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Open AccessJournal ArticleDOI

The locust genome provides insight into swarm formation and long-distance flight

TLDR
A draft 6.5 Gb genome sequence of Locusta migratoria is presented, which is the largest animal genome sequenced so far, and complex regulatory mechanisms involved in microtubule dynamic-mediated synapse plasticity during phase change are revealed.
Abstract
Locusts are one of the world's most destructive agricultural pests and represent a useful model system in entomology. Here we present a draft 6.5 Gb genome sequence of Locusta migratoria, which is the largest animal genome sequenced so far. Our findings indicate that the large genome size of L. migratoria is likely to be because of transposable element proliferation combined with slow rates of loss for these elements. Methylome and transcriptome analyses reveal complex regulatory mechanisms involved in microtubule dynamic-mediated synapse plasticity during phase change. We find significant expansion of gene families associated with energy consumption and detoxification, consistent with long-distance flight capacity and phytophagy. We report hundreds of potential insecticide target genes, including cys-loop ligand-gated ion channels, G-protein-coupled receptors and lethal genes. The L. migratoria genome sequence offers new insights into the biology and sustainable management of this pest species, and will promote its wide use as a model system.

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Integrative Genomics Viewer

TL;DR: The sheer volume and scope of data posed by this flood of data pose a significant challenge to the development of efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data.
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Long-range seasonal migration in insects: mechanisms, evolutionary drivers and ecological consequences

TL;DR: This work highlights the progress that can be made through inter-phyla comparisons, and identifies future research areas that will enhance the understanding of insect migration strategies within an eco-evolutionary perspective.
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Dynamics of genome size evolution in birds and mammals

TL;DR: The data provide evidence for an “accordion” model of genome size evolution in birds and mammals, whereby the amount of DNA gained by transposable element expansion was counteracted by DNA loss through large segmental deletions, and proposed that extensive DNA loss has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.
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Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications.

TL;DR: The molecular mechanisms promoting the birth and rapid evolution of lncRNA genes are explored, with an emphasis on the influence of bidirectional transcription and transposable elements, two pervasive features of vertebrate genomes that reveal a remarkably dynamic and malleable noncoding transcriptome.
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Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface

Duane D. McKenna, +70 more
- 11 Nov 2016 - 
TL;DR: Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle and to a lesser degree, other phytophagous insects.
References
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Journal ArticleDOI

Controlling the false discovery rate: a practical and powerful approach to multiple testing

TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
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The Sequence Alignment/Map format and SAMtools

TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
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Fast and accurate short read alignment with Burrows–Wheeler transform

TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
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MUSCLE: multiple sequence alignment with high accuracy and high throughput

TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
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Gene Ontology: tool for the unification of biology

TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
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