The i5K initiative: Advancing arthropod genomics for knowledge, human health, agriculture, and the environment
Jay D. Evans,Susan J. Brown,Kevin J. Hackett,Gene E. Robinson,Stephen Richards,Daniel Lawson,Christine G. Elsik,Jonathan A. Coddington,Owain R. Edwards,Scott J. Emrich,Toni Gabaldón,Marian R. Goldsmith,Glenn Hanes,Bernard Misof,Monica Munoz-Torres,Oliver Niehuis,Alexie Papanicolaou,Michael E. Pfrender,Monica F. Poelchau,Mary Purcell-Miramontes,Hugh M. Robertson,Oliver A. Ryder,Denis Tagu,Tatiana Teixeira Torres,Evgeny M. Zdobnov,Guojie Zhang,Xin Zhou +26 more
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TLDR
An international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics is described, which aims to deliver sequences and analytical tools for each of theArthropod branches andEach of the species having beneficial and negative effects on humankind.Abstract:
Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world's terrestrial, aquatic, and marine ecosystems Arthropods compete with humans for food and transmit devastating diseases They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists, With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankindread more
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Biosurveillance of forest insects: part I—integration and application of genomic tools to the surveillance of non-native forest insects
Amanda D. Roe,Alex S. Torson,Guillaume J. Bilodeau,Pierre Bilodeau,Gwylim S. Blackburn,Gwylim S. Blackburn,Mingming Cui,Michel Cusson,Daniel Doucet,Verena C. Griess,Valentine Lafond,Gregory Paradis,Ilga Porth,Julien Prunier,Vivek Srivastava,Émilie D. Tremblay,Adnan Uzunovic,Denys Yemshanov,Richard C. Hamelin +18 more
TL;DR: Applied biosurveillance efforts by plant health regulatory agencies will benefit substantially from the detailed insights that genomic data bring to the understanding of biological invasions.
Journal ArticleDOI
Interrogating genomic-scale data to resolve recalcitrant nodes in the Spider Tree of Life
Siddharth Kulkarni,Robert J. Kallal,Hannah M. Wood,Dimitar Dimitrov,Gonzalo Giribet,Gustavo Hormiga +5 more
TL;DR: It is found that low-occupancy data sets analyzed as nucleotides can result in more congruent relationships than high occupancy data set analyzed as amino acids, as in phylotranscriptomics, and omitting data, through amino acid translation or via retention of only high occupancy loci, may have a deleterious effect in phylogenetic reconstruction.
Journal ArticleDOI
Comparative genomics analysis of triatomines reveals common first line and inducible immunity-related genes and the absence of Imd canonical components among hemimetabolous arthropods
Federico A. Zumaya-Estrada,Jesús Martínez-Barnetche,Andrés Lavore,Rolando Rivera-Pomar,Rolando Rivera-Pomar,Mario H. Rodriguez +5 more
TL;DR: A compressive description of the humoral and cellular innate immune components of these TTTs is presented and it is revealed that the absence of various Imd canonical components is common in several hemimetabolous species.
Journal ArticleDOI
Laterally Transferred Gene Recruited as a Venom in Parasitoid Wasps
TL;DR: The GH19 chitinase gene is highly expressed in the venom gland of at least seven species, indicating a role in the complex host manipulations performed by parasitoid wasp venom.
Journal ArticleDOI
House spider genome uncovers evolutionary shifts in the diversity and expression of black widow venom proteins associated with extreme toxicity.
Kerry L. Gendreau,Kerry L. Gendreau,Robert A. Haney,Evelyn E. Schwager,Torsten Wierschin,Mario Stanke,Stephen Richards,Jessica E. Garb +7 more
TL;DR: The house spider genome sequence provides novel insights into the evolution of venom toxins once considered unique to black widows, and greatly expand the size of the latrotoxin gene family, reinforce its narrow phylogenetic distribution, and provide additional evidence for the lateral transfer of latrotoxins between spiders and bacterial endosymbionts.
References
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The genome sequence of Drosophila melanogaster
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TL;DR: The nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome is determined using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map.
Journal ArticleDOI
The genome of Tetranychus urticae reveals herbivorous pest adaptations
Miodrag Grbic,Miodrag Grbic,Thomas Van Leeuwen,Richard M. Clark,Stephane Rombauts,Pierre Rouzé,Vojislava Grbic,Vojislava Grbic,Edward J. Osborne,Wannes Dermauw,Phuong Cao Thi Ngoc,Félix Ortego,Pedro Hernández-Crespo,Isabel Diaz,Manuel Martinez,Maria Navajas,Élio Sucena,Élio Sucena,Sara Magalhães,Lisa M. Nagy,Ryan M. Pace,Sergej Djuranovic,Guy Smagghe,Masatoshi Iga,Olivier Christiaens,Jan A. Veenstra,John Ewer,Rodrigo Mancilla Villalobos,Jeffrey L. Hutter,Stephen D. Hudson,Marisela Vélez,Marisela Vélez,Soojin V. Yi,Jia Zeng,Andre Pires-daSilva,Fernando Roch,Marc Cazaux,Marie Navarro,Vladimir Zhurov,Gustavo Acevedo,Anica Bjelica,Jeffrey A. Fawcett,Jeffrey A. Fawcett,Eric Bonnet,Eric Bonnet,Cindy Martens,Guy Baele,Lothar Wissler,Aminael Sánchez-Rodríguez,Luc Tirry,Catherine Blais,Kristof Demeestere,Stefan R. Henz,T. Ryan Gregory,Johannes Mathieu,Lou Verdon,Laurent Farinelli,Jeremy Schmutz,Erika Lindquist,René Feyereisen,Yves Van de Peer +60 more
TL;DR: The Tetranychus urticae genome is the smallest known arthropod genome as discussed by the authors, which represents the first complete chelicerate genome for a pest and has been annotated with genes associated with feeding on different hosts.
Journal ArticleDOI
Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species
David Haussler,Stephen J. O'Brien,Oliver A. Ryder,F. Keith Barker,Michele Clamp,Andrew J. Crawford,Robert Hanner,Olivier Hanotte,Warren E. Johnson,Jimmy A. McGuire,Webb Miller,Robert W. Murphy,William J. Murphy,Frederick H. Sheldon,Barry Sinervo,Byrappa Venkatesh,Edward O. Wiley,Fred W. Allendorf,George Amato,C. Scott Baker,Aaron M. Bauer,Albano Beja-Pereira,Eldredge Bermingham,Giacomo Bernardi,Cibele R. Bonvicino,Sydney Brenner,Terry Burke,Joel Cracraft,Mark Diekhans,Scott V. Edwards,Per G. P. Ericson,James A. Estes,Jon Fjelsda,Nate Flesness,Tony Gamble,Philippe Gaubert,Alexander S. Graphodatsky,Jennifer A. Marshall Graves,Erik D. Green,Richard E. Green,Shannon J. Hackett,Paul D. N. Hebert,Kristofer M. Helgen,Leo Joseph,Bailey Kessing,David M. Kingsley,Harris A. Lewin,Gordon Luikart,Paola Martelli,Miguel A. M. Moreira,Ngan Nguyen,Guillermo Ortí,Brian L. Pike,David M. Rawson,Stephan C. Schuster,Héctor N. Seuánez,H. Bradley Shaffer,Mark S. Springer,Joshua M. Stuart,Joanna Sumner,Emma C. Teeling,Robert C. Vrijenhoek,Robert D. Ward,Wesley C. Warren,Robert K. Wayne,Terrie M. Williams,Nathan D. Wolfe,Ya-Ping Zhang,Adam Felsenfeld,Steve Turner +69 more
TL;DR: A precipitous drop in costs and increase in sequencing efficiency is anticipated, with concomitant development of improved annotation technology, and it is proposed to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future.
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