PacBio and Illumina RNA sequencing identify alternative splicing events
in response to cold stress in two poplar species
Abstract
In eukaryotes, alternative splicing (AS) is a crucial regulatory
mechanism that modulates mRNA diversity and stability. The contribution
of AS to stress are known in many species related to stress. But the
post-transcriptional mechanism in poplar under cold stress is still
unclear. Recent studies have utilized the advantages of Single Molecular
Real Time (SMRT) sequencing technology from Pacific Bioscience (PacBio)
to identify full-length transcripts. We, therefore, used a combination
of single-molecule long-read sequencing and Illumina RNA sequencing
(RNA-Seq) for a global analysis of AS in two poplar species (Populus
trichocarpa and P. ussuriensis) under cold stress. We further identified
1261 AS events in P. trichocarpa and 2101 in P. ussuriensis, among which
intron retention, with a frequency of more than 30%, was the most
prominent type under cold stress. RNA-Seq data analysis and annotation
revealed the importance of calcium, abscisic acid, and reactive oxygen
species signaling in cold stress response. Besides, the low temperature
rapidly induced multiple splicing factors, transcription factors, and
differentially expressed genes through AS. In P. ussuriensis, there was
a rapid occurrence of AS events. This study provides new insight into
the complexity and regulation of AS during cold stress response in two
poplar species.