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Genomewide comparative analysis of alternative splicing in plants.

Bing-Bing Wang1, Volker Brendel

  • 1Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA.

Proceedings of the National Academy of Sciences of the United States of America
|April 25, 2006
PubMed
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Alternative splicing (AS) is common in plants, with intron retention being the most frequent event. Many AS events are conserved between Arabidopsis and rice, suggesting a role in post-transcriptional regulation.

Area of Science:

  • Plant molecular biology
  • Genomics
  • Transcriptomics

Background:

  • Alternative splicing (AS) is well-studied in mammals but less so in plants.
  • Understanding AS in plants is crucial for deciphering gene regulation and evolution.

Purpose of the Study:

  • To investigate and quantify alternative splicing events in two model plants: Arabidopsis and rice.
  • To identify conserved AS events and their potential regulatory roles.
  • To establish a comprehensive database for plant AS.

Main Methods:

  • Analysis of expressed sequence tag (EST) and complementary DNA (cDNA) data.
  • Identification and classification of different types of AS events (e.g., intron retention, exon skipping).
  • Comparative analysis of AS events between Arabidopsis and rice.

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Main Results:

  • Arabidopsis exhibits 8,264 AS events in 21.8% of genes, with intron retention (56%) dominating.
  • Rice shows 14,542 AS events in 21.2% of genes, also with high intron retention (53.5%).
  • Approximately 40% of AS events are conserved between Arabidopsis and rice, indicating evolutionary significance.

Conclusions:

  • Intron retention is a prevalent AS mechanism in plants, suggesting intron definition splice site recognition.
  • Alternative splicing in plants may be conserved for post-transcriptional regulation.
  • A web-based database (ASIP) was developed to catalog plant AS events.