1. Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.

    Science 348(6239):1139 (2015) PMID 25977371

    The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings....
  2. 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...
  3. OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.

    Nucleic Acids Research 43(Database issue):D250 (2015) PMID 25428351

    Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the Or...
    PDF not found
  4. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.
    Daniel E Neafsey, Robert M Waterhouse, Mohammad R Abai, Sergey Aganezov, Max Alekseyev, James E Allen, James Amon, Bruno Arcà, Peter Arensburger, Gleb Artemov, Lauren Assour, Hamidreza Basseri, Aaron Berlin, Bruce W Birren, Stephanie A Blandin, Andrew I Brockman, Thomas R Burkot, Austin Burt, Clara S Chan, Cedric Chauve, Joanna Chiu, Mikkel Christensen, Carlo Costantini, Victoria L M Davidson, Elena Deligianni, Tania Dottorini, Vicky Dritsou, Stacey B Gabriel, Wamdaogo M Guelbeogo, Andrew B Hall, Mira V Han, Thaung Hlaing, Daniel S T Hughes, Adam M Jenkins, Xiaofang Jiang, Irwin Jungreis, Evdoxia G Kakani, Maryam Kamali, Petri Kemppainen, Ryan C Kennedy, Ioannis Kirmitzoglou, Lizette Koekemoer, Njoroge Laban, Nicholas Langridge, Mara K N Lawniczak, Manolis Lirakis, Neil F Lobo, Ernesto Lowy, Robert MacCallum, Chunhong Mao, Gareth Maslen, Charles Mbogo, Jenny McCarthy, Kristin Michel, Sara N Mitchell, Wendy Moore, Katherine A Murphy, Anastasia Naumenko, Tony Nolan, Eva M Novoa, Samantha O'Loughlin, Chioma Oringanje, Mohammad A Oshaghi, Nazzy Pakpour, Philippos A Papathanos, Ashley N Peery, Michael Povelones, Anil Prakash, David Price, Ashok Rajaraman, Lisa J Reimer, David C Rinker, Antonis Rokas, Tanya L Russell, N'Fale Sagnon, Maria V Sharakhova, Terrance Shea, Felipe A Simão, Frederic Simard, Michel A Slotman, Pradya Somboon, Vladimir Stegniy, Claudio J Struchiner, Gregg W C Thomas, Marta Tojo, Pantelis Topalis, José M C Tubio, Maria F Unger, John Vontas, Catherine Walton, Craig S Wilding, Judith H Willis, Yi-Chieh Wu, Guiyun Yan, Evgeny M Zdobnov, Xiaofan Zhou, Flaminia Catteruccia, George K Christophides, Frank H Collins, Robert S Cornman, Andrea Crisanti, Martin J Donnelly, Scott J Emrich, Michael C Fontaine, William Gelbart, Matthew W Hahn, Immo A Hansen, Paul I Howell, Fotis C Kafatos, Manolis Kellis, Daniel Lawson, Christos Louis, Shirley Luckhart, Marc A T Muskavitch, José M Ribeiro, Michael A Riehle, Igor V Sharakhov, Zhijian Tu, Laurence J Zwiebel, and Nora J Besansky

    Science 347(6217):1258522 (2015) PMID 25554792

    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 anop...
  5. OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.

    Nucleic Acids Research 43(Database issue):D250 (2015) PMID 25428351 PMCID PMC4383991

    Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the Or...
  6. A depauperate immune repertoire precedes evolution of sociality in bees.

    Genome biology 16(1):83 (2015) PMID 25908406 PMCID PMC4408586

    Sociality has many rewards, but can also be dangerous, as high population density and low genetic diversity, common in social insects, is ideal for parasite transmission. Despite this risk, honeybees and other sequenced social insects have far fewer canonical immune genes relative to solitary in...
  7. OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.

    Nucleic Acids Research 43(Database issue):D250 (2015) PMID 25428351

    Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the Or...
    PDF not found
  8. 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...
  9. 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...
  10. Gene age predicts the strength of purifying selection acting on gene expression variation in humans.

    The American Journal of Human Genetics 95(6):660 (2014) PMID 25480033 PMCID PMC4259975

    Gene expression levels can be subject to selection. We hypothesized that the age of gene origin is associated with expression constraints, given that it affects the level of gene integration into the functional cellular environment. By studying the genetic variation affecting gene expression lev...
  11. Gene age predicts the strength of purifying selection acting on gene expression variation in humans.

    The American Journal of Human Genetics 95(6):660 (2014) PMID 25480033 PMCID PMC4259975

    Gene expression levels can be subject to selection. We hypothesized that the age of gene origin is associated with expression constraints, given that it affects the level of gene integration into the functional cellular environment. By studying the genetic variation affecting gene expression lev...
  12. Gene age predicts the strength of purifying selection acting on gene expression variation in humans.

    The American Journal of Human Genetics 95(6):660 (2014) PMID 25480033 PMCID PMC4259975

    Gene expression levels can be subject to selection. We hypothesized that the age of gene origin is associated with expression constraints, given that it affects the level of gene integration into the functional cellular environment. By studying the genetic variation affecting gene expression lev...
  13. Gene age predicts the strength of purifying selection acting on gene expression variation in humans.

    The American Journal of Human Genetics 95(6):660 (2014) PMID 25480033

    Gene expression levels can be subject to selection. We hypothesized that the age of gene origin is associated with expression constraints, given that it affects the level of gene integration into the functional cellular environment. By studying the genetic variation affecting gene expression lev...
  14. Gene age predicts the strength of purifying selection acting on gene expression variation in humans.

    The American Journal of Human Genetics 95(6):660 (2014) PMID 25480033 PMCID PMC4259975

    Gene expression levels can be subject to selection. We hypothesized that the age of gene origin is associated with expression constraints, given that it affects the level of gene integration into the functional cellular environment. By studying the genetic variation affecting gene expression lev...
  15. 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. ...
  16. Comprehensive metagenomic analysis of glioblastoma reveals absence of known virus despite antiviral-like type I interferon gene response.

    International Journal of Cancer 135(6):1381 (2014) PMID 24347514

    Glioblastoma is a deadly malignant brain tumor and one of the most incurable forms of cancer in need of new therapeutic targets. As some cancers are known to be caused by a virus, the discovery of viruses could open the possibility to treat, and perhaps prevent, such a disease. Although an assoc...
  17. Comprehensive metagenomic analysis of glioblastoma reveals absence of known virus despite antiviral-like type I interferon gene response.

    International Journal of Cancer 135(6):1381 (2014) PMID 24347514 PMCID PMC4235296

    Glioblastoma is a deadly malignant brain tumor and one of the most incurable forms of cancer in need of new therapeutic targets. As some cancers are known to be caused by a virus, the discovery of viruses could open the possibility to treat, and perhaps prevent, such a disease. Although an assoc...
  18. Comprehensive metagenomic analysis of glioblastoma reveals absence of known virus despite antiviral-like type I interferon gene response.

    International Journal of Cancer 135(6):1381 (2014) PMID 24347514 PMCID PMC4235296

    Glioblastoma is a deadly malignant brain tumor and one of the most incurable forms of cancer in need of new therapeutic targets. As some cancers are known to be caused by a virus, the discovery of viruses could open the possibility to treat, and perhaps prevent, such a disease. Although an assoc...
  19. Comprehensive metagenomic analysis of glioblastoma reveals absence of known virus despite antiviral-like type I interferon gene response.

    International Journal of Cancer 135(6):1381 (2014) PMID 24347514 PMCID PMC4235296

    Glioblastoma is a deadly malignant brain tumor and one of the most incurable forms of cancer in need of new therapeutic targets. As some cancers are known to be caused by a virus, the discovery of viruses could open the possibility to treat, and perhaps prevent, such a disease. Although an assoc...
  20. Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study.

    Journal of Clinical Microbiology 52(9):3351 (2014) PMID 25009045

    High-throughput sequencing (HTS) provides the means to analyze clinical specimens in unprecedented molecular detail. While this technology has been successfully applied to virus discovery and other related areas of research, HTS methodology has yet to be exploited for use in a clinical setting f...