PDF(Pubmed)
Abstract：
Multiple studies in a range of taxa have found links between structural variants and the development of ecologically important traits. Such variants are becoming easier to find due, in large part, to the increase in the amount of genome-wide sequence data in nonmodel organisms. The salmonids (salmon, trout, and charr) are a taxonomic group with abundant genome-wide datasets due to their importance in aquaculture, fisheries, and variation in multiple ecologically important life-history traits. Previous research on rainbow trout (Oncorhynchus mykiss) has documented a large pericentric (∼55 Mb) chromosomal inversion (CI) on chromosome 5 (Omy05) and a second smaller (∼14 Mb) chromosome inversion on Omy20. While the Omy05 inversion appears to be associated with multiple adaptive traits, the inversion on Omy20 has received far less attention. In this study, we re-analyze RAD-seq and amplicon data from several populations of rainbow trout (O. mykiss) to better document the structure and geographic distribution of variation in the Omy20 CI. Moreover, we utilize phylogenomic techniques to characterize both the age- and the protein-coding gene content of the Omy20 CI. We find that the age of the Omy20 inversion dates to the early stages of O. mykiss speciation and predates the Omy05 inversion by ∼450,000 years. The 2 CIs differ further in terms of the frequency of the homokaryotypes. While both forms of the Omy05 CI are found across the eastern Pacific, the ancestral version of the Omy20 CI is restricted to the southern portion of the species range in California. Furthermore, the Omy20 inverted haplotype is comparable in genetic diversity to the ancestral form, whereas derived CIs typically show substantially reduced genetic diversity. These data contribute to our understanding of the age and distribution of a large CI in rainbow trout and provide a framework for researchers looking to document CIs in other nonmodel species.
摘要：
在一系列分类单元中的多项研究发现了结构变异与生态重要性状发展之间的联系。这样的变体变得越来越容易找到，在很大程度上,非模型生物全基因组序列数据量的增加。鲑鱼（鲑鱼，鳟鱼,和charr）是一个具有丰富的全基因组数据集的分类群，因为它们在水产养殖中的重要性，渔业,以及多种生态重要生活史特征的变异。先前对虹鳟鱼（Oncorhynchusmykiss）的研究表明，在5号染色体（Omy05）上有一个大的周心（〜55Mb）染色体倒置（CI），而在Omy20上有第二个较小的（〜14Mb）染色体倒置。虽然Omy05倒置似乎与多个适应性性状相关，Omy20的反转受到的关注要少得多。在这项研究中,我们重新分析了来自多个虹鳟鱼种群的RAD-seq和扩增子数据（O.mykiss)，以更好地记录Omy20CI变异的结构和地理分布。此外，我们利用系统基因组技术来表征Omy20CI的年龄和蛋白质编码基因含量。我们发现Omy20反转的年龄可以追溯到O.mykiss物种形成的早期阶段，并且比Omy05反转早了约450,000年。2CI在同核型的频率方面进一步不同。虽然在东太平洋发现了Omy05CI的两种形式，Omy20CI的祖先版本仅限于加利福尼亚州物种范围的南部。此外，Omy20反向单倍型在遗传多样性上与祖先形式相当，而衍生的CI通常显示出显著降低的遗传多样性。这些数据有助于我们了解虹鳟鱼中大型CI的年龄和分布，并为研究人员在其他非模型物种中记录CI提供了框架。
