Data from: Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)

Double digest restriction site-associated DNA sequencing (ddRADseq) and target capture sequencing methods are used to explore population and phylogenetic questions in non-model organisms. ddRADseq offers a simple and reliable protocol for population genomic studies, however it can result in a large amount of missing data due to allelic dropout. Target capture sequencing offers an opportunity to increase sequencing coverage with little missing data and consistent orthologous loci across samples, although this approach has generally been applied to conserved markers for deeper evolutionary questions. Here, we combine both methods to generate high quality sequencing data for population genomic studies of all marine lobster species from the genus Jasus. We designed probes based on ddRADseq libraries of two lobster species (Jasus edwardsii and Sagmariasus verreauxi) and evaluated the captured sequencing data in five other Jasus species. We validated 4,465 polymorphic loci amongst these species using a cost effective sequencing protocol, of which 1,730 were recovered from all species, and 4,026 were present in at least three species. The method was also successfully applied to DNA samples obtained from museum specimens. This data will be further used to assess spatial-temporal genetic variation in Jasus species found in the Southern Hemisphere.

双酶切限制性位点相关DNA测序（Double digest restriction site-associated DNA sequencing, ddRADseq）与目标捕获测序（target capture sequencing）技术，常用于探究非模式生物（non-model organisms）的群体遗传学与系统发育问题。ddRADseq为群体基因组学研究提供了简便可靠的实验流程，但易因等位基因脱落（allelic dropout）产生大量缺失数据。目标捕获测序可提升测序覆盖度，且样本间直系同源位点（orthologous loci）一致性高、缺失数据少，不过该方法此前多应用于保守标记以开展更深层次的进化研究。本研究结合两种技术，为波纹龙虾属（Jasus）所有海洋龙虾物种的群体基因组学研究构建高质量测序数据。我们基于两种龙虾（Jasus edwardsii与Sagmariasus verreauxi）的ddRADseq文库设计捕获探针，并在另外5种波纹龙虾属物种中对捕获测序数据进行评估。本研究通过低成本测序方案，在上述物种中验证了4465个多态性位点（polymorphic loci），其中1730个可在所有物种中被成功检出，4026个至少在3个物种中存在。该方法还成功应用于从博物馆标本（museum specimens）获取的DNA样本。本研究所得测序数据将进一步用于评估南半球分布的波纹龙虾属物种的时空遗传变异。