Summary
Alternative
splicing (AS) is a crucial regulatory mechanism in eukaryotes, which acts by greatly
increasing transcriptome diversity. The extent and complexity of AS has been
revealed in model plants using high-throughput next-generation sequencing.
However, this technique is less effective in accurately identifying transcript
isoforms in polyploid species because of the high sequence similarity between
coexisting subgenomes.
Here
we characterize AS in the polyploid species cotton. Using Pacific Biosciences
single- molecule long-read isoform sequencing (Iso-Seq), we developed an
integrated pipeline for Iso-Seq transcriptome data analysis
(https://github.com/Nextomics/pipeline-for-isoseq).
We
identified 176849 full-length transcript isoforms from 44968 gene models and
updated
gene annotation. These data led us to identify 15102 fibre-specific AS events
and estimate that c. 51.4% of homoeologous genes produce divergent isoforms in
each
subgenome.
We reveal that AS allows differential regulation of the same gene by miRNAs at the
isoform level. We also show that nucleosome occupancy and DNA methylation play
a role in defining exons at the chromatin level.
This
study provides new insights into the complexity and regulation of AS, and will
enhance our understanding of AS in polyploid species. Our methodology for
Iso-Seq data analysis will be a useful reference for the study of AS in other
species.
DOI: 10.1111/nph.14762 IF=7.33