Publications:

Veglia et al. 2018


scientific article | Marine Genomics

De novo transcriptome assembly of the coral Agaricia lamarcki (Lamarck's sheet coral) from mesophotic depth in southwest Puerto Rico

Veglia AJ, Hammerman NM, Rivera-Vicénsa RE, Schizas NV



Abstract

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 70 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; 2 × 150 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.

Keywords
Meta-data (pending validation)

Mesophotic “mentions”
9 x (total of 2012 words)

Author profiles
Alex Veglia ( 2 pubs)
Nicholas Hammerman ( 4 pubs)
Nikolaos Schizas ( 22 pubs)