1. It's more than stamp collecting: how genome sequencing can unify biological research.

    Trends in Genetics 31(7):411 (2015) PMID 26003218 PMCID PMC4490122

    The availability of reference genome sequences, especially the human reference, has revolutionized the study of biology. However, while the genomes of some species have been fully sequenced, a wide range of biological problems still cannot be effectively studied for lack of genome sequence infor...
  2. Genomic Signatures of Cooperation and Conflict in the Social Amoeba.

    Current Biology 25(12):1661 (2015) PMID 26051890

    Cooperative systems are susceptible to invasion by selfish individuals that profit from receiving the social benefits but fail to contribute. These so-called "cheaters" can have a fitness advantage in the laboratory, but it is unclear whether cheating provides an important selective advantage in...
  3. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

    Current Biology 25(5):613 (2015) PMID 25660540

    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 mec...
  4. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor.

    Current Biology 25(5):613 (2015) PMID 25660540

    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 th...
  5. The genomes of two key bumblebee species with primitive eusocial organization.
    Ben M Sadd, Seth M Barribeau, Guy Bloch, Dirk C de Graaf, Peter Dearden, Christine G Elsik, Jürgen Gadau, Cornelis J P Grimmelikhuijzen, Martin Hasselmann, Jeffrey D Lozier, Hugh M Robertson, Guy Smagghe, Eckart Stolle, Matthias Van Vaerenbergh, Robert M Waterhouse, Erich, Steffen Klasberg, Anna K Bennett, Francisco Câmara, Roderic Guigó, Katharina Hoff, Marco Mariotti, Monica Munoz-Torres, Terence Murphy, Didac Santesmasses, Gro V Amdam, Matthew Beckers, Martin Beye, Matthias Biewer, Márcia G Bitondi, Mark L Blaxter, Andrew F G Bourke, Mark J F Brown, Severine D Buechel, Rossanah Cameron, Kaat Cappelle, James Carolan, Olivier Christiaens, Kate L Ciborowski, David F Clarke, Thomas J Colgan, David H Collins, Andrew G Cridge, Tamas Dalmay, Stephanie Dreier, Louis du Plessis, Elizabeth Duncan, Silvio Erler, Jay Evans, Tiago Falcon, Kevin Flores, Flávia C P Freitas, Taro Fuchikawa, Tanja Gempe, Klaus Hartfelder, Frank Hauser, Sophie Helbing, Fernanda C Humann, Frano Irvine, Lars S Jermiin, Claire E Johnson, Reed M Johnson, Andrew K Jones, Tatsuhiko Kadowaki, Jonathan H Kidner, Vasco Koch, Arian Köhler, F Bernhard Kraus, H Michael G Lattorff, Megan Leask, Gabrielle A Lockett, Eamonn B Mallon, David S Marco Antonio, Monika Marxer, Ivan Meeus, Robin F A Moritz, Ajay Nair, Kathrin Näpflin, Inga Nissen, Jinzhi Niu, Francis M Nunes, John G Oakeshott, Amy Osborne, Marianne Otte, Daniel G Pinheiro, Nina Rossié, Olav Rueppell, Carolina G Santos, Regula Schmid-Hempel, Björn D Schmitt, Christina Schulte, Zilá L P Simões, Michelle P Soares, Luc Swevers, Eva C Winnebeck, Florian Wolschin, Na Yu, Evgeny M Zdobnov, Peshtewani K Aqrawi, Kerstin P Blankenburg, Marcus Coyle, Liezl Francisco, Alvaro G Hernandez, Michael Holder, Matthew E Hudson, LaRonda Jackson, Joy Jayaseelan, Vandita Joshi, Christie Kovar, Sandra Lee, Robert Mata, Tittu Mathew, Irene F Newsham, Robin Ngo, Geoffrey Okwuonu, Christopher Pham, Pu, Nehad Saada, Jireh Santibanez, DeNard Simmons, Rebecca Thornton, Aarti Venkat, Kimberly O Walden, Yuan-Qing Wu, Griet Debyser, Bart Devreese, Claire Asher, Julie Blommaert, Ariel D Chipman, Lars Chittka, Bertrand Fouks, Jisheng Liu, Meaghan P O'Neill, Seirian Sumner, Daniela Puiu, Jiaxin Qu, Steven L Salzberg, Steven E Scherer, Donna Muzny, Stephen Richards, Gene E Robinson, Richard A Gibbs, Paul Schmid-Hempel, and Kim C Worley

    Genome biology 16:76 (2015) PMID 25908251 PMCID PMC4414376

    The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespre...
  6. Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions.

    Nature Communications 6:7344 (2015) PMID 26108605 PMCID PMC4491171

    Lucilia cuprina is a parasitic fly of major economic importance worldwide. Larvae of this fly invade their animal host, feed on tissues and excretions and progressively cause severe skin disease (myiasis). Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cup...
  7. Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura.

    G3: Genes, Genomes, Genetics 4(12):2433 (2014) PMID 25326424 PMCID PMC4267939

    There has been a renewed interest in investigating the role of stabilizing selection acting on genome-wide traits such as codon usage bias. Codon bias, when synonymous codons are used at unequal frequencies, occurs in a wide variety of taxa. Standard evolutionary models explain the maintenance o...
  8. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima.
    Ariel D Chipman, David E K Ferrier, Carlo Brena, Jiaxin Qu, Daniel S T Hughes, Reinhard Schröder, Montserrat Torres-Oliva, Nadia Znassi, Huaiyang Jiang, Francisca C Almeida, Claudio R Alonso, Zivkos Apostolou, Peshtewani Aqrawi, Wallace Arthur, Jennifer C Barna, Kerstin P Blankenburg, Daniela Brites, Salvador Capella-Gutiérrez, Marcus Coyle, Peter K Dearden, Louis Du Pasquier, Elizabeth J Duncan, Dieter Ebert, Cornelius Eibner, Galina Erikson, Peter D Evans, Cassandra G Extavour, Liezl Francisco, Toni Gabaldón, William J Gillis, Elizabeth A Goodwin-Horn, Jack E Green, Sam Griffiths-Jones, Cornelis J P Grimmelikhuijzen, Sai Gubbala, Roderic Guigó, Yi Han, Frank Hauser, Paul Havlak, Luke Hayden, Sophie Helbing, Michael Holder, Jerome L Hui, Julia P Hunn, Vera S Hunnekuhl, LaRonda Jackson, Mehwish Javaid, Shalini N Jhangiani, Francis M Jiggins, Tamsin E Jones, Tobias S Kaiser, Divya Kalra, Nathan J Kenny, Viktoriya Korchina, Christie L Kovar, F Bernhard Kraus, François Lapraz, Sandra Lee, Jie Lv, Christigale Mandapat, Gerard Manning, Marco Mariotti, Robert Mata, Tittu Mathew, Tobias Neumann, Irene Newsham, Dinh Ngo, Maria Ninova, Geoffrey Okwuonu, Fiona Ongeri, William J Palmer, Shobha Patil, Pedro Patraquim, Christopher Pham, Pu, Nicholas H Putman, Catherine Rabouille, Olivia Mendivil Ramos, Adelaide C Rhodes, Helen E Robertson, Hugh M Robertson, Matthew Ronshaugen, Julio Rozas, Nehad Saada, Alejandro Sánchez-Gracia, Steven E Scherer, Andrew M Schurko, Kenneth W Siggens, DeNard Simmons, Anna Stief, Eckart Stolle, Maximilian J Telford, Kristin Tessmar-Raible, Rebecca Thornton, Maurijn van der Zee, Arndt von Haeseler, James M Williams, Judith H Willis, Yuanqing Wu, Xiaoyan Zou, Daniel Lawson, Donna Muzny, Kim C Worley, Richard A Gibbs, Michael Akam, and Stephen Richards

    PLoS Biology 12(11):e1002005 (2014) PMID 25423365 PMCID PMC4244043

    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 pre...
  9. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.
    Ariel D Chipman, David E K Ferrier, Carlo Brena, Jiaxin Qu, Daniel S T Hughes, Reinhard Schröder, Montserrat Torres-Oliva, Nadia Znassi, Huaiyang Jiang, Francisca C Almeida, Claudio R Alonso, Zivkos Apostolou, Peshtewani Aqrawi, Wallace Arthur, Jennifer C Barna, Kerstin P Blankenburg, Daniela Brites, Salvador Capella-Gutiérrez, Marcus Coyle, Peter K Dearden, Louis Du Pasquier, Elizabeth J Duncan, Dieter Ebert, Cornelius Eibner, Galina Erikson, Peter D Evans, Cassandra G Extavour, Liezl Francisco, Toni Gabaldón, William J Gillis, Elizabeth A Goodwin-Horn, Jack E Green, Sam Griffiths-Jones, Cornelis J P Grimmelikhuijzen, Sai Gubbala, Roderic Guigó, Yi Han, Frank Hauser, Paul Havlak, Luke Hayden, Sophie Helbing, Michael Holder, Jerome L Hui, Julia P Hunn, Vera S Hunnekuhl, LaRonda Jackson, Mehwish Javaid, Shalini N Jhangiani, Francis M Jiggins, Tamsin E Jones, Tobias S Kaiser, Divya Kalra, Nathan J Kenny, Viktoriya Korchina, Christie L Kovar, F Bernhard Kraus, François Lapraz, Sandra Lee, Jie Lv, Christigale Mandapat, Gerard Manning, Marco Mariotti, Robert Mata, Tittu Mathew, Tobias Neumann, Irene Newsham, Dinh Ngo, Maria Ninova, Geoffrey Okwuonu, Fiona Ongeri, William J Palmer, Shobha Patil, Pedro Patraquim, Christopher Pham, Pu, Nicholas H Putman, Catherine Rabouille, Olivia Mendivil Ramos, Adelaide C Rhodes, Helen E Robertson, Hugh M Robertson, Matthew Ronshaugen, Julio Rozas, Nehad Saada, Alejandro Sánchez-Gracia, Steven E Scherer, Andrew M Schurko, Kenneth W Siggens, DeNard Simmons, Anna Stief, Eckart Stolle, Maximilian J Telford, Kristin Tessmar-Raible, Rebecca Thornton, Maurijn van der Zee, Arndt von Haeseler, James M Williams, Judith H Willis, Yuanqing Wu, Xiaoyan Zou, Daniel Lawson, Donna Muzny, Kim C Worley, Richard A Gibbs, Michael Akam, and Stephen Richards

    PLoS Biology 12(11):e1002005 (2014) PMID 25423365 PMCID PMC4244043

    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 pre...
  10. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.
    Ariel D Chipman, David E K Ferrier, Carlo Brena, Jiaxin Qu, Daniel S T Hughes, Reinhard Schröder, Montserrat Torres-Oliva, Nadia Znassi, Huaiyang Jiang, Francisca C Almeida, Claudio R Alonso, Zivkos Apostolou, Peshtewani Aqrawi, Wallace Arthur, Jennifer C Barna, Kerstin P Blankenburg, Daniela Brites, Salvador Capella-Gutiérrez, Marcus Coyle, Peter K Dearden, Louis Du Pasquier, Elizabeth J Duncan, Dieter Ebert, Cornelius Eibner, Galina Erikson, Peter D Evans, Cassandra G Extavour, Liezl Francisco, Toni Gabaldón, William J Gillis, Elizabeth A Goodwin-Horn, Jack E Green, Sam Griffiths-Jones, Cornelis J P Grimmelikhuijzen, Sai Gubbala, Roderic Guigó, Yi Han, Frank Hauser, Paul Havlak, Luke Hayden, Sophie Helbing, Michael Holder, Jerome L Hui, Julia P Hunn, Vera S Hunnekuhl, LaRonda Jackson, Mehwish Javaid, Shalini N Jhangiani, Francis M Jiggins, Tamsin E Jones, Tobias S Kaiser, Divya Kalra, Nathan J Kenny, Viktoriya Korchina, Christie L Kovar, F Bernhard Kraus, François Lapraz, Sandra Lee, Jie Lv, Christigale Mandapat, Gerard Manning, Marco Mariotti, Robert Mata, Tittu Mathew, Tobias Neumann, Irene Newsham, Dinh Ngo, Maria Ninova, Geoffrey Okwuonu, Fiona Ongeri, William J Palmer, Shobha Patil, Pedro Patraquim, Christopher Pham, Pu, Nicholas H Putman, Catherine Rabouille, Olivia Mendivil Ramos, Adelaide C Rhodes, Helen E Robertson, Hugh M Robertson, Matthew Ronshaugen, Julio Rozas, Nehad Saada, Alejandro Sánchez-Gracia, Steven E Scherer, Andrew M Schurko, Kenneth W Siggens, DeNard Simmons, Anna Stief, Eckart Stolle, Maximilian J Telford, Kristin Tessmar-Raible, Rebecca Thornton, Maurijn van der Zee, Arndt von Haeseler, James M Williams, Judith H Willis, Yuanqing Wu, Xiaoyan Zou, Daniel Lawson, Donna Muzny, Kim C Worley, Richard A Gibbs, Michael Akam, and Stephen Richards

    PLoS Biology 12(11):e1002005 (2014) PMID 25423365 PMCID PMC4244043

    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 pre...
  11. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.
    Ariel D Chipman, David E K Ferrier, Carlo Brena, Jiaxin Qu, Daniel S T Hughes, Reinhard Schröder, Montserrat Torres-Oliva, Nadia Znassi, Huaiyang Jiang, Francisca C Almeida, Claudio R Alonso, Zivkos Apostolou, Peshtewani Aqrawi, Wallace Arthur, Jennifer C Barna, Kerstin P Blankenburg, Daniela Brites, Salvador Capella-Gutiérrez, Marcus Coyle, Peter K Dearden, Louis Du Pasquier, Elizabeth J Duncan, Dieter Ebert, Cornelius Eibner, Galina Erikson, Peter D Evans, Cassandra G Extavour, Liezl Francisco, Toni Gabaldón, William J Gillis, Elizabeth A Goodwin-Horn, Jack E Green, Sam Griffiths-Jones, Cornelis J P Grimmelikhuijzen, Sai Gubbala, Roderic Guigó, Yi Han, Frank Hauser, Paul Havlak, Luke Hayden, Sophie Helbing, Michael Holder, Jerome L Hui, Julia P Hunn, Vera S Hunnekuhl, LaRonda Jackson, Mehwish Javaid, Shalini N Jhangiani, Francis M Jiggins, Tamsin E Jones, Tobias S Kaiser, Divya Kalra, Nathan J Kenny, Viktoriya Korchina, Christie L Kovar, F Bernhard Kraus, François Lapraz, Sandra Lee, Jie Lv, Christigale Mandapat, Gerard Manning, Marco Mariotti, Robert Mata, Tittu Mathew, Tobias Neumann, Irene Newsham, Dinh Ngo, Maria Ninova, Geoffrey Okwuonu, Fiona Ongeri, William J Palmer, Shobha Patil, Pedro Patraquim, Christopher Pham, Pu, Nicholas H Putman, Catherine Rabouille, Olivia Mendivil Ramos, Adelaide C Rhodes, Helen E Robertson, Hugh M Robertson, Matthew Ronshaugen, Julio Rozas, Nehad Saada, Alejandro Sánchez-Gracia, Steven E Scherer, Andrew M Schurko, Kenneth W Siggens, DeNard Simmons, Anna Stief, Eckart Stolle, Maximilian J Telford, Kristin Tessmar-Raible, Rebecca Thornton, Maurijn van der Zee, Arndt von Haeseler, James M Williams, Judith H Willis, Yuanqing Wu, Xiaoyan Zou, Daniel Lawson, Donna Muzny, Kim C Worley, Richard A Gibbs, Michael Akam, and Stephen Richards

    PLoS Biology 12(11):e1002005 (2014) PMID 25423365 PMCID PMC4244043

    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 pre...
  12. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

    Current Biology (2014)

    • The plant galling Mayetiola destructor genome is replete with effector genes • The SSGP-71 effector gene family is the largest known arthropod gene family. ...
  13. Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

    Genome Research 24(7):1209 (2014) PMID 24985915 PMCID PMC4079975

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

    Genome Research 24(7):1209 (2014) PMID 24985915 PMCID PMC4079975

    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...
  15. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines.

    Genome Research 24(7):1193 (2014) PMID 24714809 PMCID PMC4079974

    The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to iden...
  16. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines.

    Genome Research 24(7):1193 (2014) PMID 24714809 PMCID PMC4079974

    The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to iden...
  17. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines.

    Genome Research 24(7):1193 (2014) PMID 24714809 PMCID PMC4079974

    The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to iden...
  18. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines.

    Genome Research 24(7):1193 (2014) PMID 24714809 PMCID PMC4079974

    The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to iden...
  19. Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

    Genome Research 24(7):1209 (2014) PMID 24985915 PMCID PMC4079975

    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...
  20. Parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects.

    Molecular Biology and Evolution 31(4):857 (2014) PMID 24398322 PMCID PMC3969561

    Bacteria confined to intracellular environments experience extensive genome reduction. In extreme cases, insect endosymbionts have evolved genomes that are so gene-poor that they blur the distinction between bacteria and endosymbiotically derived organelles such as mitochondria and plastids. To ...