Alternative Splicing during Fiber Development in G. hirsutum

Abstract

Cotton is a valuable cash crop in many countries. Cotton fiber is a trichome that develops from a single epidermal cell and serves as an excellent model for understanding cell differentiation and other life processes. Alternative splicing (AS) of genes is a common post-transcriptional regulatory process in plants that is essential for plant growth and development. The process of AS during cotton fiber formation, on the other hand, is mainly unknown. A substantial number of multi-exon genes were discovered to be alternatively spliced during cotton fiber formation in this study, accounting for 23.31% of the total number of genes in Gossypium hirsutum. Retention intron (RI) is not necessarily the most common AS type, indicating that AS genes and processes during fiber development are very temporal and tissue-specific. When compared to fiber samples, AS is more prevalent at the fiber initiation stages and in the ovule, indicating that development stages and tissues use different AS strategies. Genes involved in fiber development have gone through stage-specific AS, demonstrating that AS regulates cotton fiber development. Furthermore, AS can be regulated by trans-regulation elements such as splicing factor and cis-regulation elements such as gene length, exon numbers, and GC content, particularly at exon–intron junction sites. Our findings also suggest that increased DNA methylation may aid in the efficiency of AS, and that gene body methylation is key in AS control. Finally, our research will provide useful information about the roles of AS during the cotton fiber development process.

Alternative Splicing under Cold Stress in Paper Mulberry

“…Furthermore, we noticed that AS is more prevalent in transcripts with longer sequences and more exons. Similar results have been reported in cotton (Gossypium hirsutum) [20], as well as in soybeans [43]. This suggests that the gene structure and sequence composition in woody plants, much like in crops, have a similar influence on AS, potentially indicating a conserved phenomenon.…”

“…Research has provided evidence that AS can be regulated not only by SR genes, but also by factors such as length, the number of exons/introns, and the GC content of AS genes [20,27]. Additionally, epigenetic regulation such as DNA methylation levels has been shown to influence AS [34].…”

“…AS in plant genes is a complex and finely regulated process influenced by numerous molecular mechanisms, including splicing factors, splicing site recognition, epigenetic modifications, and the sequences within exons and introns [20]. AS occurs within the spliceosome, which comprises small nuclear ribonucleoproteins (snRNPs) and a multitude of Ser/Arg-rich proteins [4,[21][22][23].…”

Comparative analysis of key fiber characteristics in white Pima cotton (Gossypium barbadense L.): Native accessions from the Peruvian Amazon

“…Cotton, one of the most important and versatile natural fibers, has played a crucial role in the textile industry for centuries (Zheng et al., 2023). The genus Gossypium currently comprises 52 cotton species grown around the world (Campbell et al., 2010; Gallagher et al., 2017; Grover et al., 2015), and each species has distinct fiber quality traits (Y. Wang et al., 2023).…”

The Abundant and Unique Transcripts and Alternative Splicing of the Artificially Autododecaploid London Plane (Platanus × acerifolia)

“…Additionally, AS is a widespread phenomenon in eukaryotes that generates different mature mRNAs from a single mRNA precursor and is involved in encoding different proteins from a single gene [24][25][26]. During polyploidization, there are changes in the composition, abundance, and activity of splicing factors that affect alternative splicing (AS) in polyploid wheat and cotton [27][28][29]. Studies showed that AS is more complex in polyploid Brassica napus due to an increase in the number of introns that provide more exon junctions [30].…”