Transcriptomic analysis of candidate osmoregulatory genes in the eastern oyster Crassostrea virginica

Abstract

BackgroundThe eastern oyster, Crassostrea virginica, is a euryhaline species that can thrive across a wide range of salinities (5-35). As with all estuarine species, individual oysters must be able to regulate their osmotic balance in response to constant temporal variation in salinity. At the population level, recurrent viability selection may be an additional mechanism shaping adaptive osmoregulatory phenotypes at the margins of oyster salinity tolerance. To identify candidate genes for osmoregulation, we sequenced, assembled, and annotated the transcriptome of wild juvenile eastern oysters from ‘high’ and ‘low’ salinity regimes. Annotations and candidates were mostly based on the Pacific oyster (Crassostrea gigas) genome sequence so osmoregulatory relevance in C. virginica was explored by testing functional enrichment of genes showing spatially discrete patterns of expression and by quantifying coding sequence divergence.ResultsThe assembly of sequence reads and permissive clustering of potentially oversplit alleles resulted in 98,729 reftigs (contigs and singletons). Of these, 50,736 were annotated with 9,307 belonging to a set of candidate osmoregulatory genes identified from the C. gigas genome. A total of 218,777 SNPs (0.0185 SNPs/bp) were identified in annotated reftigs of C. virginica. Amino acid divergence between translations of C. virginica annotated reftigs and C. gigas coding sequence averaged 23.2 % with an average dN/dS ratio of 0.074, suggesting purifying selection on protein sequences. The high and low salinity source oysters each expressed a subset of genes unique to that group, and the functions for these annotated genes were consistent with known molecular mechanisms for osmotic regulation in molluscs.ConclusionsMost of the osmoregulatory gene candidates experimentally identified in C. gigas are present in this C. virginica transcriptome. In general these congeners show coding sequence divergence too high to make the C. gigas genome a useful reference for C. virginica bioinformatics. However, strong purifying selection is characteristic of the osmoregulatory candidates so functional annotations are likely to correspond. An initial examination of C. virginica presence/absence expression patterns across the salinity gradient in a single estuary suggests that many of these candidates have expression patterns that co-vary with salinity, consistent with osmoregulatory function in C. virginica.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-503) contains supplementary material, which is available to authorized users.

Construction of the BAC Library of Small Abalone (Haliotis diversicolor) for Gene Screening and Genome Characterization

“…The GC content is around 40.33 %, which was significantly greater than pearl oyster Pinctada fucata (34 %) (Takeuchi et al 2012), but was similar to eastern oyster Crassostrea virginica (44 %) and pacific oyster Crassostrea gigas (45.2 %) (Eierman and Hare 2014). We did not identify significant portion of repetitive elements because the Repbase library specifically designed for mollusk species was not available, which may not identify repetitive element from abalone genome comprehensively.…”

Respuesta fisiológica y molecular de Anadara tuberculosa (Arcoida: Arcidae) al estrés de salinidad

“…Estudios previos han demostrado que los FAAs intracelulares son los principales contribuyentes a la regulación de la osmolaridad intracelular y del volumen celular en bivalvos (Gosling, 2015). En este trabajo se diseñó 18 marcadores moleculares asociados al sistema de regulación por FAAs, y uno a partir de la proteína de estrés (HSP70), usando las secuencias disponibles publicadas de cuatro bivalvos modelos: las ostras C. gigas, C. angulata, C. virginica y el mejillón M. galloprovincialis (Meng et al, 2013;Cross et al, 2014;Eierman & Hare, 2014).…”

“…La primera hipótesis aparece como la más probable debido al predominio del sistema de osmorregulación mediante la utilización de FAAs en bivalvos y gasterópodos marinos; así como, porque importantes diferencias a nivel genético, en particular en los genes asociados a mecanismos de respuestas a estrés abióticos, se encontraron entre las secuencias nucleotídi-cas de C. angulata y C. virginica con C. gigas (Cross et al, 2014;Eierman & Hare, 2014).…”

“…Los genes de interés evaluados para este estudio fueron: Aminomethyltransferase, Glycine dehydrogenase, Glycine hydroxymethyltransferase, Δ-1-pyrroline-5-carboxylate synthase, Ornithine aminotransferase, Arginase, Alanine transaminase, Alanine-glyoxylate transaminase, Glutamate decarboxylase, Glutamate decarboxylase 1-2, Spermidine synthase, Aldehyde dehydrogenase, ATP-grasp domain-containing protein, Cysteine sulfinic acid decarboxylase1-2, Taurine transporter, HSP beta 1, Sodium-and chloride-dependent glycine transporter (Meng et al, 2013;Cross et al, 2014;Eierman & Hare, 2014).…”

“…Los principales mecanismos de adaptación a diferentes salinidades de la ostra y del mejillón han sido caracterizados a nivel molecular (Cross, Merlo, Rodríguez, Portela-Bens, & Rebordinos, 2014;Eierman & Hare, 2014); en particular, Meng et al (2013), resaltaron la primordial importancia de las vías de metabolismo de los FAAs para la adaptación eurihalina de la ostra Crassostrea gigas. A pesar que la mayoría de los trabajos han sido realizados en diferentes especies de bivalvos, es muy probable que los mecanismos de osmorregulación se conserven a nivel inter-específico.…”