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种蝴蝶鱼开展的大规模限制性酶切位点相关DNA测序（restriction site associated DNA sequencing, RAD-Seq）数据集，旨在验证最新发表的Chaetodon austriacus草图基因组的实用性，并评估该核基因座分离方法的明显偏倚。我们对双酶切限制性位点相关DNA测序（double-digest restriction-site associated DNA sequencing, ddRAD）数据进行了生物信息学处理，分别在有无参考基因组的条件下识别单核苷酸多态性（single nucleotide polymorphism, SNP）标记及其关联的基因功能，以探究参考基因组是否可提升RAD-Seq标记的质量。本研究的分析结果揭示：(1) 所有物种的未注释单核苷酸多态性与注释单核苷酸多态性的数量仅存在小幅差距；(2) 对于亲缘关系较近而非较远的蝴蝶鱼物种，借助基因组资源可为单核苷酸多态性位点赋予推定的基因功能，因此具备显著应用优势；(3) 姐妹蝴蝶鱼类群中的基因显著富集于钙跨膜转运与结合相关通路。上述结果表明，通过进一步研究，该实验方法有望为解析红海、阿拉伯海与阿拉伯湾等极具挑战的珊瑚礁环境中栖息种群的适应机制提供新的科学见解。