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Open Access Highly Accessed Research article

The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations

Hua Bao1, Eryang Li2, Shawn D Mansfield3, Quentin CB Cronk2, Yousry A El-Kassaby1 and Carl J Douglas2*

Author Affiliations

1 Department of Forest Sciences, University of British Columbia, Vancouver, BC V6T1Z4, Canada

2 Department of Botany, University of British Columbia, Vancouver, BC V6T1Z4, Canada

3 Department of Wood Science, University of British Columbia, Vancouver, BC V6T1Z4, Canada

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BMC Genomics 2013, 14:359  doi:10.1186/1471-2164-14-359

Published: 29 May 2013

Abstract

Background

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. However, little is known about AS patterns in wood-forming tissues and how much AS variation exists within plant populations.

Results

Here 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.

Conclusions

This 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.