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Genome-wide survey of Alternative Splicing in Sorghum Bicolor

Physiology and Molecular Biology of Plants volume 20, pages 323–329 (2014)Cite this article

Abstract

Sorghum bicolor is a member of grass family which is an attractive model plant for genome study due to interesting genome features like low genome size. In this research, we performed comprehensive investigation of Alternative Splicing and ontology aspects of genes those have undergone these events in sorghum bicolor. We used homology based alignments between gene rich transcripts, represented by tentative consensus (TC) transcript sequences, and genomic scaffolds to deduce the structure of genes and identify alternatively spliced transcripts in sorghum. Using homology mapping of assembled expressed sequence tags with genomics data, we identified 2,137 Alternative Splicing events in S. bicolor. Our study showed that complex events and intron retention are the main types of Alternative Splicing events in S. bicolor and highlights the prevalence of splicing site recognition for definition of introns in this plant. Annotations of the alternatively spliced genes revealed that they represent diverse biological process and molecular functions, suggesting a fundamental role for Alternative Splicing in affecting the development and physiology of S. bicolor.

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Abbreviations

AS:

Alternative Splicing

GO:

Gene Ontology

EST:

Expression Sequence Tag

TC:

Tentative Consensus

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Affiliations

  1. Department of Biotechnology and Plant Breeding, University of Tabriz, Tabriz, Iran

    Bahman Panahi & Mehdi Taghizadeghan

  2. Meshgin shahr Branch, Islamic Azad University, Meshgin Shahr, Iran

    Bahram Abbaszadeh

  3. School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia

    Esmaeil Ebrahimie

Authors
  1. Bahman Panahi
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  2. Bahram Abbaszadeh
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  3. Mehdi Taghizadeghan
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  4. Esmaeil Ebrahimie
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Corresponding author

Correspondence to Bahman Panahi.

Additional information

Bahman Panahi and Esmaeil Ebrahimie contributed equally to this work.

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Panahi, B., Abbaszadeh, B., Taghizadeghan, M. et al. Genome-wide survey of Alternative Splicing in Sorghum Bicolor . Physiol Mol Biol Plants 20, 323–329 (2014). https://doi.org/10.1007/s12298-014-0245-3

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  • DOI: https://doi.org/10.1007/s12298-014-0245-3

Keywords

  • Alternative splicing
  • Ontology
  • Complex events
  • Intron retention