RESUMO
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.
Assuntos
Antozoários , Animais , Antozoários/genética , Teorema de Bayes , Filogenia , Porto Rico , TranscriptomaRESUMO
Octocorals have now become the most visually dominant metazoan benthic taxa of most Caribbean reefs, following the precipitous decline of scleractinian corals. Yet taxonomic issues because of their extensive phenotypic plasticity are still abound. Briareum asbestinum one of the iconic octocorals of the shallow Caribbean coral reefs exhibits a biform morphology, the digitate and the encrusting one. The taxonomic status of each form has not been clarified, yet. Until recently, there were few genetic resources for non-model metazoans, however, affordable high-throughput DNA sequencing has removed this hindrance. We present the first transcriptome of the digitate form of Briareum asbestinum from southwest Puerto Rico. We used paired-end sequencing (Illumina NextSeq 500), with a total yield of 159,754,702 raw reads. De novo assembly was performed utilizing a multi-assembler approach generating 371,554 biologically true, non-redundant transcripts. Open reading frame analysis identified 102,839 putative ORFs of which 78,607 were with annotations. BUSCO analysis indicated a total of 96.4% complete orthologous genes from the metazoan dataset. The assembly presented here serves as an important new genomic reference for the Briareum genus that will facilitate future population and phylogenetic studies aiming to better understand the molecular basis of phenotypic plasticity exhibited throughout the genus.
Assuntos
Antozoários/genética , Transcriptoma , Animais , Antozoários/anatomia & histologia , Sequenciamento de Nucleotídeos em Larga Escala , Fases de Leitura Aberta , Porto RicoRESUMO
The plating coral, Agaricia lamarcki is a widely distributed species inhabiting reefs across the Caribbean basin and Florida. This species is of interest since it is considered a depth-generalist, found from 10 to 70â¯m. Given the scope of contemporary studies on this coral's population dynamics and physiology, as well as, the potential of mesophotic reefs to be refuge habitats for deteriorated shallow water reefs, we present the first de novo transcriptome assembly of an important mesophotic coral. Using next-generation paired-end sequencing (Illumina Hiseq4000; 2â¯×â¯150â¯bp), we obtained a total of 82,506,058 raw reads. The novel transcriptome assembly strategy included the recently developed National Center for Genome Analysis Support de novo transcriptome assembly pipeline. Assembly produced a total of 101,322 biologically true, non-redundant transcripts with an average contig length of 959 and N50 of 1830. EvidentialGene and TransDecoder were used to identify open reading frames (ORFs) with homology insight provided by the UniProtKb and PFAM databases. ORF prediction resulted in 38,517 putative ORFs of which 12,107 ORFs were annotated as genes dealing with molecular function, 1266 with biological processes and 416 with cellular components.
Assuntos
Antozoários/genética , Transcriptoma , Animais , Região do Caribe , Ecossistema , Porto RicoRESUMO
Debaryomyces hansenii J6 is a heavy-metal-tolerant, flavinogenic yeast isolated from a Swedish estuary. We present here the 11.63-Mb genome of this organism containing 5,717 open reading frames. Comparison with available Debaryomyces genomes demonstrated that J6 is closer to D. hansenii MTCC234 than D. fabry CBS789 and D. hansenii CBS767.