Despite the ecological and economic significance of stony corals (Scleractinia), a robust understanding of their phylogeny remains elusive due to patchy taxonomic and genetic sampling, as well as the limited availability of informative markers. To increase the number of genetic loci available for phylogenomic analyses in Scleractinia, we designed 15,919 DNA enrichment baits targeting 605 orthogroups (mean 565 ± SD 366 bp) over 1,139 exon regions. A further 236 and 62 barcoding baits were designed for COI and histone H3 genes respectively for quality and contamination checks. Hybrid capture using these baits was performed on 18 coral species spanning the presently understood scleractinian phylogeny, with two corallimorpharians as outgroup. On average, 74% of all loci targeted were successfully captured for each species. Barcoding baits were matched unambiguously to their respective samples and revealed low levels of cross-contamination in accordance with expectation. We put the data through a series of stringent filtering steps to ensure only scleractinian and phylogenetically informative loci were retained, and the final probe set comprised 13,479 baits, targeting 452 loci (mean 531 ± SD 307 bp) across 865 exon regions. Maximum likelihood, Bayesian and species tree analyses recovered maximally supported, topologically congruent trees consistent with previous phylogenomic reconstructions. The phylogenomic method presented here allows for consistent capture of orthologous loci among divergent coral taxa, facilitating the pooling of data from different studies and increasing the phylogenetic sampling of scleractinians in the future.

中文翻译：

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基于转录组的靶标富集饵料，用于石质珊瑚（刺ni：Anthozoa：Scleractinia）。

尽管石质珊瑚（Scleractinia）具有生态和经济意义，但由于斑驳的分类学和遗传采样以及信息性标记物的可用性有限，对它们的系统发育的深入了解仍然难以捉摸。为了增加在菌核病中用于系统生物学分析的遗传基因座的数量，我们设计了1,919个DNA富集诱饵，它们针对1,139个外显子区域上的605个正交群（平均565±SD 366 bp）。还分别为COI和组蛋白H3基因设计了236个和62个条形码诱饵，用于质量和污染检查。使用这些诱饵进行杂种捕获是在跨越目前了解的巩膜菌系统发育的18个珊瑚物种上进行的，其中有两个珊瑚类动物为外群。平均而言，每种物种成功捕获了所有目标位点的74％。条形码诱饵与它们各自的样品明确匹配，并且符合预期，显示出较低的交叉污染水平。我们将数据通过一系列严格的过滤步骤，以确保仅保留血吸虫病和系统发育信息的基因座，最终的探针组包含13,479个诱饵，靶向865个外显子区域的452个基因座（平均531±SD 307 bp）。最大似然，贝叶斯树和物种树分析可以最大程度地恢复支持的，拓扑一致的树，这些树与以前的植物学重建一致。这里介绍的系统生物学方法可以一致地捕获不同珊瑚类群中的直系同源基因座，便于汇总来自不同研究的数据，并在将来增加菌cle的系统发育取样。