Data from: Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish

Data from a large-scale restriction site associated DNA (RAD-Seq) study of nine butterflyfish species in the Red Sea and Arabian Sea provided a means to test the utility of a recently published draft genome (Chaetodon austriacus) and assess apparent bias in this method of isolating nuclear loci. We here processed double-digest restriction-site (ddRAD) associated DNA sequencing data to identify single nucleotide polymorphism (SNP) markers and their associated function with and without our reference genome to see if it improves the quality of RAD-Seq markers. Our analyses indicate (1) a modest gap between the number of non-annotated versus annotated SNPs across all species, (2) an advantage of using genomic resources for closely related but not distantly related butterflyfish species based on the ability to assign putative gene function to SNPs, and (3) an enrichment of genes among sister butterflyfish taxa related to calcium transmembrane transport and binding. The latter result highlights the potential for this approach to reveal insights into adaptive mechanisms in populations inhabiting challenging coral reef environments such as the Red Sea, Arabian Sea, and Arabian Gulf with further study.

本研究依托针对红海与阿拉伯海9种蝴蝶鱼的大规模限制性酶切位点相关DNA测序（restriction site associated DNA, RAD-Seq）数据集，为检验新近发布的Chaetodon austriacus草图基因组的应用价值，以及评估该核基因座分离方法的潜在偏倚提供了可行途径。本研究对双酶切限制性酶切位点相关DNA测序（double-digest restriction-site associated DNA, ddRAD）数据进行处理分析，分别在使用与不使用参考基因组的情境下，识别单核苷酸多态性（single nucleotide polymorphism, SNP）标记及其相关功能，以探究参考基因组能否提升RAD-Seq标记的质量。分析结果显示：① 所有物种的未注释SNP与注释SNP数量仅存在小幅差距；② 基于为SNP赋予推定基因功能的能力，使用基因组资源对亲缘关系较近的蝴蝶鱼物种具有优势，而对远缘物种则无此效果；③ 蝴蝶鱼姊妹类群中，与钙跨膜运输及结合相关的基因呈现富集现象。后续研究可依托该方法，进一步揭示红海、阿拉伯海与波斯湾等极端珊瑚礁生境中栖息种群的适应性机制，而本研究的后一项结果即凸显了该方法的应用潜力。