BACKGROUND Pteropods are planktonic gastropods that are considered as bio-indicators to monitor impacts of ocean acidification on marine ecosystems. In order to gain insight into their adaptive potential to future environmental changes, it is critical to use adequate molecular tools to delimit species and population boundaries and to assess their genetic connectivity. We developed a set of target capture probes to investigate genetic variation across their large-sized genome using a population genomics approach. Target capture is less limited by DNA amount and quality than other genome-reduced representation protocols, and has the potential for application on closely related species based on probes designed from one species. RESULTS We generated the first draft genome of a pteropod, Limacina bulimoides, resulting in a fragmented assembly of 2.9 Gbp. Using this assembly and a transcriptome as a reference, we designed a set of 2899 genome-wide target capture probes for L. bulimoides. The set of probes includes 2812 single copy nuclear targets, the 28S rDNA sequence, ten mitochondrial genes, 35 candidate biomineralisation genes, and 41 non-coding regions. The capture reaction performed with these probes was highly efficient with 97% of the targets recovered on the focal species. A total of 137,938 single nucleotide polymorphism markers were obtained from the captured sequences across a test panel of nine individuals. The probes set was also tested on four related species: L. trochiformis, L. lesueurii, L. helicina, and Heliconoides inflatus, showing an exponential decrease in capture efficiency with increased genetic distance from the focal species. Sixty-two targets were sufficiently conserved to be recovered consistently across all five species. CONCLUSION The target capture protocol used in this study was effective in capturing genome-wide variation in the focal species L. bulimoides, suitable for population genomic analyses, while providing insights into conserved genomic regions in related species. The present study provides new genomic resources for pteropods and supports the use of target capture-based protocols to efficiently characterise genomic variation in small non-model organisms with large genomes.

中文翻译：

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带壳的翼足类动物的新型基因组资源：拟南芥（Limacina bulimoides）的基因组草图和靶标捕获探针，经过跨物种相关性测试。

背景技术翼足类是浮游性腹足类动物，被认为是监测海洋酸化对海洋生态系统影响的生物指标。为了深入了解它们对未来环境变化的适应潜力，使用适当的分子工具划定物种和种群边界并评估其遗传连通性至关重要。我们使用种群基因组学方法开发了一套目标捕获探针，以研究其大型基因组中的遗传变异。与其他减少基因组的表示方案相比，目标捕获受DNA数量和质量的限制较小，并且有可能基于一种物种设计的探针应用于紧密相关的物种。结果我们产生了一个翼足类的第一个草图基因组，即Limacina bulimoides，导致碎片组装为2。9 Gbp。使用该程序集和一个转录组作为参考，我们设计了一组2899个用于bulimoides的全基因组靶捕获探针。该组探针包括2812个单拷贝核靶标，28S rDNA序列，十个线粒体基因，35个候选生物矿化基因和41个非编码区。用这些探针进行的捕获反应非常高效，有97％的靶标回收到了焦点菌种上。从九个个体的测试小组中，从捕获的序列中获得了总共137,938个单核苷酸多态性标记。还对四个相关物种测试了探针集：trochiformis，L。lesueurii，L。helicina和Heliconoides inflatus，显示捕获效率呈指数下降，且与焦点物种的遗传距离增加。保留了六十二个目标，可以在所有五个物种中一致地对其进行回收。结论本研究中使用的靶标捕获方案可有效地捕获焦点物种博美氏乳杆菌的全基因组变异，适用于种群基因组分析，同时提供对相关物种中保守基因组区域的见解。本研究为翼足类动物提供了新的基因组资源，并支持使用基于目标捕获的方案有效地表征具有大型基因组的小型非模式生物中的基因组变异。同时提供有关相关物种的保守基因组区域的见解。本研究为翼足类动物提供了新的基因组资源，并支持使用基于目标捕获的方案有效地表征具有大型基因组的小型非模式生物中的基因组变异。同时提供有关相关物种的保守基因组区域的见解。本研究为翼足类动物提供了新的基因组资源，并支持使用基于目标捕获的方案有效地表征具有大型基因组的小型非模式生物中的基因组变异。