Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment.

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...

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Autores principales:	Minako Izutsu, Jun Zhou, Yuzo Sugiyama, Osamu Nishimura, Tomoyuki Aizu, Atsushi Toyoda, Asao Fujiyama, Kiyokazu Agata, Naoyuki Fuse
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2ccc74d6d7d946ee90afec01e1618494
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spelling	oai:doaj.org-article:2ccc74d6d7d946ee90afec01e16184942021-11-18T07:25:11ZGenome features of "Dark-fly", a Drosophila line reared long-term in a dark environment.1932-620310.1371/journal.pone.0033288https://doaj.org/article/2ccc74d6d7d946ee90afec01e16184942012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22432011/?tool=EBIhttps://doaj.org/toc/1932-6203Organisms 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.Minako IzutsuJun ZhouYuzo SugiyamaOsamu NishimuraTomoyuki AizuAtsushi ToyodaAsao FujiyamaKiyokazu AgataNaoyuki FusePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 3, p e33288 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Minako Izutsu Jun Zhou Yuzo Sugiyama Osamu Nishimura Tomoyuki Aizu Atsushi Toyoda Asao Fujiyama Kiyokazu Agata Naoyuki Fuse Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment.
description	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.
format	article
author	Minako Izutsu Jun Zhou Yuzo Sugiyama Osamu Nishimura Tomoyuki Aizu Atsushi Toyoda Asao Fujiyama Kiyokazu Agata Naoyuki Fuse
author_facet	Minako Izutsu Jun Zhou Yuzo Sugiyama Osamu Nishimura Tomoyuki Aizu Atsushi Toyoda Asao Fujiyama Kiyokazu Agata Naoyuki Fuse
author_sort	Minako Izutsu
title	Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment.
title_short	Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment.
title_full	Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment.
title_fullStr	Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment.
title_full_unstemmed	Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment.
title_sort	genome features of "dark-fly", a drosophila line reared long-term in a dark environment.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/2ccc74d6d7d946ee90afec01e1618494
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Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment.

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