Transcriptome-wide N6-methyladenosine profiling of cotton root provides insights for salt stress tolerance

N6-methyladenosine (m6A) is a ubiquitous reversible epigenetic RNA modification which plays a significant role in regulation of gene expression and cell functions. However, m6A abundance, dynamics and topology remain unexplored in cotton. Here, we performed transcriptome-wide m6A profiling and comparative analysis of cotton root tissues under normal and salt stress treatments. Totally, 3360 and 3771 high confidence m6A peaks, involved in 3219 and 3566 expressed genes under normal and salt stress, were identified, respectively. Of them, 1311 mRNA transcripts from salt treatment and 964 in control were specifically detected m6A peaks. Functional analysis indicated that the 1311 methylated genes specifically from salt stress were mainly involved in zeatin biosynthesis, taurine and hypotaurine metabolism, ABC transporters, and anthocyanin biosynthesis, while 964 in control were involved in ribosome and proteasome processes. Furthermore, mRNA m6A sites were enriched around the stop codons and coding regions, and m6A methylation exhibited dynamic changes after salt treatment, with 434 m6A peaks in 430 genes up-regulated and 290 m6A peaks in 287 genes downregulated. Combined with RNA-seq analysis, we found that the m6A deposition specifically in normal or salt treatment is positively correlated with their corresponding gene transcripts abundance. We confirmed that cotton YTH (YT512-B homology) domain gene GhECT6 (evolutionarily conserved C-terminal region 6), a deduced m6A reader, played an important role against salt stress. GhECT6 was significantly induced expression after salt treatment, and silencing GhECT6 caused a decrease in salt tolerance. This first high-throughput epitranscriptomic data provide new insights into understanding the critical mRNA modification in response to salt stress in cotton.