De novo Assembly and Analysis of Tissue-Specific Transcriptomes of the Edible Red Sea Urchin Loxechinus albus Using RNA-Seq

Abstract

Edible red sea urchin (Loxechinus albus) is an endemic echinoderm species of the Chilean coasts. The worldwide demand for high-quality gonads of this species has addressed the depletion of its natural populations. Studies on this sea urchin are limited, and genomic information is almost nonexistent. Hence, generate a transcriptome is crucial information that will considerably enrich molecular data and promote future findings for the L. albus aquaculture. Here, we obtained transcriptomic data of the edible red sea urchin by Illumina platform. Total RNA was extracted from gonads, intestines, and coelomocytes of juvenile urchins, and samples were sequenced using MiSeq Illumina technology. A total of 91,119,300 paired-end reads were de novo assembled, 185,239 transcripts produced, and a reference transcriptome created with 38.8% GC content and an N50 of 1769 bp. Gene ontology analysis revealed notable differences in the expression profiles between gonads, intestines, and coelomocytes, allowing the detection of transcripts associated with specific biological processes and KEGG pathways. These data were validated using 12 candidate transcripts by real-time qPCR. This dataset will provide a valuable molecular resource for L. albus and other species of sea urchins.

Transcriptome and Genome Analyses Applied to Aquaculture Research

“…Additionally, the expression patterns of specific conserved miRNAs in particular tissues and developmental stages indicated that they are involved in organ- and developmental stage-specific functions reported in other teleost [ 24 ]. To obtain as most complete as possible a first transcriptome of edible red sea urchin, Loxechinus albus was the objective of Antiqueo et al [ 25 ]. For this, the authors sequenced gonads, intestines, and coelomocytes of juvenile urchins.…”

“…After de novo assembly, a total of 185,239 transcripts were obtained, of which 57,106 (31%) were successfully annotated. Comparative transcriptome analyses revealed that differentially expressed transcripts among tissues were specialized in different biological processes according to the specific functions of these tissues [ 25 ].…”