ArticleBMC genomics2013
The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 68 citations in OpenAlex.
- Pre-mRNA splicing and its regulation in microalgae and cyanobacteria.Advanced biotechnology · 2025Review
- Root-to-shoot mobile mRNA CmoKARI1 promotes JA-Ile biosynthesis to confer chilling tolerance in grafted cucumbers.Nature communications · 2025Article
- Genome-Wide Analyses of Copy Number Variants in 751 Populus trichocarpa Individuals From Natural Populations.Genome biology and evolution · 2025Article
- Importance of pre-mRNA splicing and its study tools in plants.Advanced biotechnology · 2024Review
- Comparative proteomic analysis provides insights into wood formation in immature xylem at different ages inFrontiers in plant science · 2024Article
- How to explore what is hidden? A review of techniques for vascular tissue expression profile analysis.Plant methods · 2023Review
- Unraveling the Guardians of Growth: A Comprehensive Analysis of thePlants (Basel, Switzerland) · 2023Article
- The PtoTCP20-miR396d-PtoGRF15 module regulates secondary vascular development in Populus.Plant communications · 2023Article
- Spatio-Temporal Modification of Lignin Biosynthesis in Plants: A Promising Strategy for Lignocellulose Improvement and Lignin Valorization.Frontiers in bioengineering and biotechnology · 2022Review
- Root-to-Shoot Long-Distance Mobile miRNAs Identified fromInternational journal of molecular sciences · 2021Article
- An alternative splicing variant of PtRD26 delays leaf senescence by regulating multiple NAC transcription factors in Populus.The Plant cell · 2021Article
- PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species.Frontiers in plant science · 2021Article
- Investigation Into Different Wood Formation Mechanisms Between Angiosperm and Gymnosperm Tree Species at the Transcriptional and Post-transcriptional Level.Frontiers in plant science · 2021Article
- PSDX: A Comprehensive Multi-Omics Association Database ofFrontiers in plant science · 2021Article
- The Genetic Regulation of Alternative Splicing inFrontiers in plant science · 2020Article
- Genome-wide profiling of alternative splicing genes in hybrid poplar (P.alba×P.glandulosa cv.84K) leaves.PloS one · 2020Article
- Transcriptional and Post-transcriptional Regulation of Lignin Biosynthesis Pathway Genes inFrontiers in plant science · 2020Review
- Genome-wide identification and comparative analysis of alternative splicing across four legume species.Planta · 2019Article
- Systems and Synthetic Biology of Forest Trees: A Bioengineering Paradigm for Woody Biomass Feedstocks.Frontiers in plant science · 2019Review
- Data Integration in Poplar: 'Omics Layers and Integration Strategies.Frontiers in genetics · 2019Review
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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