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

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 

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)

References

  1. Ast G (2004) How did alternative splicing evolve? Nat Rev Genet 5:773–782CrossRefPubMedGoogle Scholar
  2. Baek JM, Han P, Iandolino A, Cook DR (2008) Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and rice. Plant Mol Biol 674:499–510CrossRefGoogle Scholar
  3. Black DL (2003) Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 72:291–336CrossRefPubMedGoogle Scholar
  4. Campbell MA, Haas BJ, Hamilton JP, Mount SM, Buell CR (2006) Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7:327CrossRefPubMedGoogle Scholar
  5. Cana EF, Macadre C, Sevignac M, David P, Langin T, Geffroy V (2005) Distinct post-transcriptional modifications result into seven alternative transcripts of the CC-NBS-LRR gene JA1tr of Phaseolus vulgaris. Theor Appl Genet 110:895–905CrossRefGoogle Scholar
  6. Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler TC (2010) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 20:45–58CrossRefPubMedGoogle Scholar
  7. Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 8:967–974PubMedGoogle Scholar
  8. Foissac S, Sammeth M (2007) ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res 35(Web server issue):W297–W299CrossRefPubMedGoogle Scholar
  9. Garvin DF (2007) Brachypodium: a new monocot model plant system emerges. J Sci Food Agric 87:1177–1179CrossRefGoogle Scholar
  10. Gupta S, Zink D, Korn B, Vingron M, Haas SA (2004) Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics 20:2579–2585CrossRefPubMedGoogle Scholar
  11. Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877CrossRefPubMedGoogle Scholar
  12. Huo N, Lazo GR, Vogel JP, You FM, Ma Y, Hayden DM, Derr DC, Hill TA, Dvorak J, Anderson OD, Luo MC, Gu YQ (2008) The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Funct Integr Genomics 8:135–147CrossRefPubMedGoogle Scholar
  13. Johnson J, Castle J, Garrett-Engele P, Kan Z, Loerch P, Armour C, Santos R, Schadt E, Stoughton R, Shoemaker D (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302:2141–2144CrossRefPubMedGoogle Scholar
  14. Ko CH, Brendel V, Taylor RD, Walbot V (1998) U-richness is a defining feature of plant introns and may function as an intron recognition signal in maize. Plant Mol Biol 36:573–583CrossRefPubMedGoogle Scholar
  15. Kumar S, Mohan A, Balyan HS, Gupta PK (2009) Orthology between genomes of Brachypodium, wheat and rice. BMC Res Notes 2:93CrossRefPubMedGoogle Scholar
  16. Labadorf A, Link A, Rogers MF, Thomas J, Reddy ASN, Ben-Hur A (2010) Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. BMC Genomics 111:14Google Scholar
  17. Lee SW, Choi JP, Kim HJ, Hong JM, Hur CG (2008) ASPMF: a new approach for identifying alternative splicing isoforms using peptide mass fingerprinting. Biochem Biophys Res Commun 377:253–256CrossRefPubMedGoogle Scholar
  18. Lorkovic ZJ, Wieczorek Kirk DA, Lambermon MH, Filipowicz W (2000) Pre-mRNA splicing in higher plants. Trends Plant Sci 5:160–167CrossRefPubMedGoogle Scholar
  19. Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH et al (2009) CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res 37(Database issue):D205–D210CrossRefPubMedGoogle Scholar
  20. McKeown M (1992) Alternative mRNA splicing. Annu Rev Cell Biol 8:133–155CrossRefPubMedGoogle Scholar
  21. Modrek B, Resch A, Grasso C, Lee C (2001) Genome wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res 29:2850–2859CrossRefPubMedGoogle Scholar
  22. Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O (2005) Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes. Gene 364:53–62CrossRefPubMedGoogle Scholar
  23. Pan Q, Shai O, Lee L, Frey B, Blencowe B (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413–1415CrossRefPubMedGoogle Scholar
  24. Quesada V, Macknight R, Dean C, Simpson GG (2003) Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time. EMBO J 22:3142–3152CrossRefPubMedGoogle Scholar
  25. Reddy AS (2007) Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu Rev Plant Biol 58:267–294CrossRefPubMedGoogle Scholar
  26. Roca X, Sachidanandam R, Krainer AR (2005) Determinants of the inherent strength of human 5′ splice sites. RNA 11:683–698CrossRefPubMedGoogle Scholar
  27. Stamm S, Ben-Ari S, Rafalska I, Tang Y, Zhang Z, Toiber D, Thanaraj TA, Soreq H (2005) Function of alternative splicing. Gene 344:1–20CrossRefPubMedGoogle Scholar
  28. The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768CrossRefGoogle Scholar
  29. Wang B, Brendel V (2006) Genome wide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci USA 103:7175–7180CrossRefPubMedGoogle Scholar
  30. Wang BB, O’Toole M, Brendel V, Young ND (2008) Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes. BMC Plant Biol 8:17CrossRefPubMedGoogle Scholar
  31. Xiao YL, Smith SR, Ishmael N, Redman JC, Kumar N, Monaghan EL, Ayele M, Haas BJ, Wu HC, Town CD (2005) Analysis of cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants. Plant Physiol 139:1323–1337CrossRefPubMedGoogle Scholar

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

Personalised recommendations