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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Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics
Benjamin Linard,Alex Crampton-Platt,Alex Crampton-Platt,Conrad P. D. T. Gillett,Martijn J. T. N. Timmermans,Martijn J. T. N. Timmermans,Alfried P. Vogler,Alfried P. Vogler +7 more
TL;DR: The “metagenome skimming” approach is useful for capturing the genomic diversity of poorly studied, species-rich lineages and opens new prospects in environmental genomics.
Journal ArticleDOI
Birth-and-Death Evolution of the Fatty Acyl-CoA Reductase (FAR) Gene Family and Diversification of Cuticular Hydrocarbon Synthesis in Drosophila.
Cédric Finet,Kailey Slavik,Kailey Slavik,Jian Pu,Sean B. Carroll,Sean B. Carroll,Henry F.L. Chung +6 more
TL;DR: This study provides empirical evidence that a comparative approach investigating the birth-and-death evolution of gene families can identify candidate genes involved in rapidly diverging traits between species.
Journal ArticleDOI
RNA interference: a promising biopesticide strategy against the African Sweetpotato Weevil Cylas brunneus
Olivier Christiaens,Katterinne Prentice,Katterinne Prentice,Ine Pertry,Marc Ghislain,Ana M. Bailey,Charles L. Niblett,Godelieve Gheysen,Guy Smagghe +8 more
TL;DR: Results proved that dsRNAs targeting essential genes show great potential to control C. brunneus, and were analyzed as a novel crop protection strategy against this insect pest.
Journal ArticleDOI
A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system.
Sarah B. Kingan,Julie M. Urban,Christine C. Lambert,Primo Baybayan,Anna K. Childers,Brad S. Coates,Brian E. Scheffler,Kevin J. Hackett,Jonas Korlach,Scott M. Geib +9 more
TL;DR: It is demonstrated that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.
Journal ArticleDOI
Genome Annotation Generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission.
Scott M. Geib,Brian Hall,Theodore DeRego,Forest T. Bremer,Kyle Cannoles,Kyle Cannoles,Sheina B. Sim +6 more
TL;DR: The Genome Annotation Generator is a consistent and user-friendly bioinformatics tool that can be used to generate a .tbl file that is consistent with the NCBI submission pipeline.
References
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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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