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The i5K initiative: Advancing arthropod genomics for knowledge, human health, agriculture, and the environment

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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 humankind

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Journal ArticleDOI

Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

TL;DR: In this paper , the authors present a genome-wide identification of candidate genes that exhibit locally restricted expression in germ disc forming stage embryos of P. tepidariorum, based on comparative transcriptomes of isolated cells from different regions of the embryo.
Journal ArticleDOI

Topology prediction of insect olfactory receptors.

TL;DR: The current success rates by applying the algorithms on few G-protein coupled receptors of known structure and olfactory receptor sequences and outstanding challenges are discussed, and the impact of topology prediction on biology and modeling of ORs is discussed.
Posted ContentDOI

Effect of de novo transcriptome assembly on transcript quantification

TL;DR: This study comprehensively investigates how assembly quality affects the performance of quantification for RNA-Seq analysis based on de novo transcriptome assembly and proposed an open-source Python based package QuantEval that builds connected components for the assembled contigs based on sequence similarity and evaluates the quantification results for each connected component.
Journal ArticleDOI

Genome-Wide Evolutionary Analysis of Putative Non-Specific Herbicide Resistance Genes and Compilation of Core Promoters between Monocots and Dicots

Saket Chandra, +1 more
- 29 Jun 2022 - 
TL;DR: The description of putative NTSR enzymes may be used to develop innovative weed control techniques to delay the evolution of NTSR.
Book ChapterDOI

The Little Known Universe of Short Proteins in Insects: A Machine Learning Approach

TL;DR: A platform to systematically identify the functional class of short toxin-like peptides in metazoa is developed and the success of identifying overlooked neuropeptide precursors is illustrated.
References
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Journal ArticleDOI

The genome sequence of Drosophila melanogaster

Mark Raymond Adams, +194 more
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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, +60 more
- 24 Nov 2011 - 
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, +69 more
- 01 Nov 2009 - 
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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