Data from: High-throughput microsatellite marker development in two sparid species and verification of their transferability in the family Sparidae

Recently, 454 sequencing has emerged as a popular method for isolating microsatellites owing to cost-effectiveness and time saving. In this study, repeat-enriched libraries from two southern African endemic sparids (Pachymetopon blochii and Lithognathus lithognathus) were 454 GS-FLX sequenced. From these, 7370 sequences containing repeats (SCRs) were identified. A brief survey of 23 studies showed a significant difference between the number of SCRs when enrichment was performed first before 454 sequencing. We designed primers for 302 unique fragments containing more than five repeat units and suitable flanking regions. A fraction (<11%) of these loci were characterized with 18 polymorphic microsatellite loci (nine in each of the focal species) being described. Sanger sequencing of alleles confirmed that size variation was because of differences in the number of tandem repeats. However, a case of homoplasy and sequencing errors in the 454 sequencing were identified. These newly developed and four previously isolated loci were successfully used to identify polymorphic markers in nine other economically important species, representative of sparid diversity. The combination of newly developed markers with data from previous sparid cross-species studies showed a significant negative correlation between genetic divergence to focal species and microsatellite transferability. The high level of transferability we described (48% amplification success and 32% polymorphism) suggests that the 302 microsatellite loci identified represent an excellent resource for future studies on sparids. Microsatellite marker development should commonly include tests of transferability to reduce costs and increase feasibility of population genetics studies in nonmodel organisms.近年来，454测序（454 sequencing）凭借高性价比与耗时短的优势，已成为分离微卫星（microsatellite）的主流技术方法。本研究针对两种南非特有鲷科鱼类（Pachymetopon blochii与Lithognathus lithognathus）的重复序列富集文库开展了454 GS-FLX测序，最终从测序数据中鉴定出7370条含重复序列的序列（sequences containing repeats, SCRs）。对23项相关研究的简要调研显示，若先进行重复序列富集再开展454测序，所获得的SCRs数量存在显著差异。本研究为302个包含5个以上重复单元且侧翼序列适配的独特片段设计了特异性引物；对其中占比<11%的位点进行验证后，共开发得到18个多态性微卫星位点，两个目标物种各含9个。对等位基因的Sanger测序（Sanger sequencing）结果证实，片段长度变异源于串联重复单元数量的差异，但本研究同时发现了一例趋同进化（homoplasy）现象，以及454测序过程中产生的测序错误。将本研究新开发的位点与4个已分离得到的位点组合使用，可在代表鲷科物种多样性的另外9种经济鱼类中成功扩增得到多态性标记。结合新开发的标记与既往鲷科跨物种扩增研究的数据，结果显示：与目标物种的遗传分化程度和微卫星标记的跨物种可转移性之间存在显著负相关关系。本研究报道的跨物种转移效率较高：扩增成功率达48%，多态性比例达32%，这表明本次鉴定得到的302个微卫星位点可作为未来鲷科鱼类研究的优质资源。在非模式生物的群体遗传学研究中，微卫星标记开发流程通常应纳入跨物种可转移性测试环节，以降低实验成本、提升研究可行性。