Genome Features of "Dark-Fly", a Drosophila Line Reared Long-Term in a Dark Environment
Genome Features of "Dark-Fly", a Drosophila Line Reared Long-Term in a Dark Environment
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DOI：
10.1371/journal.pone.0033288
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发表时间：
2012-03-14
期刊：
影响因子：
3.7
通讯作者：
Fuse, Naoyuki
中科院分区：
文献类型：
--
作者：
Izutsu, Minako;Zhou, Jun;Fuse, Naoyuki
生物通过特殊的代谢、形态或行为显著地适应不同的环境。为了解决环境适应的分子机制，我们利用了一种果蝇品系，称为“暗蝇”，它已经在恒定的黑暗条件下保持了57年（1400代）。结果表明，暗蝇在黑暗条件下的繁殖力明显高于在光照条件下的繁殖力，表明暗蝇在黑暗条件下具有一定的优势。使用下一代测序技术，我们确定了黑蝇的全基因组序列，并与对照菌株Oregon-R-S菌株的基因组相比，在黑蝇基因组中鉴定了大约220，000个单核苷酸多态性（SNP）和4，700个插入或缺失（InDel）。1.8%的SNP被分类为非同义SNP（nsSNP：即，它们改变基因产物的氨基酸序列）。其中，我们检测到28个无义突变（即，它们在黑蝇基因组中的蛋白质序列中产生终止密码子。这些基因包括编码嗅觉受体和光受体的基因。我们还搜索了纯合性（ROH）区域的运行，作为在人口历史中选择的推定区域，并在黑蝇基因组中发现了21个ROH区域。我们鉴定了241个在ROH区域携带nsSNPs或InDel的基因。其中包括一组参与解毒过程的α-酯酶基因。此外，对黑蝇基因组结构变异的分析表明，与脂肪酸代谢相关的基因缺失。我们的研究结果揭示了黑蝇基因组的独特特征，并提供了一个参与环境适应的潜在候选基因列表。
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.