Ortiz-González, Ingrid C.

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    Transcriptome data analysis of the Millepora (Hydrozoa: Milleporidae) species complex in Puerto Rico
    (2018-05) Ortiz-González, Ingrid C.; Schizas, Nikolaos V.; College of Arts and Sciences - Sciences; Weil, Ernesto F.; Martínez Cruzado, Juan Carlos; Santos Flores, Carlos José; Otero, Ernesto; Department of Marine Sciences; Ramírez, Lilliam
    Millepora is a relative rich-species genus of hydrocorals, with 18 species distributed around the globe and no shared species between the Atlantic and Pacific Ocean. It is considered one of the important reef building cnidarians. The current diversity of the Caribbean Millepora species consist of Millepora complanata, M. alcicornis, M. squarrosa and M. striata but there are century-old taxonomic uncertainties. Here, we report the de-novo transcriptome assembly and phylotrascriptomic analysis of M. alcicornis, M. complanata, M. squarrosa and a new ecomorph (Millepora sp.) found in exposed, shallow water, Thalassia beds and mangrove areas in southwest Puerto Rico. We obtained over 345 million reads from the transcriptomes of the four taxa (Illumina HiSeq4000; 2x150bp). The analysis pipeline consisted of assembly with Trinity, BUSCO for quality check, RSEM for TPM filtration, and ORF call for each transcriptome, prior to ontology and phylogenetic analysis. The ontology analysis was performed using Blast2GO, and genes were categorized by molecular functions, biological processes, and cellular components. The phylogenetic analysis was performed using distinct custom bash programs to select homologous sequences among the transcriptomes, resulting in 10,797 homologous sequences. The concatenation analysis (with either Maximum Likelihood or Bayesian inference) resulted in a topology supporting a clade of M. complanata and M. alcicornis; with Millepora sp., the ecomorph, outside the clade, and M. squarrosa as the outgroup. However, in a coalescence-based tree estimation analysis (using RAxML and ASTRAL-II), a different topology resulted, with M. alcicornis forming a clade with Millepora sp. rather than with M. complanata. ASTRAL-II analysis indicated that there is a very high degree of incomplete lineage sorting, suggesting a very recent time of divergence among these three out of the four Caribbean Millepora species. Of the three Caribbean species and the ecomorph considered in this analysis, M. squarrosa, is the only species that can be differentiated readily as a genetically distinct milleporid species.