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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Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera).
Jacqueline Heckenhauer,Paul B. Frandsen,Paul B. Frandsen,Deepak K. Gupta,Juraj Paule,Stefan Prost,Tilman Schell,Julio V. Schneider,Russell J. Stewart,Steffen U. Pauls,Steffen U. Pauls +10 more
TL;DR: The genomic region that encodes for light (L)-chain fibroin, a protein component of larval caddisfly silk was identified and compared with existing L-fibroin gene clusters and is among the highest quality Trichoptera genomes.
Journal ArticleDOI
Application of Genomics for Understanding Plant Virus-Insect Vector Interactions and Insect Vector Control.
TL;DR: These studies demonstrate the advantages of genomics and the potential complementary studies that rapidly advance the understanding of the biology of virus transmission by insect vector and offer additional opportunities to design novel genetic strategies to manage insect vectors and the viruses they transmit.
Journal ArticleDOI
Evaluation of reference genes for gene expression analysis by real-time quantitative PCR (qPCR) in three stingless bee species (Hymenoptera: Apidae: Meliponini).
Flávia Cristina de Paula Freitas,Flávia Cristina de Paula Freitas,Thiago S. Depintor,Lucas T. Agostini,Danielle Luna-Lucena,Francis M. F. Nunes,Francis M. F. Nunes,Márcia Maria Gentile Bitondi,Zilá Luz Paulino Simões,Zilá Luz Paulino Simões,Anete Pedro Lourenço +10 more
TL;DR: To contribute to molecular studies on stingless bees, Frieseomelitta varia, Melipona quadrifasciata, and Scaptotrigona bipunctata species were used to test the expression stability of eight reference genes and the tpb-af gene showed the highest stability, thus being identified as suitable reference genes for the three stingless bee species and defined conditions.
Journal ArticleDOI
Universal fluorescence in situ hybridization (FISH) protocol for mapping repetitive DNAs in insects and other arthropods.
TL;DR: In this paper, a universal and affordable FISH protocol was proposed for the physical mapping of various sequences on chromosomes, such as multigene families, satellite DNAs, microsatellites, transposable elements, DOP-PCR products, and telomeric motif (TTAGG)n).
Journal ArticleDOI
A chromosome-scale draft sequence of the Canada fleabane genome.
Martin Laforest,Sara L. Martin,Katherine Bisaillon,Brahim Soufiane,Sydney Meloche,Eric R. Page +5 more
TL;DR: As C. canadensis has a small genome that is syntenic with other Asteraceaes, a short life cycle, and is relatively easy to cross, it has the potential to become a model weed species and contribute to a paradigm shift in the way non-target site resistance is studied.
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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