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 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.生物通过特化的代谢、形态或行为，显著适应各类环境。为解析环境适应背后的分子机制，本研究采用了一株命名为"暗果蝇"（Dark-fly）的黑腹果蝇（Drosophila melanogaster）品系，该品系已在持续黑暗环境中连续饲养57年（共计1400代）。研究发现，暗果蝇在黑暗环境中的繁殖力显著高于光照环境，表明其携带有适应黑暗环境的优势性状。本研究借助下一代测序技术完成了暗果蝇的全基因组测序，并与对照品系Oregon-R-S的基因组进行比对，共鉴定出约22万个单核苷酸多态性（single nucleotide polymorphisms，简称SNPs）以及4700个插入缺失变异（insertions or deletions，简称InDels）。其中1.8%的SNPs被归类为非同义单核苷酸多态性（non-synonymous SNPs，简称nsSNPs），即此类变异会改变基因编码产物的氨基酸序列。研究在暗果蝇基因组中共检测到28个无义突变——这类突变会在蛋白质序列中引入提前终止密码子，涉及的基因包括嗅觉受体基因与光受体基因。本研究同时筛查了群体演化历史中受选择的推定纯合子区域（runs of homozygosity，简称ROH），在暗果蝇基因组中共发现21个ROH区域。在这些区域内，我们鉴定出241个携带nsSNPs或InDels变异的基因，其中包括参与解毒过程的α酯酶基因簇。此外，对暗果蝇基因组结构变异的分析显示，存在一个与脂肪酸代谢相关的基因缺失事件。本研究结果揭示了暗果蝇基因组的独特特征，并为环境适应相关的潜在候选基因提供了候选列表。