Abstract
BackgroundAlternative splicing (AS) of genes is an efficient means of generating variation in protein structure and function. AS variation has been observed between tissues, cell types, and different treatments in non-woody plants such as Arabidopsis thaliana (Arabidopsis) and rice. However, little is known about AS patterns in wood-forming tissues and how much AS variation exists within plant populations.ResultsHere we used high-throughput RNA sequencing to analyze the Populus trichocarpa (P. trichocarpa) xylem transcriptome in 20 individuals from different populations across much of its range in western North America. Deep transcriptome sequencing and mapping of reads to the P. trichocarpa reference genome identified a suite of xylem-expressed genes common to all accessions. Our analysis suggests that at least 36% of the xylem-expressed genes in P. trichocarpa are alternatively spliced. Extensive AS was observed in cell-wall biosynthesis related genes such as glycosyl transferases and C2H2 transcription factors. 27902 AS events were documented and most of these events were not conserved across individuals. Differences in isoform-specific read densities indicated that 7% and 13% of AS events showed significant differences between individuals within geographically separated southern and northern populations, a level that is in general agreement with AS variation in human populations.ConclusionsThis genome-wide analysis of alternative splicing reveals high levels of AS in P. trichocarpa and extensive inter-individual AS variation. We provide the most comprehensive analysis of AS in P. trichocarpa to date, which will serve as a valuable resource for the plant community to study transcriptome complexity and AS regulation during wood formation.
Highlights
Alternative splicing (AS) of genes is an efficient means of generating variation in protein structure and function
Mapping of the P. trichocarpa developing xylem transcriptome Twenty P. trichocarpa individuals from a population of approximately 450 individuals from the BC Ministry of Forests collection [27,28] maintained in a common garden at the University of British Columbia were selected for xylem transcriptome analysis using the Illumina platform for ultrahigh-throughput RNA sequencing (RNA-Seq)
We found that intron retention is the most prevalent form of alternative splicing (40% of the AS events), while exon skipping only constituted 8% and alternative 3′ and 5′ splice sites were at intermediate frequencies (Tables 1 and 2)
Summary
Alternative splicing (AS) of genes is an efficient means of generating variation in protein structure and function. AS variation has been observed between tissues, cell types, and different treatments in non-woody plants such as Arabidopsis thaliana (Arabidopsis) and rice. Few studies have investigated genome-wide patterns of AS in plant species [9], but recent results from Arabidopsis [10] and rice [11] have revealed high levels of AS that can vary in different organs and under different stress conditions. Generation high throughput transcriptome sequencing (RNA-Seq) analysis suggests that 42% of the intron-containing genes in Arabidopsis undergo AS [10]. Using a normalized cDNA library derived from flower and seedling tissue, Marquez et al [5] used deep RNA-Seq transcriptome analysis to show that over 60% of Arabidopsis intron-containing genes are alternatively spliced, with intron retention (IR) being the most common form of AS. As in humans, large scale AS in plants is likely to contribute to proteome and phenotypic diversity
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