Characterization of the transcriptome and gene expression of four different tissues in the ecologically relevant sea urchin Arbacia lixula using RNA‐seq

Abstract

The sea urchin Arbacia lixula is a keystone species in Mediterranean ecosystems that drive landscape changes in littoral communities. However, genomic information available for the whole order Arbacioida is very limited. Using RNA-seq techniques, we have characterized the transcriptome of four different tissue types in A. lixula: the 'somatic' tissues (coelomocytes and digestive tissue) and the 'reproductive' tissues (ovary and testis), from two replicated cDNA libraries for each sample. Additionally, we performed a de novo assembly to build the 'reference' transcriptome, pooling reads of the four tissues, to analyse the differential expression (DE) in pairwise comparisons between tissues. The complete de novo assembly yielded 186,084 transcripts, with a sequence size limit of 100 nt, being 31% of them spliced isoforms. Approximately 21% of the transcripts had blast hits against proteins of metazoans (E < 10(-5) ), being less than 2.2% functionally annotated. Between coelomocytes and digestive, 30,794 transcripts showed DE (~11.8% of them with blast hit), and 19,567 transcripts did so between testis and ovary (~28.5% of them with blast hit). Major GO-term categories upregulated in somatic tissues were those related to muscle contraction and energy generation in digestive, and lipid metabolism associated with immune response in coelomocytes. Between reproductive tissues, the major upregulated GO categories were related to energy generation in testis, and negative regulation of nucleotide metabolism in ovary. We particularly screened for a collection of target genes in each tissue because of their relevance for further studies on evolution and adaptation of echinoids.

Delegating sex: differential gene expression in stolonizing syllids uncovers the hormonal control of reproduction in Annelida

“…Assembly statistics of the reference transcriptomes are summarized in Supplementary File S1, alongside read mapping results for each tissue and specimen. The coverage of our assemblies is similar or slightly higher than those in other studies on marine invertebrates (e.g., Meyer et al 2009;Riesgo et al 2012;Pérez-Portela et al 2016).…”

Functional insights into the testis transcriptome of the edible sea urchin Loxechinus albus

“…For instance, the GC content of the testis transcriptome of L. albus (40.4%) was closer to the testis (40.9%) and ovary (42.1%) transcriptomes of the black sea urchin Arbacia lixula 32, and showed slightly higher values in relation to the transcriptomes of the Antarctic sea urchin Sterechinus neumayeri (38.6%)15, the purple sea urchin, S. purpuratus (36.9%)33, and the kina sea urchin Evechinus chloroticus (39%)34. Moreover, in terms of the number of assembled unigene sequences, our de novo assembled transcriptome was within the range reported in other 454 sequencing projects of sea urchins15, sea cucumbers35, and sea stars36.…”

“…In order to explore the level of evolutionary conservation of gene/protein functions in male gonads of echinoderms, we compared the testis transcriptomes of the sea urchins L. albus, Arbacia lixula 32, Evechinus chloroticus 34, S. purpuratus 22 and the sea stars Patiria miniata 36 and Acanthaster planci 14. The raw unassembled datasets of these species were downloaded from the NCBI SRA database under the accessions SRP066435, SRR1014624, SRR532121, SRR573710 and SRR1197243 respectively.…”

Gene expression profiling during the embryo‐to‐larva transition in the giant red sea urchin Mesocentrotus franciscanus

“…From these unigenes, 60,439 (~34%) were blasted to known proteins in the public databases NCBI (nr) and UniProt (Swiss‐Prot and TrEMBL), while 116,446 (~66%) had no matches and may represent: (1) specific unigenes of M. franciscanus with unknown function; (2) sequences with low similarity to those compared in public databases; and/or (3) chimeric sequences. Although the percentage of unigenes with a BLAST‐hit may appear to be relatively low, we found that the number of unigenes with significant alignments (≤1 e −5 ) to known proteins in M. franciscanus is higher than those reported in other studies with nonmodel echinoderms (Delroisse et al., 2015; Dilly et al., 2015; Gaitán‐Espitia, et al, 2016; Gillard, Garama, & Brown, 2014; Pérez‐Portela, Turon, & Riesgo, 2016; Stewart, Stewart, & Rivera‐Posada, 2015; Vaughn, Garnhardt, Garey, Thomas, & Livingston, 2012; Zhou et al., 2014). Most of the annotated unigenes hit against the purple sea urchin Strongylocentrotus purpuratus (88.4%), followed by the acorn worm Saccoglossus kowalevskii (1.5%), and the Pacific oyster Crassostrea gigas (<1%; Fig.…”