Department of Biology, Texas Christian University, Fort Worth, TX 76129, USA.
Department of Animal Science, University of California Davis, Davis, CA 95616, USA.
G3 (Bethesda). 2021 Sep 27;11(10). doi: 10.1093/g3journal/jkab267.
The "genomics era" has allowed questions to be asked about genome organization and genome architecture of non-model species at a rate not previously seen. Analyses of these genome-wide datasets have documented many examples of novel structural variants (SVs) such as chromosomal inversions, copy number variants, and chromosomal translocations, many of which have been linked to adaptation. The salmonids are a taxonomic group with abundant genome-wide datasets due to their importance in aquaculture and fisheries. However, the number of documented SVs in salmonids is surprisingly low and is most likely due to removing loci in high linkage disequilibrium when analyzing structure and gene flow. Here we re-analyze RAD-seq data from several populations of Arctic charr (Salvelinus alpinus) and document a novel ∼1.2 MB SV at the distal end of LG12. This variant contains 15 protein-coding genes connected to a wide-range of functions including cell adhesion and signal transduction. Interestingly, we studied the frequency of this polymorphism in four disjointed populations of charr-one each from Nunavut, Newfoundland, Eastern Russia, and Scotland-and found evidence of the variant only in Nunavut, Canada, suggesting the polymorphism is novel and recently evolved.
“基因组学时代”使得人们以前所未有的速度开始研究非模式生物的基因组组织和基因组结构。对这些全基因组数据集的分析记录了许多新的结构变异（SVs）的例子，如染色体倒位、拷贝数变异和染色体易位，其中许多与适应有关。鲑鱼是一个具有丰富全基因组数据集的分类群，这主要是因为它们在水产养殖和渔业中的重要性。然而，鲑鱼中记录的 SVs 的数量却出人意料地低，这很可能是由于在分析结构和基因流时，去除了处于高度连锁不平衡的基因座。在这里，我们重新分析了来自几个北极红点鲑（Salvelinus alpinus）种群的 RAD-seq 数据，并在 LG12 的远端记录了一个新的约 1.2MB 的 SV。这个变体包含 15 个编码蛋白质的基因，与多种功能相关，包括细胞黏附和信号转导。有趣的是，我们研究了来自努纳武特、纽芬兰、俄罗斯东部和苏格兰的四个不连续的红点鲑种群中这个多态性的频率，仅在加拿大的努纳武特地区发现了该变体的证据，这表明该多态性是新的，是最近进化而来的。
