Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

The rapid evolution of alternative splicing in plants

Zhihao Ling, Thomas Brockmöller, Ian T. Baldwin, Shuqing Xu
doi: https://doi.org/10.1101/107938
Zhihao Ling
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: zling@ice.mpg.de
Thomas Brockmöller
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: tbrockmoeller@ice.mpg.de
Ian T. Baldwin
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: baldwin@ice.mpg.de
Shuqing Xu
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: sxu@ice.mpg.de
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Alternative pre-mRNA splicing (AS) is prevalent among all plants and is involved in many interactions with environmental stresses. However, the evolutionary patterns and underlying mechanisms of AS in plants remain unclear. By analyzing the transcriptomes of six plant species, we revealed that AS diverged rapidly among closely related species, largely due to the gains and losses of AS events among orthologous genes. Furthermore, AS that generates transcripts containing premature termination codons (PTC), although only representing a small fraction of the total AS, are more conserved than those that generate non-PTC containing transcripts, suggesting that AS coupled with nonsense-mediated decay (NMD) might play an important role in regulating mRNA levels post-transcriptionally. With a machine learning approach we analyzed the key determinants of AS to understand the mechanisms underlying its rapid divergence. Among the studied species, the presence/absence of alternative splicing site (SS) within the junction, the distance between the authentic SS and the nearest alternative SS, the size of exon-exon junctions were the major determinants for both alternative 5’ donor site and 3’acceptor site, suggesting a relatively conserved AS mechanism. Comparative analysis further demonstrated that variations of the identified AS determinants, mostly are located in introns, significantly contributed to the AS turnover among closely related species in both Solanaceae and Brassicaceae taxa. These new mechanistic insights into the evolution of AS in plants highlight the importance of post-transcriptional regulation in mediating plant-environment interactions.

One sentence summary Changes of intron located splicing regulators contributed to the rapid evolution of alternative splicing in plants.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted February 13, 2017.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
The rapid evolution of alternative splicing in plants
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
The rapid evolution of alternative splicing in plants
Zhihao Ling, Thomas Brockmöller, Ian T. Baldwin, Shuqing Xu
bioRxiv 107938; doi: https://doi.org/10.1101/107938
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
The rapid evolution of alternative splicing in plants
Zhihao Ling, Thomas Brockmöller, Ian T. Baldwin, Shuqing Xu
bioRxiv 107938; doi: https://doi.org/10.1101/107938

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Plant Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4865)
  • Biochemistry (10821)
  • Bioengineering (8065)
  • Bioinformatics (27374)
  • Biophysics (14020)
  • Cancer Biology (11160)
  • Cell Biology (16099)
  • Clinical Trials (138)
  • Developmental Biology (8807)
  • Ecology (13329)
  • Epidemiology (2067)
  • Evolutionary Biology (17394)
  • Genetics (11705)
  • Genomics (15961)
  • Immunology (11057)
  • Microbiology (26155)
  • Molecular Biology (10679)
  • Neuroscience (56729)
  • Paleontology (422)
  • Pathology (1737)
  • Pharmacology and Toxicology (3012)
  • Physiology (4567)
  • Plant Biology (9666)
  • Scientific Communication and Education (1617)
  • Synthetic Biology (2699)
  • Systems Biology (6994)
  • Zoology (1513)