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Title: Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment
Authors: Izutsu, Minako
Zhou, Jun
Sugiyama, Yuzo
Nishimura, Osamu
Aizu, Tomoyuki
Toyoda, Atsushi
Fujiyama, Asao
Agata, Kiyokazu
Fuse, Naoyuki
Author's alias: 布施, 直之
Issue Date: 14-Mar-2012
Publisher: Public Library of Science
Citation: Izutsu M, Zhou J, Sugiyama Y, Nishimura O, Aizu T, et al. (2012) Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment. PLoS ONE 7(3): e33288. doi:10.1371/journal.pone.0033288
Journal title: PLoS ONE
Volume: 7
Issue: 3
Start page: e33288
Abstract: Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a Drosophila melanogaster line, termed “Dark-fly”, which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation.
Description: 「暗黒ショウジョウバエ」のゲノム解読-暗闇への適応のメカニズム. 京都大学プレスリリース. 2012-03-15.
Rights: © 2012 Izutsu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
DOI(Published Version): 10.1371/journal.pone.0033288
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