., and Murray, Barbara E.

Subjects
Streptococcus -- Physiological aspects, Streptococcus -- Genetic aspects, Streptococcus -- Research, Endocarditis -- Development and progression, Endocarditis -- Research, Gene expression -- Research, Bacteria -- Adhesion, Bacteria -- Physiological aspects, Bacteria -- Genetic aspects, Bacteria -- Research, Biological sciences
Abstract

Members of the Streptococcus bovis group are important causes of endocarditis. However, factors associated with their pathogenicity, such as adhesins, remain uncharacterized. We recently demonstrated that endocarditis-derived Streptococcus gallolyticus subsp, gallolyticus isolates frequently adhere to extracellular matrix (ECM) proteins. Here, we generated a draft genome sequence of an ECM protein-adherent S. gallolyticus subsp. gallolyticus strain and found, by genome-wide analyses, 11 predicted LPXTG-type cell wall-anchored proteins with characteristics of MSCRAMMs, including a modular architecture of domains predicted to adopt immunoglobulin (Ig)-like folding. A recombinant segment of one of these, Acb, showed high-affinity binding to immobilized collagen, and cell surface expression of Acb correlated with the presence of acb and collagen adherence of isolates. Three of the 11 proteins have similarities to major pilus subunits and are organized in separate clusters, each including a second Ig-fold-containing MSCRAMM and a class C sortase, suggesting that the sequenced strain encodes three distinct types of pili. Reverse transcription-PCR demonstrated that all three genes of one cluster, acb-sbs7-srtC1, are cotranscribed, consistent with pilus operons of other grampositive bacteria. Further analysis detected expression of all 11 genes in cells grown to mid to late exponential growth phases. Wide distribution of 9 of the 11 genes was observed among S. gallolyticus subsp, gallolyticus isolates with fewer genes present in other S. bovis group species/subspecies. The high prevalence of genes encoding putative MSCRAMMs and pili, including a collagen-binding MSCRAMM, among S. gallolyticus subsp, gallolyticus isolates may play an important role in the predominance of this subspecies in S. bovis endocarditis. doi: 10.1128/JB.00909-09

Published
2009

16. A framework for human microbiome research

Author

Methé, Barbara A., Nelson, Karen E., Pop, Mihai, Creasy, Heather H., Giglio, Michelle G., Huttenhower, Curtis, Gevers, Dirk, Petrosino, Joseph F., Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien R., Brooks, Paul, Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Michael W., Jr, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry, Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, Kinder-Haake, Susan, King, Nicholas B., Knight, Rob, Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavrommatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Chris S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, Yuan Qing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Weinstock, George M., Wilson, Richard K., and White, Owen

Published
2012
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17. Structure, function and diversity of the healthy human microbiome

Author

Huttenhower, Curtis, Gevers, Dirk, Knight, Rob, Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Creasy, Heather H., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Giglio, Michelle G., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien, Brooks, Paul J., Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S. G., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Wm Michael, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry J., Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haake, Susan Kinder, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, King, Nicholas B., Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavromatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Pop, Mihai, Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Christopher S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, YuanQing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Methé, Barbara A., Nelson, Karen E., Petrosino, Joseph F., Weinstock, George M., Wilson, Richard K., and White, Owen

Published
2012
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18. 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., Elsik, Christine G., Tellam, Ross L, Gibbs, Richard A., Muzny, Donna M., Weinstock, George M., Adelson, David L, Eichler, Evan E., Elnitski, Laura, Elsik, Christine G., Guigó, Roderic, Hamernik, Debora L., Kappes, Steve M., Lewin, Harris A, Lynn, David J., Nicholas, Frank W., Reymond, Alexandre, Rijnkels, Monique, Skow, Loren C., Tellam, Ross L, Worley, Kim C., Zdobnov, Evgeny M., Gibbs, Richard A., Kappes, Steve M., Schook, Lawrence, Skow, Loren C., Weinstock, George M., Womack, James, Alioto, Tyler, Antonarakis, Stylianos E., Astashyn, Alex, Chapple, Charles E., Chen, Hsiu-Chuan, Chrast, Jacqueline, Câmara, Francisco, Elsik, Christine G., Ermolaeva, Olga, Guigó, Roderic, Henrichsen, Charlotte N., Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Kokocinski, Felix, Landrum, Melissa, Maglott, Donna, Pruitt, Kim, Reymond, Alexandre, Sapojnikov, Victor, Searle, Stephen M., Solovyev, Victor, Souvorov, Alexandre, Ucla, Catherine, Weinstock, George M., Wyss, Carine, Alioto, Tyler, Antonarakis, Stylianos E., Chapple, Charles E., Chrast, Jacqueline, Câmara, Francisco, Guigó, Roderic, Henrichsen, Charlotte N., Reymond, Alexandre, Ucla, Catherine, Wyss, Carine, Anzola, Juan M., Gerlach, Daniel, Zdobnov, Evgeny M., Elhaik, Eran, Elsik, Christine G., Graur, Dan, Reese, Justin T., Adelson, David L., Edgar, Robert C., McEwan, John C., Payne, Gemma M., Raison, Joy M., Junier, Thomas, Kriventseva, Evgenia V., Zdobnov, Evgeny M., Chrast, Jacqueline, Eyras, Eduardo, Henrichsen, Charlotte N., Plass, Mireya, Reymond, Alexandre, Donthu, Ravikiran, Larkin, Denis M., Lewin, Harris A., Nicholas, Frank W., Elnitski, Laura, Larkin, Denis M., Lewin, Harris A., Reecy, James, Yang, Mary Q., Adelson, David L, Chen, Lin, Cheng, Ze, Chitko-McKown, Carol G., Eichler, Evan E., Elnitski, Laura, Elsik, Christine G., Liu, George E., Matukumalli, Lakshmi K., Song, Jiuzhou, Zhu, Bin, Elsik, Christine G., Lynn, David J., Reese, Justin T., Bradley, Daniel G., Brinkman, Fiona S.L, Lau, Lilian P.L., Lynn, David J., Whiteside, Matthew D., Tellam, Ross L, Walker, Angela, Wheeler, Thomas T., Casey, Theresa, German, Bruce J., Lemay, Danielle G., Lynn, David J., Maqbool, Nauman J., Molenaar, Adrian J., Rijnkels, Monique, Lewin, Harris A., Seo, Seongwon, Stothard, Paul, Baldwin, Cynthia L., Baxter, Rebecca, Brinkmeyer-Langford, Candice L., Brown, Wendy C., Childers, Christopher P., Connelley, Timothy, Ellis, Shirley A., Fritz, Krista, Glass, Elizabeth J., Herzig, Carolyn T.A., livanainen, Antti, Lahmers, Kevin K., Skow, Loren C., Bennett, Anna K., Childers, Christopher P., Dickens, Michael C., Elsik, Christine G., Gilbert, James G.R., Hagen, Darren E., Reese, Justin T., Salih, Hanni, Aerts, Jan, Caetano, Alexandre R., Dalrymple, Brian, Elsik, Christine G., Fernando Garcia, Jose, Gibbs, Richard A., Gill, Clare A., Hamernik, Debora L, Hiendleder, Stefan G., Memili, Erdogan, Nicholas, Frank W., Reecy, James, Rijnkels, Monique, Skow, Loren C., Spurlock, Diane, Stothard, Paul, Tellam, Ross L, Weinstock, George M., Williams, John L, Worley, Kim C., Alexander, Lee, Brownstein, Michael J., Guan, Leluo, Holt, Robert A., Jones, Steven J.M., Marra, Marco A., Moore, Richard, Moore, Stephen S., Roberts, Andy, Taniguchi, Masaaki, Waterman, Richard C., Chacko, Joseph, Chandrabose, Mimi M., Cree, Andy, Diep Dao, Marvin, Dinh, Huyen H., Ayiesha Gabisi, Ramatu, Hines, Sandra, Hume, Jennifer, Jhangiani, Shalini N., Joshi, Vandita, Kovar, Christie L., Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Muzny, Donna M., Bich Nguyen, Ngoc, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Buhay, Christian, Ding, Yan, Dugan-Rocha, Shannon, Herdandez, Judith, Holder, Michael, Sabo, Aniko, Egan, Amy, Goodell, Jason, Wilczek-Boney, Katarzyna, Fowler, Gerald R., Edward Hitchens, Matthew, Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Chiu, Readman, Jones, Steven J.M., Marra, Marco A., Schein, Jacqueline E., James Durbin, K., Havlak, Paul, Jiang, Huaiyang, Liu, Yue, Qin, Xiang, Ren, Yanru, Shen, Yufeng, Song, Henry, Weinstock, George M., Worley, Kim C., Nicole Bell, Stephanie, Davis, Clay, Jolivet Johnson, Angela, Lee, Sandra, Nazareth, Lynne V., Patel, Bella Mayurkumar, Pu, Ling-Ling, Vattathil, Selina, Williams, Rex Lee, Jr., Curry, Stacey, Hamilton, Cerissa, Sodergren, Erica, Nazareth, Lynne V., Wheeler, David A., Adelson, David L, Aerts, Jan, Barris, Wes, Bennett, Gary L, Dalrymple, Brian, Eggen, André, Gill, Clare A., Green, Ronnie D., Harhay, Gregory P., Hobbs, Matthew, Jann, Oliver, Kappes, Steve M., Keele, John W., Kent, Matthew P., Larkin, Denis M., Lewin, Harris A., Lien, Sigbjørn, McEwan, John C., McKay, Stephanie D., McWilliam, Sean, Moore, Stephen S., Nicholas, Frank W., Payne, Gemma M., Ratnakumar, Abhirami, Salih, Hanni, Schnabel, Robert D., Smith, Timothy, Snelling, Warren M., Sonstegard, Tad S., Stone, Roger T., Sugimoto, Yoshikazu, Takasuga, Akiko, Taylor, Jeremy F., Tellam, Ross L., Van Tassell, Curtis P., Williams, John L, MacNeil, Michael D., Abatepaulo, Antonio R.R., Abbey, Colette A., Aerts, Jan, Ahola, Virpi, Almeida, Iassudara G., Amadio, Ariel F., Anatriello, Elen, Bahadue, Suria M., Baldwin, Cynthia L., Baxter, Rebecca, Bennett, Anna K., Biase, Fernando H., Boldt, Clayton R., Brinkmeyer-Langford, Candice L, Brown, Wendy C., Caetano, Alexandre R., Carroll, Jeffery A., Carvalho, Wanessa A, Casey, Theresa, Cervelatti, Eliane P., Chacko, Elsa, Chapin, Jennifer E., Cheng, Ye, Childers, Christopher P., Choi, Jungwoo, Colley, Adam J., Connelley, Timothy, de Campos, Tatiana A., De Donato, Marcos, de Miranda Santos, Isabel K.F., de Oliveira, Carlo J.F., Deobald, Heather, Devinoy, Eve, Dickens, Michael C., Donohue, Kaitlin E., Dovc, Peter, Eberlein, Annett, Ellis, Shirley A., Fitzsimmons, Carolyn J., Franzin, Alessandra M., Fritz, Krista, Garcia, Gustavo R., Fernando Garcia, Jose, Genini, Sem, German, Bruce J., Gilbert, James G.R., Gill, Clare A., Gladney, Cody J., Glass, Elizabeth J., Grant, Jason R., Greaser, Marion L., Green, Jonathan A., Hadsell, Darryl L., Hagen, Darren E., Hakimov, Hatam A., Halgren, Rob, Harrow, Jennifer L, Hart, Elizabeth A., Hastings, Nicola, Hernandez, Marta, Herzig, Carolyn T.A., Hiendleder, Stefan G., Hobbs, Matthew, Hu, Zhi-Liang, livanainen, Antti, Ingham, Aaron, Iso-Touru, Terhi, Jamis, Catherine, Jann, Oliver, Jensen, Kirsty, Kapetis, Dimos, Kerr, Tovah, Khalil, Sari S., Khatib, Hasan, Kolbehdari, Davood, Kumar, Charu G., Kumar, Dinesh, Leach, Richard, Lee, Justin C-M, Lemay, Danielle G., Li, Changxi, Liu, George E., Logan, Krystin M., Malinverni, Roberto, Maqbool, Nauman J., Marques, Elisa, Martin, William F., Martins, Natalia F., Maruyama, Sandra R., Mazza, Raffaele, McLean, Kim L, Medrano, Juan F., Memili, Erdogan, Molenaar, Adrian J., Moreno, Barbara T., Moré, Daniela D., Muntean, Carl T., Nandakumar, Hari P., Nogueira, Marcelo F.G., Olsaker, Ingrid, Pant, Sameer D., Panzitta, Francesca, Pastor, Rosemeire C.P., Poli, Mario A., Poslusny, Nathan, Rachagani, Satyanarayana, Ranganathan, Shoba, Razpet, Andrej, Reecy, James, Riggs, Penny K., Rijnkels, Monique, Rincon, Gonzalo, Rodriguez-Osorio, Nelida, Rodriguez-Zas, Sandra L., Romero, Natasha E., Rosenwald, Anne, Sando, Lillian, Schmutz, Sheila M., Seo, Seongwon, Shen, Libing, Sherman, Laura, Skow, Loren C., Southey, Bruce R., Spurlock, Diane, Strandberg Lutzow, Ylva, Sweedler, Jonathan V., Tammen, Imke, Taniguchi, Masaaki, Tellam, Ross L, Telugu, Bhanu Prakash V.L, Urbanski, Jennifer M., Utsunomiya, Yuri T., Verschoor, Chris P., Waardenberg, Ashley J., Walker, Angela, Wang, Zhiquan, Ward, Robert, Weikard, Rosemarie, Welsh, Thomas H., Jr., Wheeler, Thomas T., White, Stephen N., Williams, John L, Wilming, Laurens G., Wunderlich, Kris R., Yang, Jianqi, and Zhao, Feng-Qi

Published
2009

20. Cohort Profile: The Right Drug, Right Dose, Right Time: Using Genomic Data to Individualize Treatment Protocol (RIGHT Protocol)

Author

Bielinski, Suzette J, primary, St Sauver, Jennifer L, primary, Olson, Janet E, primary, Larson, Nicholas B, primary, Black, John L, primary, Scherer, Steven E, primary, Bernard, Matthew E, primary, Boerwinkle, Eric, primary, Borah, Bijan J, primary, Caraballo, Pedro J, primary, Curry, Timothy B, primary, Doddapaneni, HarshaVardhan, primary, Formea, Christine M, primary, Freimuth, Robert R, primary, Gibbs, Richard A, primary, Giri, Jyothsna, primary, Hathcock, Matthew A, primary, Hu, Jianhong, primary, Jacobson, Debra J, primary, Jones, Leila A, primary, Kalla, Sara, primary, Koep, Tyler H, primary, Korchina, Viktoriya, primary, Kovar, Christie L, primary, Lee, Sandra, primary, Liu, Hongfang, primary, Matey, Eric T, primary, McGree, Michaela E, primary, McAllister, Tammy M, primary, Moyer, Ann M, primary, Muzny, Donna M, primary, Nicholson, Wayne T, primary, Oyen, Lance J, primary, Qin, Xiang, primary, Raj, Ritika, primary, Roger, Véronique L, primary, Rohrer Vitek, Carolyn R, primary, Ross, Jason L, primary, Sharp, Richard R, primary, Takahashi, Paul Y, primary, Venner, Eric, primary, Walker, Kimberly, primary, Wang, Liwei, primary, Wang, Qiaoyan, primary, Wright, Jessica A, primary, Wu, Tsung-Jung, primary, Wang, Liewei, primary, and Weinshilboum, Richard M, primary

Published
2019
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21. 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, and Gibbs, Richard A

Subjects
Apis mellifera, GC content, Gene annotation, Gene prediction, Genome assembly, Genome improvement, Genome sequencing, Repetitive DNA, Transcriptome, fungi
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

22. ADAM19 and HTR4 Variants and Pulmonary Function: Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study

Author

Kovar, Christie L., Zhou, Yanhua, Franceschini, Nora, Muzny, Donna M., Psaty, Bruce M., House, John S., Gibbs, Richard A., North, Kari E., Gharib, Sina A., Heckbert, Susan R., Brody, Jennifer A., Hancock, Dana B., Lumley, Thomas, Morrison, Alanna Cée, London, Stephanie J., Wilk, Jemma B., Gao, Wei, and Coresh, Josef

Subjects
respiratory system, circulatory and respiratory physiology, respiratory tract diseases
Abstract

The pulmonary function measures of forced expiratory volume in one second (FEV1) and its ratio to forced vital capacity (FVC) are used in the diagnosis and monitoring of lung diseases and predict cardiovascular mortality in the general population. Genome wide association studies (GWAS) have identified numerous loci associated with FEV1 and FEV1/FVC but the causal variants remain uncertain. We hypothesized that novel or rare variants poorly tagged by GWAS may explain the significant associations between FEV1/FVC and two genes: ADAM19 and HTR4.

Published
2014
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23. An open access pilot freely sharing cancer genomic data from participants in Texas

Author

Becnel, Lauren B., primary, Pereira, Stacey, additional, Drummond, Jennifer A., additional, Gingras, Marie-Claude, additional, Covington, Kyle R., additional, Kovar, Christie L., additional, Doddapaneni, Harsha Vardhan, additional, Hu, Jianhong, additional, Muzny, Donna, additional, McGuire, Amy L., additional, Wheeler, David A., additional, and Gibbs, Richard A., additional

Published
2016
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24. A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor

Author

Zhao, Chaoyang, Escalante, Lucio Navarro, Chen, Hang, Benatti, Thiago R., Qu, Jiaxin, Chellapilla, Sanjay, Waterhouse, Robert M., Wheeler, David, Andersson, Martin N, Bao, Riyue, Batterton, Matthew, Behura, Susanta K, Blankenburg, Kerstin P, Caragea, Doina, Carolan, James C, Coyle, Marcus, El-Bouhssini, Mustapha, Francisco, Liezl, Friedrich, Markus, Gill, Navdeep, Grace, Tony, Grimmelikhuijzen, Cornelis, Han, Yi, Hauser, Frank, Herndon, Nicolae, Holder, Michael, Ioannidis, Panagiotis, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Johnson, Alisha J, Kalra, Divya, Korchina, Viktoriya, Kovar, Christie L, Lara, Fremiet, Lee, Sandra L, Liu, Xuming, Löfstedt, Christer, Mata, Robert, Mathew, Tittu, Muzny, Donna M, Nagar, Swapnil, Nazareth, Lynne V, Okwuonu, Geoffrey, Ongeri, Fiona, Perales, Lora, Peterson, Brittany F, Pu, Ling-Ling, Robertson, Hugh M, Schemerhorn, Brandon J, Scherer, Steven E, Shreve, Jacob T, Simmons, DeNard, Subramanyam, Subhashree, Thornton, Rebecca L, Xue, Kun, Weissenberger, George M, Williams, Christie E, Worley, Kim C, Zhu, Dianhui, Zhu, Yiming, Harris, Marion O, Shukle, Richard H, Werren, John H, Zdobnov, Evgeny M, Chen, Ming-Shun, Brown, Susan J, Stuart, Jeffery J, Richards, Stephen, Zhao, Chaoyang, Escalante, Lucio Navarro, Chen, Hang, Benatti, Thiago R., Qu, Jiaxin, Chellapilla, Sanjay, Waterhouse, Robert M., Wheeler, David, Andersson, Martin N, Bao, Riyue, Batterton, Matthew, Behura, Susanta K, Blankenburg, Kerstin P, Caragea, Doina, Carolan, James C, Coyle, Marcus, El-Bouhssini, Mustapha, Francisco, Liezl, Friedrich, Markus, Gill, Navdeep, Grace, Tony, Grimmelikhuijzen, Cornelis, Han, Yi, Hauser, Frank, Herndon, Nicolae, Holder, Michael, Ioannidis, Panagiotis, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Johnson, Alisha J, Kalra, Divya, Korchina, Viktoriya, Kovar, Christie L, Lara, Fremiet, Lee, Sandra L, Liu, Xuming, Löfstedt, Christer, Mata, Robert, Mathew, Tittu, Muzny, Donna M, Nagar, Swapnil, Nazareth, Lynne V, Okwuonu, Geoffrey, Ongeri, Fiona, Perales, Lora, Peterson, Brittany F, Pu, Ling-Ling, Robertson, Hugh M, Schemerhorn, Brandon J, Scherer, Steven E, Shreve, Jacob T, Simmons, DeNard, Subramanyam, Subhashree, Thornton, Rebecca L, Xue, Kun, Weissenberger, George M, Williams, Christie E, Worley, Kim C, Zhu, Dianhui, Zhu, Yiming, Harris, Marion O, Shukle, Richard H, Werren, John H, Zdobnov, Evgeny M, Chen, Ming-Shun, Brown, Susan J, Stuart, Jeffery J, and Richards, Stephen

Abstract

Gall-forming arthropods are highly specialized herbivores that, in combination with their hosts, produce extended phenotypes with unique morphologies [1]. Many are economically important, and others have improved our understanding of ecology and adaptive radiation [2]. However, the mechanisms that these arthropods use to induce plant galls are poorly understood. We sequenced the genome of the Hessian fly (Mayetiola destructor; Diptera: Cecidomyiidae), a plant parasitic gall midge and a pest of wheat (Triticum spp.), with the aim of identifying genic modifications that contribute to its plant-parasitic lifestyle. Among several adaptive modifications, we discovered an expansive reservoir of potential effector proteins. Nearly 5% of the 20,163 predicted gene models matched putative effector gene transcripts present in the M. destructor larval salivary gland. Another 466 putative effectors were discovered among the genes that have no sequence similarities in other organisms. The largest known arthropod gene family (family SSGP-71) was also discovered within the effector reservoir. SSGP-71 proteins lack sequence homologies to other proteins, but their structures resemble both ubiquitin E3 ligases in plants and E3-ligase-mimicking effectors in plant pathogenic bacteria. SSGP-71 proteins and wheat Skp proteins interact in vivo. Mutations in different SSGP-71 genes avoid the effector-triggered immunity that is directed by the wheat resistance genes H6 and H9. Results point to effectors as the agents responsible for arthropod-induced plant gall formation.

Published
2015

25. Genomic Signatures of Cooperation and Conflict in the Social Amoeba

Author

Ostrowski, Elizabeth A., primary, Shen, Yufeng, additional, Tian, Xiangjun, additional, Sucgang, Richard, additional, Jiang, Huaiyang, additional, Qu, Jiaxin, additional, Katoh-Kurasawa, Mariko, additional, Brock, Debra A., additional, Dinh, Christopher, additional, Lara-Garduno, Fremiet, additional, Lee, Sandra L., additional, Kovar, Christie L., additional, Dinh, Huyen H., additional, Korchina, Viktoriya, additional, Jackson, LaRonda, additional, Patil, Shobha, additional, Han, Yi, additional, Chaboub, Lesley, additional, Shaulsky, Gad, additional, Muzny, Donna M., additional, Worley, Kim C., additional, Gibbs, Richard A., additional, Richards, Stephen, additional, Kuspa, Adam, additional, Strassmann, Joan E., additional, and Queller, David C., additional

Published
2015
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26. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

Author

Zhao, Chaoyang, primary, Escalante, Lucio Navarro, additional, Chen, Hang, additional, Benatti, Thiago R., additional, Qu, Jiaxin, additional, Chellapilla, Sanjay, additional, Waterhouse, Robert M., additional, Wheeler, David, additional, Andersson, Martin N., additional, Bao, Riyue, additional, Batterton, Matthew, additional, Behura, Susanta K., additional, Blankenburg, Kerstin P., additional, Caragea, Doina, additional, Carolan, James C., additional, Coyle, Marcus, additional, El-Bouhssini, Mustapha, additional, Francisco, Liezl, additional, Friedrich, Markus, additional, Gill, Navdeep, additional, Grace, Tony, additional, Grimmelikhuijzen, Cornelis J.P., additional, Han, Yi, additional, Hauser, Frank, additional, Herndon, Nicolae, additional, Holder, Michael, additional, Ioannidis, Panagiotis, additional, Jackson, LaRonda, additional, Javaid, Mehwish, additional, Jhangiani, Shalini N., additional, Johnson, Alisha J., additional, Kalra, Divya, additional, Korchina, Viktoriya, additional, Kovar, Christie L., additional, Lara, Fremiet, additional, Lee, Sandra L., additional, Liu, Xuming, additional, Löfstedt, Christer, additional, Mata, Robert, additional, Mathew, Tittu, additional, Muzny, Donna M., additional, Nagar, Swapnil, additional, Nazareth, Lynne V., additional, Okwuonu, Geoffrey, additional, Ongeri, Fiona, additional, Perales, Lora, additional, Peterson, Brittany F., additional, Pu, Ling-Ling, additional, Robertson, Hugh M., additional, Schemerhorn, Brandon J., additional, Scherer, Steven E., additional, Shreve, Jacob T., additional, Simmons, DeNard, additional, Subramanyam, Subhashree, additional, Thornton, Rebecca L., additional, Xue, Kun, additional, Weissenberger, George M., additional, Williams, Christie E., additional, Worley, Kim C., additional, Zhu, Dianhui, additional, Zhu, Yiming, additional, Harris, Marion O., additional, Shukle, Richard H., additional, Werren, John H., additional, Zdobnov, Evgeny M., additional, Chen, Ming-Shun, additional, Brown, Susan J., additional, Stuart, Jeffery J., additional, and Richards, Stephen, additional

Published
2015
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27. 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

28. 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

29. Associations of NINJ2 Sequence Variants with Incident Ischemic Stroke in the Cohorts for Heart and Aging in Genomic Epidemiology (CHARGE) Consortium

Author

Bis, Joshua C., primary, DeStefano, Anita, additional, Liu, Xiaoming, additional, Brody, Jennifer A., additional, Choi, Seung Hoan, additional, Verhaaren, Benjamin F. J., additional, Debette, Stéphanie, additional, Ikram, M. Arfan, additional, Shahar, Eyal, additional, Butler, Kenneth R., additional, Gottesman, Rebecca F., additional, Muzny, Donna, additional, Kovar, Christie L., additional, Psaty, Bruce M., additional, Hofman, Albert, additional, Lumley, Thomas, additional, Gupta, Mayetri, additional, Wolf, Philip A., additional, van Duijn, Cornelia, additional, Gibbs, Richard A., additional, Mosley, Thomas H., additional, Longstreth, W. T., additional, Boerwinkle, Eric, additional, Seshadri, Sudha, additional, and Fornage, Myriam, additional

Published
2014
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30. Strategies to Design and Analyze Targeted Sequencing Data

Author

Lin, Honghuang, primary, Wang, Min, additional, Brody, Jennifer A., additional, Bis, Joshua C., additional, Dupuis, Josée, additional, Lumley, Thomas, additional, McKnight, Barbara, additional, Rice, Kenneth M., additional, Sitlani, Colleen M., additional, Reid, Jeffrey G., additional, Bressler, Jan, additional, Liu, Xiaoming, additional, Davis, Brian C., additional, Johnson, Andrew D., additional, O’Donnell, Christopher J., additional, Kovar, Christie L., additional, Dinh, Huyen, additional, Wu, Yuanqing, additional, Newsham, Irene, additional, Chen, Han, additional, Broka, Andi, additional, DeStefano, Anita L., additional, Gupta, Mayetri, additional, Lunetta, Kathryn L., additional, Liu, Ching-Ti, additional, White, Charles C., additional, Xing, Chuanhua, additional, Zhou, Yanhua, additional, Benjamin, Emelia J., additional, Schnabel, Renate B., additional, Heckbert, Susan R., additional, Psaty, Bruce M., additional, Muzny, Donna M., additional, Cupples, L. Adrienne, additional, Morrison, Alanna C., additional, and Boerwinkle, Eric, additional

Published
2014
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31. ADAM19 and HTR4 Variants and Pulmonary Function

Author

London, Stephanie J., primary, Gao, Wei, additional, Gharib, Sina A., additional, Hancock, Dana B., additional, Wilk, Jemma B., additional, House, John S., additional, Gibbs, Richard A., additional, Muzny, Donna M., additional, Lumley, Thomas, additional, Franceschini, Nora, additional, North, Kari E., additional, Psaty, Bruce M., additional, Kovar, Christie L., additional, Coresh, Josef, additional, Zhou, Yanhua, additional, Heckbert, Susan R., additional, Brody, Jennifer A., additional, Morrison, Alanna C., additional, and Dupuis, Josée, additional

Published
2014
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32. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Author

Renfree, Marilyn B., Papenfuss, Anthony T., Deakin, Janine E., Lindsay, James, Heider, Thomas, Belov, Katherine, Rens, Willem, Waters, Paul D., Pharo, Elizabeth A., Shaw, Geoff, Wong, Emily S. W., Gibbs, Richard A, Cooper, Desmond W, Speed, Terence P, Fujiyama, Asao, Graves, Jennifer A. M., O'Neill, Rachel J., Pask, Andrew J., Forrest, Susan M., Worley, Kim C., Lefèvre, Christophe M., Nicholas, Kevin R., Kuroki, Yoko, Wakefield, Matthew J., Zenger, Kyall R., Wang, Chenwei, Ferguson-Smith, Malcolm, Nicholas, Frank W., Hickford, Danielle, Yu, Hongshi, Short, Kirsty R., Siddle, Hannah V., Frankenberg, Stephen R., Chew, Keng, Menzies, Brandon R., Stringer, Jessica M., Suzuki, Shunsuke, Hore, Timothy A., Delbridge, Margaret L., Mohammadi, Amir, Schneider, Nanette Y., Hu, Yanqiu, O'Hara, William, Al Nadaf, Shafagh, Wu, Chen, Feng, Zhi-Ping, Cocks, Benjamin G., Wang, Jianghui, Flicek, Paul, Searle, Stephen M. J., Fairley, Susan, Beal, Kathryn, Herrero, Javier, Carone, Dawn M., Suzuki, Yutaka, Sugano, Sumio, Toyoda, Atsushi, Sakaki, Yoshiyuki, Kondo, Shinji, Nishida, Yuichiro, Tatsumoto, Shoji, Mandiou, Ion, Hsu, Arthur, McColl, Kaighin A., Lansdell, Benjamin, Weinstock, George, Kuczek, Elizabeth, McGrath, Annette, Wilson, Peter, Men, Artem, Hazar-Rethinam, Mehlika, Hall, Allison, Davis, John, Wood, David, Williams, Sarah, Sundaravadanam, Yogi, Muzny, Donna M, Jhangiani, Shalini N, Lewis, Lora R, Morgan, Margaret B, Okwuonu, Geoffrey O, Ruiz, San, Santibanez, Jireh, Nazareth, Lynne, Cree, Andrew, Fowler, Gerald, Kovar, Christie L, Dinh, Huyen H, Joshi, Vandita, Jing, Chyn, Lara, Fremiet, Thornton, Rebecca, Chen, Lei, Deng, Jixin, Liu, Yue, Shen, Joshua Y, Song, Xing-Zhi, Edson, Janette, Troon, Carmen, Thomas, Daniel, Stephens, Amber, Yapa, Lankesha, Levchenko, Tanya, Renfree, Marilyn B., Papenfuss, Anthony T., Deakin, Janine E., Lindsay, James, Heider, Thomas, Belov, Katherine, Rens, Willem, Waters, Paul D., Pharo, Elizabeth A., Shaw, Geoff, Wong, Emily S. W., Gibbs, Richard A, Cooper, Desmond W, Speed, Terence P, Fujiyama, Asao, Graves, Jennifer A. M., O'Neill, Rachel J., Pask, Andrew J., Forrest, Susan M., Worley, Kim C., Lefèvre, Christophe M., Nicholas, Kevin R., Kuroki, Yoko, Wakefield, Matthew J., Zenger, Kyall R., Wang, Chenwei, Ferguson-Smith, Malcolm, Nicholas, Frank W., Hickford, Danielle, Yu, Hongshi, Short, Kirsty R., Siddle, Hannah V., Frankenberg, Stephen R., Chew, Keng, Menzies, Brandon R., Stringer, Jessica M., Suzuki, Shunsuke, Hore, Timothy A., Delbridge, Margaret L., Mohammadi, Amir, Schneider, Nanette Y., Hu, Yanqiu, O'Hara, William, Al Nadaf, Shafagh, Wu, Chen, Feng, Zhi-Ping, Cocks, Benjamin G., Wang, Jianghui, Flicek, Paul, Searle, Stephen M. J., Fairley, Susan, Beal, Kathryn, Herrero, Javier, Carone, Dawn M., Suzuki, Yutaka, Sugano, Sumio, Toyoda, Atsushi, Sakaki, Yoshiyuki, Kondo, Shinji, Nishida, Yuichiro, Tatsumoto, Shoji, Mandiou, Ion, Hsu, Arthur, McColl, Kaighin A., Lansdell, Benjamin, Weinstock, George, Kuczek, Elizabeth, McGrath, Annette, Wilson, Peter, Men, Artem, Hazar-Rethinam, Mehlika, Hall, Allison, Davis, John, Wood, David, Williams, Sarah, Sundaravadanam, Yogi, Muzny, Donna M, Jhangiani, Shalini N, Lewis, Lora R, Morgan, Margaret B, Okwuonu, Geoffrey O, Ruiz, San, Santibanez, Jireh, Nazareth, Lynne, Cree, Andrew, Fowler, Gerald, Kovar, Christie L, Dinh, Huyen H, Joshi, Vandita, Jing, Chyn, Lara, Fremiet, Thornton, Rebecca, Chen, Lei, Deng, Jixin, Liu, Yue, Shen, Joshua Y, Song, Xing-Zhi, Edson, Janette, Troon, Carmen, Thomas, Daniel, Stephens, Amber, Yapa, Lankesha, and Levchenko, Tanya

Abstract

BACKGROUND We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.

Published
2011

33. 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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34. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Author

Renfree, Marilyn B, primary, Papenfuss, Anthony T, additional, Deakin, Janine E, additional, Lindsay, James, additional, Heider, Thomas, additional, Belov, Katherine, additional, Rens, Willem, additional, Waters, Paul D, additional, Pharo, Elizabeth A, additional, Shaw, Geoff, additional, Wong, Emily SW, additional, Lefèvre, Christophe M, additional, Nicholas, Kevin R, additional, Kuroki, Yoko, additional, Wakefield, Matthew J, additional, Zenger, Kyall R, additional, Wang, Chenwei, additional, Ferguson-Smith, Malcolm, additional, Nicholas, Frank W, additional, Hickford, Danielle, additional, Yu, Hongshi, additional, Short, Kirsty R, additional, Siddle, Hannah V, additional, Frankenberg, Stephen R, additional, Chew, Keng Y, additional, Menzies, Brandon R, additional, Stringer, Jessica M, additional, Suzuki, Shunsuke, additional, Hore, Timothy A, additional, Delbridge, Margaret L, additional, Patel, Hardip, additional, Mohammadi, Amir, additional, Schneider, Nanette Y, additional, Hu, Yanqiu, additional, O'Hara, William, additional, Al Nadaf, Shafagh, additional, Wu, Chen, additional, Feng, Zhi-Ping, additional, Cocks, Benjamin G, additional, Wang, Jianghui, additional, Flicek, Paul, additional, Searle, Stephen MJ, additional, Fairley, Susan, additional, Beal, Kathryn, additional, Herrero, Javier, additional, Carone, Dawn M, additional, Suzuki, Yutaka, additional, Sugano, Sumio, additional, Toyoda, Atsushi, additional, Sakaki, Yoshiyuki, additional, Kondo, Shinji, additional, Nishida, Yuichiro, additional, Tatsumoto, Shoji, additional, Mandiou, Ion, additional, Hsu, Arthur, additional, McColl, Kaighin A, additional, Lansdell, Benjamin, additional, Weinstock, George, additional, Kuczek, Elizabeth, additional, McGrath, Annette, additional, Wilson, Peter, additional, Men, Artem, additional, Hazar-Rethinam, Mehlika, additional, Hall, Allison, additional, Davis, John, additional, Wood, David, additional, Williams, Sarah, additional, Sundaravadanam, Yogi, additional, Muzny, Donna M, additional, Jhangiani, Shalini N, additional, Lewis, Lora R, additional, Morgan, Margaret B, additional, Okwuonu, Geoffrey O, additional, Ruiz, San J, additional, Santibanez, Jireh, additional, Nazareth, Lynne, additional, Cree, Andrew, additional, Fowler, Gerald, additional, Kovar, Christie L, additional, Dinh, Huyen H, additional, Joshi, Vandita, additional, Jing, Chyn, additional, Lara, Fremiet, additional, Thornton, Rebecca, additional, Chen, Lei, additional, Deng, Jixin, additional, Liu, Yue, additional, Shen, Joshua Y, additional, Song, Xing-Zhi, additional, Edson, Janette, additional, Troon, Carmen, additional, Thomas, Daniel, additional, Stephens, Amber, additional, Yapa, Lankesha, additional, Levchenko, Tanya, additional, Gibbs, Richard A, additional, Cooper, Desmond W, additional, Speed, Terence P, additional, Fujiyama, Asao, additional, M Graves, Jennifer A, additional, O'Neill, Rachel J, additional, Pask, Andrew J, additional, Forrest, Susan M, additional, and Worley, Kim C, additional

Published
2011
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35. Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus

Author

Highlander, Sarah K, primary, Hultén, Kristina G, additional, Qin, Xiang, additional, Jiang, Huaiyang, additional, Yerrapragada, Shailaja, additional, Mason, Edward O, additional, Shang, Yue, additional, Williams, Tiffany M, additional, Fortunov, Régine M, additional, Liu, Yamei, additional, Igboeli, Okezie, additional, Petrosino, Joseph, additional, Tirumalai, Madhan, additional, Uzman, Akif, additional, Fox, George E, additional, Cardenas, Ana Maria, additional, Muzny, Donna M, additional, Hemphill, Lisa, additional, Ding, Yan, additional, Dugan, Shannon, additional, Blyth, Peter R, additional, Buhay, Christian J, additional, Dinh, Huyen H, additional, Hawes, Alicia C, additional, Holder, Michael, additional, Kovar, Christie L, additional, Lee, Sandra L, additional, Liu, Wen, additional, Nazareth, Lynne V, additional, Wang, Qiaoyan, additional, Zhou, Jianling, additional, Kaplan, Sheldon L, additional, and Weinstock, George M, additional

Published
2007
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36. Associations of NINJ2 Sequence Variants with Incident Ischemic Stroke in the Cohorts for Heart and Aging in Genomic Epidemiology (CHARGE) Consortium.

Author

Bis, Joshua C., DeStefano, Anita, Liu, Xiaoming, Brody, Jennifer A., Choi, Seung Hoan, Verhaaren, Benjamin F. J., Debette, Stéphanie, Ikram, M. Arfan, Shahar, Eyal, Butler Jr, Kenneth R., Gottesman, Rebecca F., Muzny, Donna, Kovar, Christie L., Psaty, Bruce M., Hofman, Albert, Lumley, Thomas, Gupta, Mayetri, Wolf, Philip A., van Duijn, Cornelia, and Gibbs, Richard A.

Subjects
NUCLEOTIDE sequence, GENETIC polymorphisms, ISCHEMIA, STROKE risk factors, CAUSES of death, LONGITUDINAL method, MOLECULAR epidemiology, PATIENTS
Abstract

Background: Stroke, the leading neurologic cause of death and disability, has a substantial genetic component. We previously conducted a genome-wide association study (GWAS) in four prospective studies from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium and demonstrated that sequence variants near the NINJ2 gene are associated with incident ischemic stroke. Here, we sought to fine-map functional variants in the region and evaluate the contribution of rare variants to ischemic stroke risk. Methods and Results: We sequenced 196 kb around NINJ2 on chromosome 12p13 among 3,986 European ancestry participants, including 475 ischemic stroke cases, from the Atherosclerosis Risk in Communities Study, Cardiovascular Health Study, and Framingham Heart Study. Meta-analyses of single-variant tests for 425 common variants (minor allele frequency [MAF] ≥ 1%) confirmed the original GWAS results and identified an independent intronic variant, rs34166160 (MAF = 0.012), most significantly associated with incident ischemic stroke (HR = 1.80, p = 0.0003). Aggregating 278 putatively-functional variants with MAF≤ 1% using count statistics, we observed a nominally statistically significant association, with the burden of rare NINJ2 variants contributing to decreased ischemic stroke incidence (HR = 0.81; p = 0.026). Conclusion: Common and rare variants in the NINJ2 region were nominally associated with incident ischemic stroke among a subset of CHARGE participants. Allelic heterogeneity at this locus, caused by multiple rare, low frequency, and common variants with disparate effects on risk, may explain the difficulties in replicating the original GWAS results. Additional studies that take into account the complex allelic architecture at this locus are needed to confirm these findings. [ABSTRACT FROM AUTHOR]

Published
2014
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37. ADAM19and HTR4Variants and Pulmonary Function

Author

London, Stephanie J., Gao, Wei, Gharib, Sina A., Hancock, Dana B., Wilk, Jemma B., House, John S., Gibbs, Richard A., Muzny, Donna M., Lumley, Thomas, Franceschini, Nora, North, Kari E., Psaty, Bruce M., Kovar, Christie L., Coresh, Josef, Zhou, Yanhua, Heckbert, Susan R., Brody, Jennifer A., Morrison, Alanna C., and Dupuis, Josée

Abstract

The pulmonary function measures of forced expiratory volume in 1 second (FEV1) and its ratio to forced vital capacity (FVC) are used in the diagnosis and monitoring of lung diseases and predict cardiovascular mortality in the general population. Genome-wide association studies (GWASs) have identified numerous loci associated with FEV1 and FEV1FVC, but the causal variants remain uncertain. We hypothesized that novel or rare variants poorly tagged by GWASs may explain the significant associations between FEV1FVC and 2 genes: ADAM19and HTR4.

Published
2014
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38. Comparative and demographic analysis of orang-utan genomes

Author

Matthew W. Hahn, Andreas Heger, Carolin Kosiol, Lisa Cook, Arindam RoyChoudhury, Arcadi Navarro, Catrina Fronick, Lin Chen, Devin P. Locke, Oliver A. Ryder, Olga Fernando, Tomas Vinar, Adam Siepel, Jian Ma, Jeremiah D. Degenhardt, Giuliano Della Valle, Brona Brejova, Oronzo Capozzi, Christie Kovar, Nicoletta Archidiacono, Lucinda Fulton, Jerilyn A. Walker, Albert J. Vilella, Domènec Farré, Julien Y. Dutheil, Xose S. Puente, Mikkel H. Schierup, Carlos Bustamante, George M. Weinstock, Lynne V. Nazareth, Can Alkan, Robert S. Fulton, Brian J. Raney, Mark A. Batzer, Tina Graves, Stephen M. J. Searle, Miriam K. Konkel, Yuko Yoshinaga, Donna M. Muzny, Mariano Rocchi, Carlos López-Otín, Bernard B. Suh, Thomas Mailund, Gonzalo R. Ordóñez, Robert Hubley, Claudio Casola, Huyen Dinh, Rui Faria, Joanne O. Nelson, Tomas Marques-Bonet, Vincent Magrini, Chris Markovic, Makedonka Mitreva, Zhengyuan Wang, Elaine R. Mardis, Arian F.A. Smit, Asger Hobolth, Javier Herrero, David Haussler, Pieter J. de Jong, Kim C. Worley, Heather Schmidt, Ryan N. Gutenkunst, Webb Miller, Yuan Chen, Richard Burhans, Gerton Lunter, Simon D. M. White, André L. Martins, Richard A. Gibbs, Wesley C. Warren, Richard K. Wilson, Patrick Minx, Elodie Gazave, Xin Ma, Daniel R. Schrider, Chris P. Ponting, Roberta Roberto, Shiaw-Pyng Yang, Víctor Quesada, Stefania Purgato, Evan E. Eichler, Andy Cree, Brygg Ullmer, Jeffrey Rogers, Fleur Darré, Robert S. Harris, Vikas Taliwal, Jeffrey M. Kidd, Craig Pohl, Aakrosh Ratan, Paul Flicek, Meritxell Oliva, Kim D. Delehaunty, LaDeana W. Hillier, Jennifer Hume, Stephen Meader, Ze Cheng, Asif T. Chinwalla, Heather A. Lawson, Gerald R. Fowler, National Human Genome Research Institute (US), National Institutes of Health (US), National Science Foundation (US), David and Lucile Packard Foundation, Cornell University, Medical Research Council (UK), European Commission, Ministerio de Ciencia e Innovación (España), Fundación Botín, Instituto Nacional de Bioinformática (España), Fundação para a Ciência e a Tecnologia (Portugal), Locke, Devin P, Hillier, Ladeana W., Warren, Wesley C., Worley, Kim C., Nazareth, Lynne V., Muzny, Donna M., Yang, Shiaw-Pyng, Wang, Zhengyuan, Chinwalla, Asif T., Minx, Pat, Mitreva, Makedonka, Cook, Lisa, Delehaunty, Kim D., Fronick, Catrina, Schmidt, Heather, Fulton, Lucinda A., Fulton, Robert S., Nelson, Joanne O., Magrini, Vincent, Pohl, Craig, Graves, Tina A., Markovic, Chri, Cree, Andy, Dinh, Huyen H., Hume, Jennifer, Kovar, Christie L., Fowler, Gerald R., Lunter, Gerton, Meader, Stephen, Heger, Andrea, Ponting, Chris P., Marques-Bonet, Toma, Alkan, Can, Chen, Lin, Cheng, Ze, Kidd, Jeffrey M., Eichler, Evan E., White, Simon, Searle, Stephen, Vilella, Albert J., Chen, Yuan, Flicek, Paul, Ma, Jian, Raney, Brian, Suh, Bernard, Burhans, Richard, Herrero, Javier, Haussler, David, Faria, Rui, Fernando, Olga, Darré, Fleur, Farré, Doménec, Gazave, Elodie, Oliva, Meritxell, Navarro, Arcadi, Roberto, Roberta, Capozzi, Oronzo, Archidiacono, Nicoletta, Della Valle, Giuliano, Purgato, Stefania, Rocchi, Mariano, Konkel, Miriam K., Walker, Jerilyn A., Ullmer, Brygg, Batzer, Mark A., Smit, Arian F. A., Hubley, Robert, Casola, Claudio, Schrider, Daniel R., Hahn, Matthew W., Quesada, Victor, Puente, Xose S., Ordõez, Gonzalo R., Ĺpez-Otín, Carlo, Vinar, Toma, Brejova, Brona, Ratan, Aakrosh, Harris, Robert S., Miller, Webb, Kosiol, Carolin, Lawson, Heather A., Taliwal, Vika, Martins, André L., Siepel, Adam, Roychoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos D., Gutenkunst, Ryan N., Mailund, Thoma, Dutheil, Julien Y., Hobolth, Asger, Schierup, Mikkel H., Ryder, Oliver A., Yoshinaga, Yuko, De Jong, Pieter J., Weinstock, George M., Rogers, Jeffrey, Mardis, Elaine R., Gibbs, Richard A., and Wilson, Richard K.

Subjects
Male, Pongo abelii, Genetic Speciation, Population, Population Dynamics, Centromere, Zoology, Biology, Southeast asian, Chromosome, Genome, Chromosomes, Article, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Pongo pygmaeus, Effective population size, Cerebrosides, Species Specificity, Animals, Humans, education, Phylogeny, 030304 developmental biology, Comparative genomics, Cerebroside, Gene Rearrangement, Population Density, 0303 health sciences, education.field_of_study, Population Dynamic, Multidisciplinary, Animal, Medicine (all), Genetic Variation, Gene rearrangement, 3. Good health, Genetics, Population, Evolutionary biology, Female, Pongo pygmaeu, 030217 neurology & neurosurgery, Human
Abstract

5 páginas, 5 figuras, 2 tablas.-- This paper is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike Licence, and is freely available to all readers atwww.nature.com/nature.-- et al., ‘Orang-utan’ is derived from a Malay term meaning ‘man of the forest’ and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts., The orang-utan genome project was funded by the National Human Genome Research Institute (NHGRI), including grantsU54HG003079 (R.K.W.) and U54 HG003273 (R.A.G), with further support from National Institutes of Health R01 GM59290 (M.A.B.), PO1 AG022064 (M.A.B.), HG002385 (E.E.E.) and HG002238 (W.M.), National Science Foundation DBI-0644111 (A.S. and B.B.), David and Lucile Packard Foundation(A.S., V.T. and T.V.),CornellUniversity Provost’s Fellowship (A.L.M.), UK Medical Research Council (C.P.P., G.L., S.M. and A.H.), Marie Curie Fellowship (T.M.-B.), Ministerio de Ciencia e Innovación-Spain (MCI-Spain) and Fundación M. Botín (V.Q., X.S.P., G.R.O. and C.L.-O.), MCI-Spain BFU2006-15413-C02-01 and BFU2009-13409-C02-02 (A.N.), Spanish National Institute for Bioinformatics (INAB) and Fundação para a Ciência e a Tecnologia (Portugal), SFRH/BPD/26384/2006(R.F.) and SFRH/BD/15856/2005 (O.F.), PRIN and CEGBA (M.R., N.A. and G.D.V.), and the Commission of the European Communities IRG-224885 (T.V.), IRG-231025 (B.B.).

Published
2011

39. Cohort Profile: The Right Drug, Right Dose, Right Time: Using Genomic Data to Individualize Treatment Protocol (RIGHT Protocol).

Author

Bielinski SJ, St Sauver JL, Olson JE, Larson NB, Black JL, Scherer SE, Bernard ME, Boerwinkle E, Borah BJ, Caraballo PJ, Curry TB, Doddapaneni H, Formea CM, Freimuth RR, Gibbs RA, Giri J, Hathcock MA, Hu J, Jacobson DJ, Jones LA, Kalla S, Koep TH, Korchina V, Kovar CL, Lee S, Liu H, Matey ET, McGree ME, McAllister TM, Moyer AM, Muzny DM, Nicholson WT, Oyen LJ, Qin X, Raj R, Roger VL, Rohrer Vitek CR, Ross JL, Sharp RR, Takahashi PY, Venner E, Walker K, Wang L, Wang Q, Wright JA, Wu TJ, Wang L, and Weinshilboum RM

Subjects
Cohort Studies, Female, Humans, Male, Precision Medicine, Clinical Protocols, Genomics, Pharmacogenetics
Published
2020
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40. Finding the missing honey bee genes: lessons learned from a genome upgrade.

Author

Elsik CG, Worley KC, Bennett AK, Beye M, Camara F, Childers CP, de Graaf DC, Debyser G, Deng J, Devreese B, Elhaik E, Evans JD, Foster LJ, Graur D, Guigo R, Hoff KJ, Holder ME, Hudson ME, Hunt GJ, Jiang H, Joshi V, Khetani RS, Kosarev P, Kovar CL, Ma J, Maleszka R, Moritz RF, Munoz-Torres MC, Murphy TD, Muzny DM, Newsham IF, Reese JT, Robertson HM, Robinson GE, Rueppell O, Solovyev V, Stanke M, Stolle E, Tsuruda JM, Vaerenbergh MV, Waterhouse RM, Weaver DB, Whitfield CW, Wu Y, Zdobnov EM, Zhang L, Zhu D, and Gibbs RA

Subjects
Animals, Base Composition, Databases, Genetic, Interspersed Repetitive Sequences genetics, Molecular Sequence Annotation, Open Reading Frames genetics, Peptides analysis, Sequence Analysis, RNA, Sequence Homology, Amino Acid, Bees genetics, Genes, Insect
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&#95;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
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41. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

Author

Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, and Gibbs RA

Subjects
Animals, Arthropods parasitology, DNA Methylation, DNA Transposable Elements, Female, Gene Transfer, Horizontal, Genes, Insect, Genetic Speciation, Genetic Variation, Host-Parasite Interactions, Insect Proteins genetics, Insect Proteins metabolism, Insect Viruses genetics, Insecta genetics, Male, Molecular Sequence Data, Quantitative Trait Loci, Recombination, Genetic, Sequence Analysis, DNA, Wasp Venoms chemistry, Wasp Venoms toxicity, Wasps physiology, Wolbachia genetics, Biological Evolution, Genome, Insect, Wasps genetics
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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