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Reference Report
| Reference | |||
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| Citation | Izutsu, M., Zhou, J., Sugiyama, Y., Nishimura, O., Aizu, T., Toyoda, A., Fujiyama, A., Agata, K., Fuse, N. (2012). Genome features of "dark-fly", a Drosophila line reared long-term in a dark environment. PLoS ONE 7(3): e33288. (Export to RIS) | ||
| FlyBase ID | FBrf0217825 | ||
| Publication Type | Research paper | ||
| PubMed ID | 22432011 | ||
| PubMed 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. | ||
| DOI | 10.1371/journal.pone.0033288 | ||
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| Language of Publication | English | ||
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| Publication Type | Journal | ||
| Abbreviation | PLoS ONE | ||
| Title | PLoS ONE | ||
| Publication Year | 2006- | ||
| ISBN/ISSN | 1932-6203 | ||
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Data from Reference
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| Alleles (1)
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| Genes (241)
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