Genome-wide profiling of alternative splicing genes in hybrid poplar (P.alba×P.glandulosa cv.84K) leaves

PLoS One. 2020 Nov 18;15(11):e0241914. doi: 10.1371/journal.pone.0241914. eCollection 2020.

Abstract

Alternative splicing (AS) is a post-transcriptional process common in plants and essential for regulation of environmental fitness of plants. In the present study, we focus on the AS events in poplar leaves to understand their effects on plant growth and development. The hybrid poplar (P.alba×P.glandulosa cv.84K) leaves were collected for RNA extraction. The extracted RNA was sequenced using on an Illumina HiSeq™ 2000 platform. Using the Populus trichocarpa genome as the reference, a total of 3810 AS genes were identified (9225 AS events), which accounted for 13.51% of all the expressed genes. Intron retention was the most common AS event, accounting for 43.86% of all the AS events, followed by alternative 3' splice sites (23.75%), alternative 5' splice sites (23.71%), and exon skipping (8.68%). Chromosomes 10 had the most condensed AS events (33.67 events/Mb) and chromosome 19 had the least (12.42 events/Mb). Association analysis showed that AS in the poplar leaves was positively correlated with intron length, exon number, exon length, and gene expression level, and was negatively correlated with GC content. AS genes in the poplar leaves were associated mainly with inositol phosphate metabolism and phosphatidylinositol signaling system pathways that would be significant on wooden plant production.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing*
  • Chimera / genetics*
  • Chimera / growth & development
  • Chromosomes, Plant / genetics
  • Exons
  • Gene Expression Regulation, Plant
  • High-Throughput Nucleotide Sequencing
  • Introns
  • Plant Leaves / genetics
  • Plant Leaves / growth & development
  • Plant Proteins / genetics*
  • Populus / genetics
  • Populus / growth & development*
  • RNA Splice Sites
  • Whole Genome Sequencing / methods*

Substances

  • Plant Proteins
  • RNA Splice Sites

Grants and funding

The National Natural Science Foundation of China (#31672189) and Beijing Forestry University Undergraduate Training Program for Inovation and Entrepreneurship (#202010022062). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.