Abstract
BackgroundNumerous studies have focused on the regulation of gene expression in response to salt stress at the transcriptional level; however, little is known about this process at the post-transcriptional level.ResultsUsing a diploid D genome wild salinity-tolerant cotton species, Gossypium davidsonii, we analyzed alternative splicing (AS) of genes related to salt stress by comparing high-throughput transcriptomes from salt-treated and well-watered roots and leaves. A total of 14,172 AS events were identified involving 6798 genes, of which intron retention (35.73%) was the most frequent, being detected in 3492 genes. Under salt stress, 1287 and 1228 differential alternative splicing (DAS) events were identified in roots and leaves, respectively. These DAS genes were associated with specific functional pathways, such as “responses to stress”, “metabolic process” and “RNA splicing”, implying that AS represents an important pathway of gene regulation in response to salt stress. Several salt response genes, such as pyrroline-5-carboxylate synthase (P5CS), K+ channel outward (KCO1), plasma membrane intrinsic protein (PIP) and WRKY33 which were involved in osmotic balance, ion homeostasis, water transportation and transcriptional regulation, respectively, were identified with differential alternative splicing under salt stress. Moreover, we revealed that 13 genes encoding Ser/Arg-rich (SR) proteins related to AS regulation were differentially alternatively spliced under salt stress.ConclusionThis study first provide a comprehensive view of AS in G. davidsonii, and highlight novel insights into the potential roles of AS in plant responses to salt stress.
Highlights
Numerous studies have focused on the regulation of gene expression in response to salt stress at the transcriptional level; little is known about this process at the post-transcriptional level
Using RNA-seq data (Accessions: SRP061663), which were collected from both roots and leaves at 12, 24, 48, 96, and 144 h post salt stress (200 mM NaCl) in G. davidsonii, with data in normal conditions as controls [26], the splicing events involved in novel exons and novel intergenic transcripts were identified by mapping these data to the sequenced G. raimondii genome
It means more than 70 percentage isoforms predicted in our data will not be translated into function proteins
Summary
Numerous studies have focused on the regulation of gene expression in response to salt stress at the transcriptional level; little is known about this process at the post-transcriptional level. The removal of introns from immature mRNA by a process called “pre-mRNA splicing” occurs in the vast majority of eukaryotic protein-coding genes. In this process, particular exons of a gene may be included in or excluded from the final, processed messenger RNA (mRNA) from that gene. AS is accomplished by spliceosomes, which are high molecular weight complexes that are assembled at every intron [8, 9]. They contain five small nuclear ribonucleoprotein particles (snRNPs) and over 200 additional proteins. The identification of splice sites under particular cellular conditions is related to the interaction of additional proteins, globally designated as splicing factors (SFs), that guide spliceosomal components and thereby
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