Dataset Information

Transcriptomic analysis of Crassostrea sikamea × Crassostrea angulata hybrids in response to low salinity stress.

ABSTRACT: Hybrid oysters often show heterosis in growth rate, weight, survival and adaptability to extremes of salinity. Oysters have also been used as model organisms to study the evolution of host-defense system. To gain comprehensive knowledge about various physiological processes in hybrid oysters under low salinity stress, we performed transcriptomic analysis of gill tissue of Crassostrea sikamea ? × Crassostrea angulata? hybrid using the deep-sequencing platform Illumina HiSeq. We exploited the high-throughput technique to delineate differentially expressed genes (DEGs) in oysters maintained in hypotonic conditions. A total of 199,391 high quality unigenes, with average length of 644 bp, were generated. Of these 35 and 31 genes showed up- and down-regulation, respectively. Functional categorization and pathway analysis of these DEGs revealed enrichment for immune mechanism, apoptosis, energy metabolism and osmoregulation under low salinity stress. The expression patterns of 41 DEGs in hybrids and their parental species were further analyzed by quantitative real-time PCR (qRT-PCR). This study will serve as a platform for subsequent gene expression analysis regarding environmental stress. Our findings will also provide valuable information about gene expression to better understand the immune mechanism, apoptosis, energy metabolism and osmoregulation in hybrid oysters under low salinity stress.

SUBMITTER: Yan L

PROVIDER: S-EPMC5300195 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Transcriptomic analysis of Crassostrea sikamea × Crassostrea angulata hybrids in response to low salinity stress.

Yan Lulu L Su Jiaqi J Wang Zhaoping Z Yan Xiwu X Yu Ruihai R Ma Peizhen P Li Yangchun Y Du Junpeng J

PloS one 20170209 2

Hybrid oysters often show heterosis in growth rate, weight, survival and adaptability to extremes of salinity. Oysters have also been used as model organisms to study the evolution of host-defense system. To gain comprehensive knowledge about various physiological processes in hybrid oysters under low salinity stress, we performed transcriptomic analysis of gill tissue of Crassostrea sikamea ♀ × Crassostrea angulata♂ hybrid using the deep-sequencing platform Illumina HiSeq. We exploited the high ...[more]

PMID: 28182701

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Project description:BackgroundLow salinity is one of the main factors limiting the distribution and survival of marine species. As a euryhaline species, the Pacific oyster Crassostrea gigas is considered to be tolerant to relative low salinity. The genes that regulate C. gigas responses to osmotic stress were monitored using the next-generation sequencing of whole transcriptome with samples taken from gills. By RNAseq technology, transcript catalogs of up- and down-regulated genes were generated from the oysters exposed to low and optimal salinity seawater.Methodology/principal findingsThrough Illumina sequencing, we reported 1665 up-regulated transcripts and 1815 down-regulated transcripts. A total of 45771 protein-coding contigs were identified from two groups based on sequence similarities with known proteins. As determined by GO annotation and KEGG pathway mapping, functional annotation of the genes recovered diverse biological functions and processes. The genes that changed expression significantly were highly represented in cellular process and regulation of biological process, intracellular and cell, binding and protein binding according to GO annotation. The results highlighted genes related to osmoregulation, signaling and interactions of osmotic stress response, anti-apoptotic reactions as well as immune response, cell adhesion and communication, cytoskeleton and cell cycle.Conclusions/significanceThrough more than 1.5 million sequence reads and the expression data of the two libraries, the study provided some useful insights into signal transduction pathways in oysters and offered a number of candidate genes as potential markers of tolerance to hypoosmotic stress for oysters. In addition, the characterization of C. gigas transcriptome will not only provide a better understanding of the molecular mechanisms about the response to osmotic stress of the oysters, but also facilitate research into biological processes to find underlying physiological adaptations to hypoosmotic shock for marine invertebrates.

Project description:Sturgeons are euryhaline fish species that have developed specific mechanisms of osmotic and ion regulation to adapt to waters of varying salinity. For the aim to elucidate the osmoregulation strategy behind its high salinity tolerance of sturgeons, the transcriptomes of gills in Siberian sturgeon Acipenser baeri under salinity stress (30 ppt) were sequenced using deep-sequencing platform Illumina/HiSeq-2500 and differential expression genes (DEGs) were identified. A total of 167, 501, 278 clean reads were obtained and 280, 238 unigenes were composed of those clean reads with the mean length of 520nt, and the N50 of 630?bp. Unigenes Sequence alignment was implemented via KEGG, KOG, NT, NR, PFAM, Swiss-Prot, and GO databases. 62, 242 unigenes (22.21%) were annoated in at least one database. 11380 significantly differentially expressed unigenes were found, 6969 of which were up-regulated and 4411 were down-regulated by salinity stress. Amongst the top 20 KEGG pathways with the most amount of annotation sequences, some pathways such as glycerophospholipid metabolism, fatty-acid biosynthesis, glycolysis/gluconeogenesis, oxidative phosphorylation have been comprehensively proved to be relevant to osmoregulation. Despite of these, three possible osmoregulation-related signaling pathways as lipid metabolism related pathways, tight junction pathway and thyroid hormone signaling pathway have been widely analyzed in the current study. In all DEGs, some of the typical genes involved in osmoregulation, including calcium-transporting ATPase 4 (ATP2B4), Na+/K+-ATPase alpha subunit (?-NKA), potassium-transporting ATPase alpha chain 1 (ATP4A) and Ras GTPase-activating protein (RasGAP) etc were also identified. RNA-seq results were validated with quantitative real-time PCR (qPCR), the 12 selected genes showed a consistent direction in both DGE library and qPCR analysis, proving that the RNA-seq results are reliable. The present results would be helpful to elucidate the osmoregulation mechanism of aquatic animals adapting to salinity challenge.

Dataset Information

Transcriptomic analysis of Crassostrea sikamea × Crassostrea angulata hybrids in response to low salinity stress.

Publications

Transcriptomic analysis of Crassostrea sikamea × Crassostrea angulata hybrids in response to low salinity stress.

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