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Biotechnology Letters

, Volume 33, Issue 3, pp 629–636 | Cite as

Genome-wide survey of alternative splicing in the grass Brachypodium distachyon: a emerging model biosystem for plant functional genomics

  • Gaurav Sablok
  • P. K. Gupta
  • Jong-Min Baek
  • Franck Vazquez
  • Xiang Jia Min
Original Research Paper
First Online:
Received:
Accepted:

Abstract

A draft sequence of the genome of Brachypodium distachyon, the emerging grass model, was recently released. This represents a unique opportunity to determine its functional diversity compared to the genomes of other model species. Using homology mapping of assembled expressed sequence tags with chromosome scale pseudomolecules, we identified 128 alternative splicing events in B. distachyon. Our study identified that retention of introns is the major type of alternative splicing events (53%) in this plant and highlights the prevalence of splicing site recognition for definition of introns in plants. We have analyzed the compositional profiles of exon–intron junctions by base-pairing nucleotides with U1 snRNA which serves as a model for describing the possibility of sequence conservation. The alternative splicing isoforms identified in this study are novel and represent one of the potentially biologically significant means by which B. distachyon controls the function of its genes. Our observations serve as a basis to understand alternative splicing events of cereal crops with more complex genomes, like wheat or barley.

Keywords

Alternative splicing Brachypodium distachyon Exon–intron junction Intron retention U1 snRNA 
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Notes

Acknowledgments

G Sablok and PK Gupta thanks Department of Genetics and Plant Breeding for providing the computational facilities. XJ Min was supported by the YSU Research Professorship and the STEM Dean’s reassigned time. Research work in F. Vazquez lab is supported by an Ambizione Grant (PZ00P3_126329/1) of the Swiss National Science Foundation.

Supplementary material

10529_2010_475_MOESM1_ESM.xls (48 kb)
Supplementary material 1 (XLS 47 kb)

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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Gaurav Sablok
    • 1
  • P. K. Gupta
    • 1
  • Jong-Min Baek
    • 2
  • Franck Vazquez
    • 3
  • Xiang Jia Min
    • 4
  1. 1.Molecular Biology and Bioinformatics Laboratory, Department of Genetics and Plant BreedingChaudhary Charan Singh UniversityMeerutIndia
  2. 2.College of Agricultural and Environmental Sciences, Genomics FacilityUniversity of CaliforniaDavisUSA
  3. 3.Botanical InstituteZurich-Basel Plant Science Center, University of BaselBaselSwitzerland
  4. 4.Department of Biological Sciences, Center for Applied Chemical BiologyYoungstown State UniversityYoungstownUSA

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