RNA-seq analysis reveals alternative splicing under salt stress in cotton, Gossypium davidsonii

BACKGROUND: Numerous 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. RESULTS: Using 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. CONCLUSION: This 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4449-8) contains supplementary material, which is available to authorized users.