Millepora is a relatively species-rich genus of hydrocorals, with 16 species distributed around the globe. It is considered an important reef building cnidarian. The current diversity of Caribbean Millepora species consists of Millepora complanata, M. alcicornis, M. squarrosa and M. striata. Here, we report the de novo transcriptome assembly and phylotranscriptomic analysis of M. alcicornis, M. complanata, M. squarrosa and a undescribed morphotype (Millepora sp.) found in exposed Thalassia beds and mangrove areas in southwest Puerto Rico. Over 345 million sequence reads were obtained for the analysis of the Millepora transcriptomes (Illumina HiSeq4000; 2x150bp). The analysis pipeline consisted of assembly with Trinity, BUSCO, RSEM and ORFs calling for each transcriptome, followed by ontology (Blast2GO) and phylogenetic analysis. The phylogenetic analysis was performed after selecting homologous genes among the transcriptomes, resulting in 10,596 sequences. Concatenation analysis (Maximum Likelihood and Bayesian inference) and a coalescence-based analysis were performed to the dataset too. Concatenation analysis yielded a topology supporting a clade of M. complanata and M. alcicornis, with Millepora sp. outside this clade and M. squarrosa as an outgroup. The coalescence-based tree estimation analysis (ASTRAL-II), presented a different topology placing M. alcicornis and Millepora sp. as sister taxa, rather than grouping with M. alcicornis with M. complanata. Our coalescence analysis indicated that there is a high degree of incomplete lineage sorting, suggesting a very recent time of species emergence among three out of the four Caribbean Millepora species. Calculations of ABBA-BABA statistics derived from transcriptome-wide SNP data indicate the possible presence of introgression between Millepora complanata and M. alcicornis.

Millepora是一个物种相对丰富的水珊瑚属，在全球有 16 种分布。它被认为是一种重要的造礁刺胞动物。加勒比海当前分Millepora种类包括Millepora complanata，M. alcicornis，M.草和M.芨。在这里，我们报告了在波多黎各西南部暴露的地中海床和红树林地区发现的M. alcicornis、M. complanata、M. squarrosa和未描述的形态型（Millepora sp.）的从头转录组组装和系统转录组学分析。获得了超过 3.45 亿个序列读数用于分析Millepora转录组（Illumina HiSeq4000；2x150bp）。分析流程包括与 Trinity、BUSCO、RSEM 和 ORF 的组装，调用每个转录组，然后是本体 (Blast2GO) 和系统发育分析。在转录组中选择同源基因后进行系统发育分析，得到 10,596 个序列。还对数据集进行了串联分析（最大似然和贝叶斯推理）和基于合并的分析。串联分析产生了支持M. complanata和M. alcicornis进化枝的拓扑结构，以及Millepora sp。在这个进化枝和M. squarrosa 之外作为外群。基于合并的树估计分析 (ASTRAL-II) 提出了一种不同的拓扑结构，放置M. alcicornis和Millepora sp。作为姐妹分类群，而不是与M. alcicornis与M. complanata分组。我们的合并分析表明，存在高度不完整的谱系分类，这表明四种加勒比千里珊瑚物种中的三种物种出现在最近的时间。来自全转录组 SNP 数据的 ABBA-BABA 统计数据的计算表明Millepora complanata和M. alcicornis之间可能存在基因渗入。