title: Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment.
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.
authors.affiliation: Laboratory for Biodiversity, Global COE Program, Graduate School of Science, Kyoto University, Kyoto, Japan.
authors.forename: Minako
authors.initials: M
authors.lastname: Izutsu
authors.forename: Jun
authors.initials: J
authors.lastname: Zhou
authors.forename: Yuzo
authors.initials: Y
authors.lastname: Sugiyama
authors.forename: Osamu
authors.initials: O
authors.lastname: Nishimura
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Aizu
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
authors.forename: Kiyokazu
authors.initials: K
authors.lastname: Agata
authors.forename: Naoyuki
authors.initials: N
authors.lastname: Fuse
mesh_terms: D000818:Animals; D018389:Codon, Nonsense / Q000235:genetics; D056915:DNA Copy Number Variations / Q000235:genetics; D003624:Darkness; D004331:Drosophila melanogaster / Q000235:genetics*; D004777:Environment; D005260:Female; D005298:Fertility / Q000235:genetics; D017353:Gene Deletion; D017344:Genes, Insect / Q000235:genetics; D049750:Genome, Insect / Q000235:genetics*; D006720:Homozygote; D054643:INDEL Mutation / Q000235:genetics; D008297:Male; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D016019:Survival Analysis; D013997:Time Factors
chemical_list: D018389:Codon, Nonsense