Abstract
Transcriptome complexity plays crucial roles in regulating the biological functions of eukaryotes. Except for functional genes, alternative splicing and fusion transcripts produce a vast expansion of transcriptome diversity. In this study, we applied PacBio single-molecule long-read sequencing technology to unveil the whole transcriptome landscape of Lateolabrax maculatus. We obtained 28,809 high-quality non-redundant transcripts, including 18,280 novel isoforms covering 8,961 annotated gene loci within the current reference genome and 3,172 novel isoforms. A total of 10,249 AS events were detected, and intron retention was the predominant AS event. In addition, 1,359 alternative polyadenylation events, 3,112 lncRNAs, 29,609 SSRs, 365 fusion transcripts, and 1,194 transcription factors were identified in this study. Furthermore, we performed RNA-Seq analysis combined with Iso-Seq results to investigate salinity regulation mechanism at the transcripts level. A total of 518 transcripts were differentially expressed, which were further divided into 8 functional groups. Notably, transcripts from the same genes exhibited similar or opposite expression patterns. Our study provides a comprehensive view of the transcriptome complexity in L. maculatus, which significantly improves current gene models. Moreover, the diversity of the expression patterns of transcripts may enhance the understanding of salinity regulatory mechanism in L. maculatus and other euryhaline teleosts.
Highlights
With the development of high-throughput sequencing of the transcriptome, biologists have begun to pay more attention to multiple post-transcriptional processes of precursor-messenger RNA
reads of insert (ROIs) were further classified into full-length non-chimeric (FLNC) and NFL reads based on the presence of 5’ primer, 3’ primer, and poly(A) tails
These consensus sequences were collapsed by the TOFU process, yielding 28,809 non-redundant transcripts retained for the following study (Table 1)
Summary
With the development of high-throughput sequencing of the transcriptome, biologists have begun to pay more attention to multiple post-transcriptional processes of precursor-messenger RNA (premRNA). Transcriptome complexity plays an important role in increasing the coding capacity of genes, generating proteome diversity, regulating gene expression, cellular physiological and developmental processes (Lareau et al, 2004; Abdel-Ghany et al, 2016; Wang et al, 2016). Alternative polyadenylation (APA), another post-transcriptional regulatory events in which RNA molecules with different 3’ ends originate from distinct polyadenylation sites of a single gene, is emerging as a mechanism widely used to regulate gene expression (Chen et al, 2017b). APA events may alter sequence elements and/or the coding capacity of transcripts, and could be considered as a mechanism that adds another layer to regulation of transcriptome diversity (Shen et al, 2011; Abdel-Ghany et al, 2016; Ha et al, 2018)
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