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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Evolutionarily Conserved Alternative Splicing Across Monocots.

Wenbin Mei1, Lucas Boatwright1, Guanqiao Feng2

  • 1Department of Biology, University of Florida, Gainesville, Florida 32611.

Genetics
|August 26, 2017
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Summary
This summary is machine-generated.

Conserved alternative splicing (AS) events were identified across nine plant species using RNA-Seq. These conserved AS events, particularly in grasses, offer insights into genotype-phenotype connections and crop improvement.

Keywords:
R2R3-MYBRS and RS2Z subfamiliesconserved alternative splicing eventsgrass familymonocot

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Area of Science:

  • Plant molecular biology
  • Genomics
  • Bioinformatics

Background:

  • Distinguishing functional alternative splicing (AS) from splicing noise in plants is challenging.
  • Conserved AS events across species can validate splice isoform functionality.

Purpose of the Study:

  • To identify and analyze junction-based conserved AS events across nine diverse plant species.
  • To investigate the relationship between conserved AS events and genomic features like conserved synteny.
  • To explore the role of conserved AS in plant-specific splice factor subfamilies and functional networks.

Main Methods:

  • High-throughput RNA-Seq data analysis across nine plant species.
  • Identification of conserved junction-based AS events.
  • Analysis of AS event frequency in relation to conserved synteny blocks.
  • Construction of STRING functional protein association networks for genes with conserved AS.

Main Results:

  • 9804 AS events were conserved across two or more species.
  • Conserved AS events were twice as frequent in grasses within conserved synteny regions.
  • Conservation and divergence of AS were observed in maize-specific SR protein subfamilies post-genome duplication.
  • Conserved AS networks are enriched for signaling pathway genes (phosphatases, kinases, ubiquitylation).

Conclusions:

  • This study provides a foundational resource for conserved AS events in monocots, especially grasses.
  • Conserved AS represents an additional layer connecting genotype to phenotype.
  • Understanding conserved AS can impact crop improvement strategies.