Characterization and analysis of transcriptome complexity using SMRT-Seq combined with RNA-Seq for a better understanding of Acanthogobius ommaturus in response to temperature stress

Acanthogobius ommaturus is a eurythermic fish, which is widely distributed in coastal, estuarine and bay waters of China, Japan and Korea. Due to the lack of whole genomic information, full-length transcriptome of A. ommaturus was firstly generated by single molecule real-time sequencing (SMRT-seq) in this study. A total of 49,833 full-length non-redundant transcripts (FLNRTs), 2255 alternative splices, 46,856 simple sequence repeats, 5094 long non-coding RNAs and 2708 transcription factors were obtained. Additionally, FLNRTs were used as reference sequences for the following transcriptome analysis of the temperature stress (7 °C, 14 °C, 21 °C (control), 28 °C and 35 °C). GO and KEGG enrichment analysis using GSEA were performed on all genes in 10 response modules which were screened out by WGCNA. Enrichment analysis showed that protein degradation, immune response and energy metabolism play an active role in the temperature stress of A. ommaturus. The differentially expressed hub genes (DEHGs) in response modules were closely related to adhesion, vascular remodeling and disease. The results of this study provided the first systematical full-length transcriptome profile of A. ommaturus and characterized its temperature stress responses, which will serve as the foundation for further exploring the molecular mechanism of the temperature stress in fish. •The combined analysis of SMRT-Seq and RNA-Seq data can combine their respective advantages to improve the accuracy and value of research.•The combination of weighted gene co-expression network analysis (WGCNA) and gene set enrichment analysis (GSEA) is a new method for transcriptome analysis.•49,833 full-length non-redundant transcripts (FLNRTs), 2,255 alternative splices (ASs), 46,856 simple sequence repeats (SSRs) and other genetic information were mined in A. ommaturus.•The results showed that protein degradation, immune response and energy metabolism play an active role in temperature regulation of A. ommaturus.•Combined with its geographical distribution, we inferred that 28°C may be the tolerance temperature of A. ommaturus.