Description of four Millepora spp. transcriptomes and their potential to delimit the Caribbean fire coral species
Autor: | Nikolaos V. Schizas, Ingrid Corasí Ortiz González, Ramón E. Rivera-Vicéns |
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Rok vydání: | 2021 |
Předmět: |
0106 biological sciences
0303 health sciences Phylogenetic tree Puerto Rico De novo transcriptome assembly Millepora complanata Introgression Bayes Theorem Aquatic Science Biology Anthozoa 010603 evolutionary biology 01 natural sciences Coalescent theory 03 medical and health sciences Sister group Genus Evolutionary biology Genetics Animals Transcriptome Clade Phylogeny 030304 developmental biology |
Zdroj: | Marine Genomics. 59:100863 |
ISSN: | 1874-7787 |
DOI: | 10.1016/j.margen.2021.100863 |
Popis: | 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. |
Databáze: | OpenAIRE |
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