Derežanin Lorena, Blažytė Asta, Dobrynin Pavel, Duchêne David A, Grau José Horacio, Jeon Sungwon, Kliver Sergei, Koepfli Klaus-Peter, Meneghini Dorina, Preick Michaela, Tomarovsky Andrey, Totikov Azamat, Fickel Jörns, Förster Daniel W
Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany.
Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea.
Mol Ecol. 2022 May;31(10):2898-2919. doi: 10.1111/mec.16443. Epub 2022 Apr 5.
Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species-specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.
鼬科貂亚科的物种栖息于多个大陆的不同栖息地，并占据着各种各样的生态位。它们在觅食生态、繁殖策略和形态适应方面存在差异。为了确定与适应各自环境相关的候选基因座，我们对貂亚科中最早分化的物种——蓬尾浣熊（Eira barbara）进行了从头组装，并将其与狼獾（Gulo gulo）和紫貂（Martes zibellina）的可用基因组进行了比较。我们的比较基因组分析包括寻找正选择的迹象、检查基因家族大小的变化以及寻找物种特异性结构变异。在与表型特征相关的候选基因座中，我们观察到许多与饮食、身体状况和繁殖有关的基因座。例如，对于具有非典型貂亚科繁殖策略（季节性繁殖）的蓬尾浣熊，我们在许多与妊娠相关的基因中观察到了物种特异性变化。对于必须应对季节性食物短缺的环北极超级食肉动物狼獾，我们在与饮食和身体状况相关的基因中观察到了许多变化。所检测的所有类型的基因组变异（单核苷酸多态性、基因家族扩展、结构变异）对候选基因座的鉴定都有很大贡献。这有力地证明了在旨在鉴定具有适应性意义的基因座的比较基因组学研究中，除了单核苷酸多态性之外，还应考虑其他变异。
