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14 results on '"Hughes, Daniel"'

1. Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest

Author

Sparks, Michael E, Bansal, Raman, Benoit, Joshua B, Blackburn, Michael B, Chao, Hsu, Chen, Mengyao, Cheng, Sammy, Childers, Christopher, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Elpidina, Elena N, Farrow, David W, Friedrich, Markus, Gibbs, Richard A, Hall, Brantley, Han, Yi, Hardy, Richard W, Holmes, Christopher J, Hughes, Daniel ST, Ioannidis, Panagiotis, Cheatle Jarvela, Alys M, Johnston, J Spencer, Jones, Jeffery W, Kronmiller, Brent A, Kung, Faith, Lee, Sandra L, Martynov, Alexander G, Masterson, Patrick, Maumus, Florian, Munoz-Torres, Monica, Murali, Shwetha C, Murphy, Terence D, Muzny, Donna M, Nelson, David R, Oppert, Brenda, Panfilio, Kristen A, Paula, Débora Pires, Pick, Leslie, Poelchau, Monica F, Qu, Jiaxin, Reding, Katie, Rhoades, Joshua H, Rhodes, Adelaide, Richards, Stephen, Richter, Rose, Robertson, Hugh M, Rosendale, Andrew J, Tu, Zhijian Jake, Velamuri, Arun S, Waterhouse, Robert M, Weirauch, Matthew T, Wells, Jackson T, Werren, John H, Worley, Kim C, Zdobnov, Evgeny M, and Gundersen-Rindal, Dawn E

Subjects
Genetics, Biotechnology, Human Genome, Animals, Ecosystem, Gene Transfer, Horizontal, Genome Size, Heteroptera, Insect Proteins, Insecticide Resistance, Introduced Species, Phylogeny, Whole Genome Sequencing, Brown marmorated stink bug genome, Pentatomid genomics, polyphagy, chemoreceptors, odorant binding proteins, opsins, cathepsins, xenobiotic detoxification, invasive species, Biological Sciences, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics
Abstract

BackgroundHalyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species' feeding and habitat traits, defining potential targets for pest management strategies.ResultsAnalysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys' capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications.ConclusionsAvailability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.

Published
2020

2. Gene content evolution in the arthropods

Author

Thomas, Gregg WC, Dohmen, Elias, Hughes, Daniel ST, Murali, Shwetha C, Poelchau, Monica, Glastad, Karl, Anstead, Clare A, Ayoub, Nadia A, Batterham, Phillip, Bellair, Michelle, Binford, Greta J, Chao, Hsu, Chen, Yolanda H, Childers, Christopher, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Duan, Jian J, Dugan, Shannon, Esposito, Lauren A, Friedrich, Markus, Garb, Jessica, Gasser, Robin B, Goodisman, Michael AD, Gundersen-Rindal, Dawn E, Han, Yi, Handler, Alfred M, Hatakeyama, Masatsugu, Hering, Lars, Hunter, Wayne B, Ioannidis, Panagiotis, Jayaseelan, Joy C, Kalra, Divya, Khila, Abderrahman, Korhonen, Pasi K, Lee, Carol Eunmi, Lee, Sandra L, Li, Yiyuan, Lindsey, Amelia RI, Mayer, Georg, McGregor, Alistair P, McKenna, Duane D, Misof, Bernhard, Munidasa, Mala, Munoz-Torres, Monica, Muzny, Donna M, Niehuis, Oliver, Osuji-Lacy, Nkechinyere, Palli, Subba R, Panfilio, Kristen A, Pechmann, Matthias, Perry, Trent, Peters, Ralph S, Poynton, Helen C, Prpic, Nikola-Michael, Qu, Jiaxin, Rotenberg, Dorith, Schal, Coby, Schoville, Sean D, Scully, Erin D, Skinner, Evette, Sloan, Daniel B, Stouthamer, Richard, Strand, Michael R, Szucsich, Nikolaus U, Wijeratne, Asela, Young, Neil D, Zattara, Eduardo E, Benoit, Joshua B, Zdobnov, Evgeny M, Pfrender, Michael E, Hackett, Kevin J, Werren, John H, Worley, Kim C, Gibbs, Richard A, Chipman, Ariel D, Waterhouse, Robert M, Bornberg-Bauer, Erich, Hahn, Matthew W, and Richards, Stephen

Subjects
Human Genome, Genetics, Biotechnology, Generic health relevance, Animals, Arthropods, DNA Methylation, Evolution, Molecular, Genetic Speciation, Genetic Variation, Phylogeny, Genome assembly, Genomics, Protein domains, Gene content, Evolution, DNA methylation, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundArthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods.ResultsUsing 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception.ConclusionsThese analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.

Published
2020

3. Genome-enabled insights into the biology of thrips as crop pests

Author

Rotenberg, Dorith, Baumann, Aaron A, Ben-Mahmoud, Sulley, Christiaens, Olivier, Dermauw, Wannes, Ioannidis, Panagiotis, Jacobs, Chris GC, Vargas Jentzsch, Iris M, Oliver, Jonathan E, Poelchau, Monica F, Rajarapu, Swapna Priya, Schneweis, Derek J, Snoeck, Simon, Taning, Clauvis NT, Wei, Dong, Widana Gamage, Shirani MK, Hughes, Daniel ST, Murali, Shwetha C, Bailey, Samuel T, Bejerman, Nicolas E, Holmes, Christopher J, Jennings, Emily C, Rosendale, Andrew J, Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A, Cheng, Sammy, Childers, Christopher, Simão, Felipe A, Dietzgen, Ralf G, Chao, Hsu, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Han, Yi, Lee, Sandra L, Muzny, Donna M, Qu, Jiaxin, Worley, Kim C, Benoit, Joshua B, Friedrich, Markus, Jones, Jeffery W, Panfilio, Kristen A, Park, Yoonseong, Robertson, Hugh M, Smagghe, Guy, Ullman, Diane E, van der Zee, Maurijn, Van Leeuwen, Thomas, Veenstra, Jan A, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Whitfield, Anna E, Zdobnov, Evgeny M, Gibbs, Richard A, and Richards, Stephen

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Animals, Crops, Agricultural, Feeding Behavior, Food Chain, Genome, Insect, Immunity, Innate, Life History Traits, Perception, Phylogeny, Reproduction, Thysanoptera, Transcriptome, Western flower thrips, Hemipteroid assemblage, Insect genomics, Tospovirus, Salivary glands, Chemosensory receptors, Opsins, Detoxification, Innate immunity, Developmental Biology, Biological sciences
Abstract

BackgroundThe western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set.ResultsWe report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta.ConclusionsAnalysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.

Published
2020

4. Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera

Author

Oeyen, Jan Philip, Baa-Puyoulet, Patrice, Benoit, Joshua B, Beukeboom, Leo W, Bornberg-Bauer, Erich, Buttstedt, Anja, Calevro, Federica, Cash, Elizabeth I, Chao, Hsu, Charles, Hubert, Chen, Mei-Ju May, Childers, Christopher, Cridge, Andrew G, Dearden, Peter, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dolan, Amanda, Donath, Alexander, Dowling, Daniel, Dugan, Shannon, Duncan, Elizabeth, Elpidina, Elena N, Friedrich, Markus, Geuverink, Elzemiek, Gibson, Joshua D, Grath, Sonja, Grimmelikhuijzen, Cornelis JP, Große-Wilde, Ewald, Gudobba, Cameron, Han, Yi, Hansson, Bill S, Hauser, Frank, Hughes, Daniel ST, Ioannidis, Panagiotis, Jacquin-Joly, Emmanuelle, Jennings, Emily C, Jones, Jeffery W, Klasberg, Steffen, Lee, Sandra L, Lesný, Peter, Lovegrove, Mackenzie, Martin, Sebastian, Martynov, Alexander G, Mayer, Christoph, Montagné, Nicolas, Moris, Victoria C, Munoz-Torres, Monica, Murali, Shwetha Canchi, Muzny, Donna M, Oppert, Brenda, Parisot, Nicolas, Pauli, Thomas, Peters, Ralph S, Petersen, Malte, Pick, Christian, Persyn, Emma, Podsiadlowski, Lars, Poelchau, Monica F, Provataris, Panagiotis, Qu, Jiaxin, Reijnders, Maarten JMF, von Reumont, Björn Marcus, Rosendale, Andrew J, Simao, Felipe A, Skelly, John, Sotiropoulos, Alexandros G, Stahl, Aaron L, Sumitani, Megumi, Szuter, Elise M, Tidswell, Olivia, Tsitlakidis, Evangelos, Vedder, Lucia, Waterhouse, Robert M, Werren, John H, Wilbrandt, Jeanne, Worley, Kim C, Yamamoto, Daisuke S, van de Zande, Louis, Zdobnov, Evgeny M, Ziesmann, Tanja, Gibbs, Richard A, Richards, Stephen, Hatakeyama, Masatsugu, Misof, Bernhard, and Niehuis, Oliver

Subjects
Human Genome, Genetics, Life Below Water, Amino Acid Sequence, Animals, Conserved Sequence, DNA Transposable Elements, Female, Gene Dosage, Genetic Speciation, Genome, Insect, Glycoproteins, Herbivory, Host-Parasite Interactions, Hymenoptera, Immunity, Insect Proteins, Male, Multigene Family, Receptors, Odorant, Social Behavior, Vision, Ocular, hexamerin, major royal jelly protein, microsynteny, odorant receptor, opsin, phytophagy, Biochemistry and Cell Biology, Evolutionary Biology, Developmental Biology
Abstract

The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.

Published
2020

5. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

Author

Panfilio, Kristen A, Vargas Jentzsch, Iris M, Benoit, Joshua B, Erezyilmaz, Deniz, Suzuki, Yuichiro, Colella, Stefano, Robertson, Hugh M, Poelchau, Monica F, Waterhouse, Robert M, Ioannidis, Panagiotis, Weirauch, Matthew T, Hughes, Daniel ST, Murali, Shwetha C, Werren, John H, Jacobs, Chris GC, Duncan, Elizabeth J, Armisén, David, Vreede, Barbara MI, Baa-Puyoulet, Patrice, Berger, Chloé S, Chang, Chun-che, Chao, Hsu, Chen, Mei-Ju M, Chen, Yen-Ta, Childers, Christopher P, Chipman, Ariel D, Cridge, Andrew G, Crumière, Antonin JJ, Dearden, Peter K, Didion, Elise M, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dolan, Amanda, Dugan, Shannon, Extavour, Cassandra G, Febvay, Gérard, Friedrich, Markus, Ginzburg, Neta, Han, Yi, Heger, Peter, Holmes, Christopher J, Horn, Thorsten, Hsiao, Yi-min, Jennings, Emily C, Johnston, J Spencer, Jones, Tamsin E, Jones, Jeffery W, Khila, Abderrahman, Koelzer, Stefan, Kovacova, Viera, Leask, Megan, Lee, Sandra L, Lee, Chien-Yueh, Lovegrove, Mackenzie R, Lu, Hsiao-ling, Lu, Yong, Moore, Patricia J, Munoz-Torres, Monica C, Muzny, Donna M, Palli, Subba R, Parisot, Nicolas, Pick, Leslie, Porter, Megan L, Qu, Jiaxin, Refki, Peter N, Richter, Rose, Rivera-Pomar, Rolando, Rosendale, Andrew J, Roth, Siegfried, Sachs, Lena, Santos, M Emília, Seibert, Jan, Sghaier, Essia, Shukla, Jayendra N, Stancliffe, Richard J, Tidswell, Olivia, Traverso, Lucila, van der Zee, Maurijn, Viala, Séverine, Worley, Kim C, Zdobnov, Evgeny M, Gibbs, Richard A, and Richards, Stephen

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Amino Acid Sequence, Animals, CYS2-HIS2 Zinc Fingers, Evolution, Molecular, Feeding Behavior, Gene Dosage, Gene Expression Profiling, Gene Transfer, Horizontal, Genes, Homeobox, Genome, Insect, Hemiptera, Pigmentation, Smell, Transcription Factors, Evolution of development, Gene family evolution, Gene structure, Lateral gene transfer, Phytophagy, RNAi, Transcription factors, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundThe Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.ResultsThe 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding.ConclusionsWith the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.

Published
2019

6. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.

Author

Panfilio, Kristen A, Vargas Jentzsch, Iris M, Benoit, Joshua B, Erezyilmaz, Deniz, Suzuki, Yuichiro, Colella, Stefano, Robertson, Hugh M, Poelchau, Monica F, Waterhouse, Robert M, Ioannidis, Panagiotis, Weirauch, Matthew T, Hughes, Daniel ST, Murali, Shwetha C, Werren, John H, Jacobs, Chris GC, Duncan, Elizabeth J, Armisén, David, Vreede, Barbara MI, Baa-Puyoulet, Patrice, Berger, Chloé S, Chang, Chun-Che, Chao, Hsu, Chen, Mei-Ju M, Chen, Yen-Ta, Childers, Christopher P, Chipman, Ariel D, Cridge, Andrew G, Crumière, Antonin JJ, Dearden, Peter K, Didion, Elise M, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dolan, Amanda, Dugan, Shannon, Extavour, Cassandra G, Febvay, Gérard, Friedrich, Markus, Ginzburg, Neta, Han, Yi, Heger, Peter, Holmes, Christopher J, Horn, Thorsten, Hsiao, Yi-Min, Jennings, Emily C, Johnston, J Spencer, Jones, Tamsin E, Jones, Jeffery W, Khila, Abderrahman, Koelzer, Stefan, Kovacova, Viera, Leask, Megan, Lee, Sandra L, Lee, Chien-Yueh, Lovegrove, Mackenzie R, Lu, Hsiao-Ling, Lu, Yong, Moore, Patricia J, Munoz-Torres, Monica C, Muzny, Donna M, Palli, Subba R, Parisot, Nicolas, Pick, Leslie, Porter, Megan L, Qu, Jiaxin, Refki, Peter N, Richter, Rose, Rivera-Pomar, Rolando, Rosendale, Andrew J, Roth, Siegfried, Sachs, Lena, Santos, M Emília, Seibert, Jan, Sghaier, Essia, Shukla, Jayendra N, Stancliffe, Richard J, Tidswell, Olivia, Traverso, Lucila, van der Zee, Maurijn, Viala, Séverine, Worley, Kim C, Zdobnov, Evgeny M, Gibbs, Richard A, and Richards, Stephen

Subjects
Animals, Hemiptera, Transcription Factors, Pigmentation, Gene Expression Profiling, Feeding Behavior, Smell, Evolution, Molecular, Gene Transfer, Horizontal, Amino Acid Sequence, Gene Dosage, Genes, Homeobox, Genome, Insect, CYS2-HIS2 Zinc Fingers, Evolution of development, Gene family evolution, Gene structure, Lateral gene transfer, Phytophagy, RNAi, Transcription factors, Biotechnology, Human Genome, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BACKGROUND:The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS:The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS:With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.

Published
2019

7. Integrated Molecular Characterization of Testicular Germ Cell Tumors

Author

Shen, Hui, Shih, Juliann, Hollern, Daniel P, Wang, Linghua, Bowlby, Reanne, Tickoo, Satish K, Thorsson, Vésteinn, Mungall, Andrew J, Newton, Yulia, Hegde, Apurva M, Armenia, Joshua, Sánchez-Vega, Francisco, Pluta, John, Pyle, Louise C, Mehra, Rohit, Reuter, Victor E, Godoy, Guilherme, Jones, Jeffrey, Shelley, Carl S, Feldman, Darren R, Vidal, Daniel O, Lessel, Davor, Kulis, Tomislav, Cárcano, Flavio M, Leraas, Kristen M, Lichtenberg, Tara M, Brooks, Denise, Cherniack, Andrew D, Cho, Juok, Heiman, David I, Kasaian, Katayoon, Liu, Minwei, Noble, Michael S, Xi, Liu, Zhang, Hailei, Zhou, Wanding, ZenKlusen, Jean C, Hutter, Carolyn M, Felau, Ina, Zhang, Jiashan, Schultz, Nikolaus, Getz, Gad, Meyerson, Matthew, Stuart, Joshua M, Akbani, Rehan, Wheeler, David, Laird, Peter W, Nathanson, Katherine L, Cortessis, Victoria K, Hoadley, Katherine A, Wheeler, David A, Hughes, Daniel, Covington, Kyle, Jayaseelan, Joy C, Korchina, Viktoriya, Lewis, Lora, Hu, Jianhong, Doddapaneni, HarshaVardhan, Muzny, Donna, Gibbs, Richard, Hollern, Daniel, Vincent, Benjamin G, Chai, Shengjie, Smith, Christof C, Auman, J Todd, Shi, Yan, Meng, Shaowu, Skelly, Tara, Tan, Donghui, Veluvolu, Umadevi, Mieczkowski, Piotr A, Jones, Corbin D, Wilkerson, Matthew D, Balu, Saianand, Bodenheimer, Tom, Hoyle, Alan P, Jefferys, Stuart R, Mose, Lisle E, Simons, Janae V, Soloway, Matthew G, Roach, Jeffrey, Parker, Joel S, Hayes, D Neil, Perou, Charles M, Saksena, Gordon, Cibulskis, Carrie, Schumacher, Steven E, Beroukhim, Rameen, Gabriel, Stacey B, and Ally, Adrian

Subjects
Urologic Diseases, Rare Diseases, Human Genome, Cancer, Biotechnology, Genetics, DNA Copy Number Variations, DNA Methylation, Gene Expression Regulation, Neoplastic, Humans, Male, MicroRNAs, Neoplasms, Germ Cell and Embryonal, Proto-Oncogene Proteins c-kit, Seminoma, Testicular Neoplasms, ras Proteins, Cancer Genome Atlas Research Network, DNA methylation, KIT, The Cancer Genome Atlas, copy number, exome sequencing, miR-375, nonseminoma, seminoma, testicular germ cell tumors, Biochemistry and Cell Biology, Medical Physiology
Abstract

We studied 137 primary testicular germ cell tumors (TGCTs) using high-dimensional assays of genomic, epigenomic, transcriptomic, and proteomic features. These tumors exhibited high aneuploidy and a paucity of somatic mutations. Somatic mutation of only three genes achieved significance-KIT, KRAS, and NRAS-exclusively in samples with seminoma components. Integrated analyses identified distinct molecular patterns that characterized the major recognized histologic subtypes of TGCT: seminoma, embryonal carcinoma, yolk sac tumor, and teratoma. Striking differences in global DNA methylation and microRNA expression between histology subtypes highlight a likely role of epigenomic processes in determining histologic fates in TGCTs. We also identified a subset of pure seminomas defined by KIT mutations, increased immune infiltration, globally demethylated DNA, and decreased KRAS copy number. We report potential biomarkers for risk stratification, such as miRNA specifically expressed in teratoma, and others with molecular diagnostic potential, such as CpH (CpA/CpC/CpT) methylation identifying embryonal carcinomas.

Published
2018

8. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

Author

Schwager, Evelyn E, Sharma, Prashant P, Clarke, Thomas, Leite, Daniel J, Wierschin, Torsten, Pechmann, Matthias, Akiyama-Oda, Yasuko, Esposito, Lauren, Bechsgaard, Jesper, Bilde, Trine, Buffry, Alexandra D, Chao, Hsu, Dinh, Huyen, Doddapaneni, HarshaVardhan, Dugan, Shannon, Eibner, Cornelius, Extavour, Cassandra G, Funch, Peter, Garb, Jessica, Gonzalez, Luis B, Gonzalez, Vanessa L, Griffiths-Jones, Sam, Han, Yi, Hayashi, Cheryl, Hilbrant, Maarten, Hughes, Daniel ST, Janssen, Ralf, Lee, Sandra L, Maeso, Ignacio, Murali, Shwetha C, Muzny, Donna M, Nunes da Fonseca, Rodrigo, Paese, Christian LB, Qu, Jiaxin, Ronshaugen, Matthew, Schomburg, Christoph, Schönauer, Anna, Stollewerk, Angelika, Torres-Oliva, Montserrat, Turetzek, Natascha, Vanthournout, Bram, Werren, John H, Wolff, Carsten, Worley, Kim C, Bucher, Gregor, Gibbs, Richard A, Coddington, Jonathan, Oda, Hiroki, Stanke, Mario, Ayoub, Nadia A, Prpic, Nikola-Michael, Flot, Jean-François, Posnien, Nico, Richards, Stephen, and McGregor, Alistair P

Subjects
Human Genome, Genetics, Generic health relevance, Animals, Evolution, Molecular, Female, Gene Duplication, Genome, Male, Spiders, Synteny, Parasteatoda tepidariorum, Centruroides sculpturatus, Gene duplication, Evolution, Hox genes, Developmental Biology
Abstract

BackgroundThe duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum.ResultsWe found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication.ConclusionsOur results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.

Published
2017

9. Whole genome analysis of a schistosomiasis-transmitting freshwater snail.

Author

Adema, Coen M, Hillier, LaDeana W, Jones, Catherine S, Loker, Eric S, Knight, Matty, Minx, Patrick, Oliveira, Guilherme, Raghavan, Nithya, Shedlock, Andrew, do Amaral, Laurence Rodrigues, Arican-Goktas, Halime D, Assis, Juliana G, Baba, Elio Hideo, Baron, Olga L, Bayne, Christopher J, Bickham-Wright, Utibe, Biggar, Kyle K, Blouin, Michael, Bonning, Bryony C, Botka, Chris, Bridger, Joanna M, Buckley, Katherine M, Buddenborg, Sarah K, Lima Caldeira, Roberta, Carleton, Julia, Carvalho, Omar S, Castillo, Maria G, Chalmers, Iain W, Christensens, Mikkel, Clifton, Sandra, Cosseau, Celine, Coustau, Christine, Cripps, Richard M, Cuesta-Astroz, Yesid, Cummins, Scott F, di Stephano, Leon, Dinguirard, Nathalie, Duval, David, Emrich, Scott, Feschotte, Cédric, Feyereisen, Rene, FitzGerald, Peter, Fronick, Catrina, Fulton, Lucinda, Galinier, Richard, Gava, Sandra G, Geusz, Michael, Geyer, Kathrin K, Giraldo-Calderón, Gloria I, de Souza Gomes, Matheus, Gordy, Michelle A, Gourbal, Benjamin, Grunau, Christoph, Hanington, Patrick C, Hoffmann, Karl F, Hughes, Daniel, Humphries, Judith, Jackson, Daniel J, Jannotti-Passos, Liana K, de Jesus Jeremias, Wander, Jobling, Susan, Kamel, Bishoy, Kapusta, Aurélie, Kaur, Satwant, Koene, Joris M, Kohn, Andrea B, Lawson, Dan, Lawton, Scott P, Liang, Di, Limpanont, Yanin, Liu, Sijun, Lockyer, Anne E, Lovato, TyAnna L, Ludolf, Fernanda, Magrini, Vince, McManus, Donald P, Medina, Monica, Misra, Milind, Mitta, Guillaume, Mkoji, Gerald M, Montague, Michael J, Montelongo, Cesar, Moroz, Leonid L, Munoz-Torres, Monica C, Niazi, Umar, Noble, Leslie R, Oliveira, Francislon S, Pais, Fabiano S, Papenfuss, Anthony T, Peace, Rob, Pena, Janeth J, Pila, Emmanuel A, Quelais, Titouan, Raney, Brian J, Rast, Jonathan P, Rollinson, David, Rosse, Izinara C, Rotgans, Bronwyn, Routledge, Edwin J, and Ryan, Kathryn M

Subjects
Animals, Schistosoma mansoni, Biomphalaria, Schistosomiasis mansoni, Proteome, DNA Transposable Elements, Pheromones, Sequence Analysis, DNA, Animal Communication, Fresh Water, Evolution, Molecular, Gene Expression Regulation, Genome, Host-Parasite Interactions, Stress, Physiological, Genetics, Human Genome, Digestive Diseases, Vector-Borne Diseases, Infectious Diseases, Infection, Good Health and Well Being
Abstract

Biomphalaria snails are instrumental in transmission of the human blood fluke Schistosoma mansoni. With the World Health Organization's goal to eliminate schistosomiasis as a global health problem by 2025, there is now renewed emphasis on snail control. Here, we characterize the genome of Biomphalaria glabrata, a lophotrochozoan protostome, and provide timely and important information on snail biology. We describe aspects of phero-perception, stress responses, immune function and regulation of gene expression that support the persistence of B. glabrata in the field and may define this species as a suitable snail host for S. mansoni. We identify several potential targets for developing novel control measures aimed at reducing snail-mediated transmission of schistosomiasis.

Published
2017

10. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome

Author

Benoit, Joshua B, Adelman, Zach N, Reinhardt, Klaus, Dolan, Amanda, Poelchau, Monica, Jennings, Emily C, Szuter, Elise M, Hagan, Richard W, Gujar, Hemant, Shukla, Jayendra Nath, Zhu, Fang, Mohan, M, Nelson, David R, Rosendale, Andrew J, Derst, Christian, Resnik, Valentina, Wernig, Sebastian, Menegazzi, Pamela, Wegener, Christian, Peschel, Nicolai, Hendershot, Jacob M, Blenau, Wolfgang, Predel, Reinhard, Johnston, Paul R, Ioannidis, Panagiotis, Waterhouse, Robert M, Nauen, Ralf, Schorn, Corinna, Ott, Mark-Christoph, Maiwald, Frank, Johnston, J Spencer, Gondhalekar, Ameya D, Scharf, Michael E, Peterson, Brittany F, Raje, Kapil R, Hottel, Benjamin A, Armisén, David, Crumière, Antonin Jean Johan, Refki, Peter Nagui, Santos, Maria Emilia, Sghaier, Essia, Viala, Sèverine, Khila, Abderrahman, Ahn, Seung-Joon, Childers, Christopher, Lee, Chien-Yueh, Lin, Han, Hughes, Daniel ST, Duncan, Elizabeth J, Murali, Shwetha C, Qu, Jiaxin, Dugan, Shannon, Lee, Sandra L, Chao, Hsu, Dinh, Huyen, Han, Yi, Doddapaneni, Harshavardhan, Worley, Kim C, Muzny, Donna M, Wheeler, David, Panfilio, Kristen A, Vargas Jentzsch, Iris M, Vargo, Edward L, Booth, Warren, Friedrich, Markus, Weirauch, Matthew T, Anderson, Michelle AE, Jones, Jeffery W, Mittapalli, Omprakash, Zhao, Chaoyang, Zhou, Jing-Jiang, Evans, Jay D, Attardo, Geoffrey M, Robertson, Hugh M, Zdobnov, Evgeny M, Ribeiro, Jose MC, Gibbs, Richard A, Werren, John H, Palli, Subba R, Schal, Coby, and Richards, Stephen

Subjects
Human Genome, Genetics, Biotechnology, Good Health and Well Being, Animals, Bedbugs, Ectoparasitic Infestations, Feeding Behavior, Gene Transfer, Horizontal, Genome, Host-Parasite Interactions, Humans, Insecticide Resistance, Insecticides, Sequence Analysis, DNA
Abstract

The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.

Published
2016

11. Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

Author

Neafsey, Daniel E, Waterhouse, Robert M, Abai, Mohammad R, Aganezov, Sergey S, Alekseyev, Max A, Allen, James E, Amon, James, Arcà, Bruno, Arensburger, Peter, Artemov, Gleb, Assour, Lauren A, Basseri, Hamidreza, Berlin, Aaron, Birren, Bruce W, Blandin, Stephanie A, Brockman, Andrew I, Burkot, Thomas R, Burt, Austin, Chan, Clara S, Chauve, Cedric, Chiu, Joanna C, Christensen, Mikkel, Costantini, Carlo, Davidson, Victoria LM, Deligianni, Elena, Dottorini, Tania, Dritsou, Vicky, Gabriel, Stacey B, Guelbeogo, Wamdaogo M, Hall, Andrew B, Han, Mira V, Hlaing, Thaung, Hughes, Daniel ST, Jenkins, Adam M, Jiang, Xiaofang, Jungreis, Irwin, Kakani, Evdoxia G, Kamali, Maryam, Kemppainen, Petri, Kennedy, Ryan C, Kirmitzoglou, Ioannis K, Koekemoer, Lizette L, Laban, Njoroge, Langridge, Nicholas, Lawniczak, Mara KN, Lirakis, Manolis, Lobo, Neil F, Lowy, Ernesto, MacCallum, Robert M, Mao, Chunhong, Maslen, Gareth, Mbogo, Charles, McCarthy, Jenny, Michel, Kristin, Mitchell, Sara N, Moore, Wendy, Murphy, Katherine A, Naumenko, Anastasia N, Nolan, Tony, Novoa, Eva M, O'Loughlin, Samantha, Oringanje, Chioma, Oshaghi, Mohammad A, Pakpour, Nazzy, Papathanos, Philippos A, Peery, Ashley N, Povelones, Michael, Prakash, Anil, Price, David P, Rajaraman, Ashok, Reimer, Lisa J, Rinker, David C, Rokas, Antonis, Russell, Tanya L, Sagnon, N'Fale, Sharakhova, Maria V, Shea, Terrance, Simão, Felipe A, Simard, Frederic, Slotman, Michel A, Somboon, Pradya, Stegniy, Vladimir, Struchiner, Claudio J, Thomas, Gregg WC, Tojo, Marta, Topalis, Pantelis, Tubio, José MC, Unger, Maria F, Vontas, John, Walton, Catherine, Wilding, Craig S, Willis, Judith H, Wu, Yi-Chieh, Yan, Guiyun, Zdobnov, Evgeny M, Zhou, Xiaofan, Catteruccia, Flaminia, Christophides, George K, Collins, Frank H, and Cornman, Robert S

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Medical Microbiology, Infectious Diseases, Rare Diseases, Vector-Borne Diseases, Biotechnology, Malaria, Infection, Good Health and Well Being, Animals, Anopheles, Base Sequence, Chromosomes, Insect, Drosophila, Evolution, Molecular, Genome, Insect, Humans, Insect Vectors, Molecular Sequence Data, Phylogeny, Sequence Alignment, General Science & Technology
Abstract

Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.

Published
2015

12. Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis

Author

Initiative, International Glossina Genome, Attardo, Geoffrey M, Abila, Patrick P, Auma, Joanna E, Baumann, Aaron A, Benoit, Joshua B, Brelsfoard, Corey L, Ribeiro, José MC, Cotton, James A, Pham, Daphne QD, Darby, Alistair C, Van Den Abbeele, Jan, Denlinger, David L, Field, Linda M, Nyanjom, Steven RG, Gaunt, Michael W, Geiser, Dawn L, Gomulski, Ludvik M, Haines, Lee R, Hansen, Immo A, Jones, Jeffery W, Kibet, Caleb K, Kinyua, Johnson K, Larkin, Denis M, Lehane, Michael J, Rio, Rita VM, Macdonald, Sandy J, Macharia, Rosaline W, Malacrida, Anna R, Marco, Heather G, Marucha, Kevin K, Masiga, Daniel K, Meuti, Megan E, Mireji, Paul O, Obiero, George FO, Koekemoer, Jacobus JO, Okoro, Chinyere K, Omedo, Irene A, Osamor, Victor C, Balyeidhusa, Apollo SP, Peyton, Justin T, Price, David P, Quail, Michael A, Ramphul, Urvashi N, Rawlings, Neil D, Riehle, Michael A, Robertson, Hugh M, Sanders, Mandy J, Scott, Maxwell J, Dashti, Zahra Jalali Sefid, Snyder, Anna K, Srivastava, Tulika P, Stanley, Eleanor J, Swain, Martin T, Hughes, Daniel ST, Tarone, Aaron M, Taylor, Todd D, Telleria, Erich L, Thomas, Gavin H, Walshe, Deirdre P, Wilson, Richard K, Winzerling, Joy J, Acosta-Serrano, Alvaro, Aksoy, Serap, Arensburger, Peter, Aslett, Martin, Bateta, Rosemary, Benkahla, Alia, Berriman, Matthew, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christoffels, Alan, Falchetto, Marco, Friedrich, Markus, Fu, Shuhua, Gäde, Gerd, Githinji, George, Gregory, Richard, Hall, Neil, Harkins, Gordon, Hattori, Masahira, Hertz-Fowler, Christiane, Hide, Winston, Hu, Wanqi, Imanishi, Tadashi, Inoue, Noboru, Jonas, Mario, Kawahara, Yoshihiro, Koffi, Mathurin, Kruger, Adele, Lawson, Daniel, Lehane, Stella, Lehväslaiho, Heikki, Luiz, Thiago, Makgamathe, Mmule, Malele, Imna, Manangwa, Oliver, Manga, Lucien, and Megy, Karyn

Subjects
Vector-Borne Diseases, Genetics, Prevention, Infectious Diseases, Biotechnology, 2.2 Factors relating to the physical environment, Aetiology, Infection, Good Health and Well Being, Animals, Blood, Feeding Behavior, Female, Genes, Insect, Genome, Insect, Insect Proteins, Insect Vectors, Microbiota, Molecular Sequence Annotation, Molecular Sequence Data, Reproduction, Salivary Glands, Sensation, Sequence Analysis, DNA, Symbiosis, Trypanosoma, Trypanosomiasis, African, Tsetse Flies, Wolbachia, International Glossina Genome Initiative, General Science & Technology
Abstract

Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.

Published
2014

13. 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

14. VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics

Author

Megy, Karine, Emrich, Scott J, Lawson, Daniel, Campbell, David, Dialynas, Emmanuel, Hughes, Daniel ST, Koscielny, Gautier, Louis, Christos, MacCallum, Robert M, Redmond, Seth N, Sheehan, Andrew, Topalis, Pantelis, and Wilson, Derek

Subjects
Emerging Infectious Diseases, Human Genome, Infectious Diseases, Genetics, Vector-Borne Diseases, Prevention, Biotechnology, 3.2 Interventions to alter physical and biological environmental risks, Prevention of disease and conditions, and promotion of well-being, Infection, Generic health relevance, Good Health and Well Being, Animals, Culicidae, Databases, Genetic, Genetic Variation, Genome, Insect, Genomics, Insect Vectors, Insecticide Resistance, Ixodes, Pediculus, Rhodnius, Tsetse Flies, VectorBase Consortium, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

VectorBase (http://www.vectorbase.org) is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data for nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis), body louse (Pediculus humanus), kissing bug (Rhodnius prolixus) and tsetse fly (Glossina morsitans). Hosted data range from genomic features and expression data to population genetics and ontologies. We describe improvements and integration of new data that expand our taxonomic coverage. Releases are bi-monthly and include the delivery of preliminary data for emerging genomes. Frequent updates of the genome browser provide VectorBase users with increasing options for visualizing their own high-throughput data. One major development is a new population biology resource for storing genomic variations, insecticide resistance data and their associated metadata. It takes advantage of improved ontologies and controlled vocabularies. Combined, these new features ensure timely release of multiple types of data in the public domain while helping overcome the bottlenecks of bioinformatics and annotation by engaging with our user community.

Published
2012

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