Data from: Development and preliminary evaluation of a genome-wide single-nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis)

Recent advances in high-throughput sequencing technologies have offered the possibility to generate genome-wide sequence data to delineate previously unidentified genetic structure, obtain more accurate estimates of demographic parameters, and to evaluate potential adaptive divergence. Here, we identified 27 556 single-nucleotide polymorphisms for the small yellow croaker (Larimichthys polyactis) using restriction-site-associated DNA (RAD) sequencing of 24 individuals from two populations. Significant sources of genetic variation was identified, with an average nucleotide diversity (π) of 0.00105 ± 0.000425 across individuals and long-term effective population size was thus estimated to range between 26 172 and 261 716. According to the results, no differentiation between the two populations was detected based on the SNP dataset of top quality score per contig or neutral loci. However, the two analyzed populations were highly differentiated based on SNP dataset of both top FST value per contig and the outlier SNPs. Moreover, local adaptation was highlighted by an FST-based outlier tests implemented in LOSITAN and a total of 538 potentially locally selected SNPs were identified. BLAST2GO annotation of contigs containing the outlier SNPs yielded hits for 37 (66%) of 56 significant BLASTX matches. Candidate genes for local adaptation constituted a wide array of biological functions, including cellular response to oxidative stress, actin filament binding, ion transmembrane transport and synapse assembly. The generated SNP resources in the present study provided a valuable tool for future population genetics and genomics studies of L. polyactis.

高通量测序技术的近期进展，为获取全基因组序列数据以解析此前未被探明的遗传结构、更精准地估算种群统计参数，以及评估潜在的适应性分化提供了可能。本研究针对2个种群共24个个体开展限制性位点相关DNA（restriction-site-associated DNA, RAD）测序，成功为小黄鱼（Larimichthys polyactis）鉴定出27556个单核苷酸多态性（single-nucleotide polymorphism, SNP）位点。研究检测到显著的遗传变异，所有个体的平均核苷酸多样性（π）为0.00105 ± 0.000425，并据此估算出长期有效种群大小介于26172至261716之间。基于每个重叠群（contig）高质量得分的SNP数据集或中性位点数据集，未检测到两个种群间存在遗传分化；然而，基于每个重叠群的最高遗传分化系数FST值SNP数据集以及离群SNP位点数据集，两个分析种群却呈现出高度的遗传分化。此外，借助LOSITAN软件开展的基于FST的离群位点检测，共鉴定出538个潜在受局部选择作用的SNP位点，进一步证实了局部适应性分化的存在。对携带离群SNP位点的重叠群进行BLAST2GO注释后，在56个显著BLASTX匹配结果中，有37个（占比66%）获得了注释信息。局部适应性分化的候选基因涵盖了丰富的生物学功能，包括细胞氧化应激应答、肌动蛋白丝结合、离子跨膜运输以及突触组装等。本研究构建的SNP资源，为未来小黄鱼的种群遗传学与基因组学研究提供了极具价值的研究工具。