Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching

Frontiers in Plant Science
Sergei A FilichkinPankaj Jaiswal

Abstract

Abiotic stresses affect plant physiology, development, growth, and alter pre-mRNA splicing. Western poplar is a model woody tree and a potential bioenergy feedstock. To investigate the extent of stress-regulated alternative splicing (AS), we conducted an in-depth survey of leaf, root, and stem xylem transcriptomes under drought, salt, or temperature stress. Analysis of approximately one billion of genome-aligned RNA-Seq reads from tissue- or stress-specific libraries revealed over fifteen millions of novel splice junctions. Transcript models supported by both RNA-Seq and single molecule isoform sequencing (Iso-Seq) data revealed a broad array of novel stress- and/or tissue-specific isoforms. Analysis of Iso-Seq data also resulted in the discovery of 15,087 novel transcribed regions of which 164 show AS. Our findings demonstrate that abiotic stresses profoundly perturb transcript isoform profiles and trigger widespread intron retention (IR) events. Stress treatments often increased or decreased retention of specific introns - a phenomenon described here as differential intron retention (DIR). Many differentially retained introns were regulated in a stress- and/or tissue-specific manner. A subset of transcripts harboring super st...Continue Reading

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Datasets Mentioned

BETA
E-MTAB-5540

Methods Mentioned

BETA
environmental stresses
RNA-Seq
PCR
Iso-Seq
salt treatments

Software Mentioned

STAR ( Spliced Transcripts Alignment to a Reference )
STAR aligner
iDiffIR
TAPIS
GBrowse
Transcriptome Analysis Pipeline for Isoform Sequencing ( TAPIS )
STAR read mapping
Cufflinks
Seq
SpliceGrapher

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