Gill Transcriptome Sequencing and De Novo Annotation of Acanthogobius ommaturus in Response to Salinity Stress

Abstract

Acanthogobius ommaturus is a euryhaline fish widely distributed in coastal, bay and estuarine areas, showing a strong tolerance to salinity. In order to understand the mechanism of adaptation to salinity stress, RNA-seq was used to compare the transcriptome responses of Acanthogobius ommaturus to the changes of salinity. Four salinity gradients, 0 psu, 15 psu (control), 30 psu and 45 psu were set to conduct the experiment. In total, 131,225 unigenes were obtained from the gill tissue of A. ommaturus using the Illumina HiSeq 2000 platform (San Diego, USA). Compared with the gene expression profile of the control group, 572 differentially expressed genes (DEGs) were screened, with 150 at 0 psu, 170 at 30 psu, and 252 at 45 psu. Additionally, among these DEGs, Gene Ontology (GO) analysis indicated that binding, metabolic processes and cellular processes were significantly enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis detected 3, 5 and 8 pathways related to signal transduction, metabolism, digestive and endocrine systems at 0 psu, 30 psu and 45 psu, respectively. Based on GO enrichment analysis and manual literature searches, the results of the present study indicated that A. ommaturus mainly responded to energy metabolism, ion transport and signal transduction to resist the damage caused by salinity stress. Eight DEGs were randomly selected for further validation by quantitative real-time PCR (qRT-PCR) and the results were consistent with the RNA-seq data.

Keywords: Acanthogobius ommaturus; RNA-seq; differentially expressed genes (DEGs); salinity stress.

Figure 1

Global overview of differentially expressed unigenes based on Venn diagram.

Figure 2

Results of the enrichment analysis of gene ontology (GO) terms of differentially expressed genes (DEGs) of A. ommaturus exposed to salinity changes.

Figure 2

Results of the enrichment analysis of gene ontology (GO) terms of differentially expressed genes (DEGs) of A. ommaturus exposed to salinity changes.

Figure 3

Scatterplot of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched in the DEGs. Rich factor is the ratio of the DEGs number to the total gene number in a given pathway. The size and color of the dots represent the gene number and range of the q value, respectively.

Figure 3

Scatterplot of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched in the DEGs. Rich factor is the ratio of the DEGs number to the total gene number in a given pathway. The size and color of the dots represent the gene number and range of the q value, respectively.

Figure 4

Relative change of the transcriptomes data and qRT-PCR data of 8 DEGs. Log₂fold changes are expressed as the ratio of gene expression after normalization to β-actin. The data are means ± SD from three independent replicates, and “*” indicates statistical significance between experimental group and control group (p < 0.05).