Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States.
J Hered. 2023 Jun 22;114(4):404-409. doi: 10.1093/jhered/esad009.
The surfperches (family Embiotocidae) are a unique group of mostly marine fishes whose phylogenetic position within the Ovalentaria clade (Percomorpha) is still unresolved. As a result of their viviparity and lack of a dispersive larval stage, surfperches are an excellent model for the study of speciation, gene flow, and local adaptation in the ocean. They are also the target of an immensely popular recreational fishery. Very few high-quality molecular resources, however, are available for this group and only for a single species. Here, we describe a highly complete reference genome for the kelp surfperch, Brachyistius frenatus, assembled using a combination of short-read (Illumina, ~47× coverage) and long-read (Oxford Nanopore Technologies, ~27× coverage) sequencing. The 596 Mb assembly has a completeness level of 98.1% (BUSCO), a contig N50 of 2.6 Mb (n = 56), and a contig N90 of 406.6 kb (n = 293). Comparative analysis revealed a high level of synteny between B. frenatus and its close relative, Embiotoca jacksoni. This assembly will serve as a valuable molecular resource upon which future evolutionary dynamics research will build, such as the investigation of local adaptation and the genomic potential for climate adaptation in wild populations.
拟石首鱼科（Embiotocidae）是一组独特的海洋鱼类，其在 Ovalentaria 分支（鲈形目）中的系统发育位置仍未解决。由于它们的胎生和缺乏分散的幼虫阶段，拟石首鱼是研究海洋物种形成、基因流动和局部适应的绝佳模型。它们也是一项非常受欢迎的休闲渔业的目标。然而，这个群体只有一个物种有很少的高质量分子资源。在这里，我们描述了一种高度完整的海草拟石首鱼（Brachyistius frenatus）参考基因组，该基因组是使用短读（Illumina，约 47×覆盖度）和长读（Oxford Nanopore Technologies，约 27×覆盖度）测序技术组合组装而成的。这个 596Mb 的组装具有 98.1%（BUSCO）的完整性水平，2.6Mb 的 contig N50（n = 56）和 406.6kb 的 contig N90（n = 293）。比较分析显示，B. frenatus 与其近亲 Embiotoca jacksoni 之间存在高度的同线性。这个组装将成为未来进化动态研究的有价值的分子资源，例如对野生种群的局部适应和气候适应的基因组潜力的研究。
