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Genomic Approaches to Analyze Alternative Splicing, A Key Regulator of Transcriptome and Proteome Diversity in Brachypodium distachyon

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Brachypodium Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1667))

Abstract

Alternative splicing (AS) promotes transcriptome and proteome diversity in plants, which influences growth and development, and host responses to stress. Advancements in next-generation sequencing, bioinformatics, and computational biology tools have allowed biologists to investigate AS landscapes on a genome-wide scale in several plant species. Furthermore, the development of Brachypodium distachyon (Brachypodium) as a model system for grasses has facilitated comparative studies of AS within the Poaceae. These analyses revealed a plethora of genes in several biological processes that are alternatively spliced and identified conserved AS patterns among monocot and dicot plants. In this chapter, using a Brachypodium-virus pathosystem as a research template, we provide an overview of genomic and bioinformatic tools that can be used to investigate constitutive and alternative splicing in plants.

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Acknowledgment

This study was supported by funds from USDA-NIFA-AFRI (2016-67013-24738) to K-B.G.S. and K.K.M., Texas A&M AgriLife Research Bioenergy/Bioproducts Grant (124738-96210) to K.K.M.

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Authors and Affiliations

  1. Texas A&M AgriLife Research & Extension Center, 2415 E. Highway 83, Weslaco, TX, 78596, USA

    Sonia Irigoyen, Renesh H. Bedre & Kranthi K. Mandadi

  2. Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX, 77843, USA

    Karen-Beth G. Scholthof & Kranthi K. Mandadi

Authors
  1. Sonia Irigoyen
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  2. Renesh H. Bedre
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  3. Karen-Beth G. Scholthof
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  4. Kranthi K. Mandadi
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Corresponding author

Correspondence to Kranthi K. Mandadi .

Editor information

Editors and Affiliations

  1. Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach IASMA, Trentino, Italy

    Gaurav Sablok

  2. Sabanci University, Istanbul, Turkey

    Hikmet Budak

  3. Climate Change Cluster (C3), University of Technology Sydney, Sydney, New South Wales, Australia

    Peter J. Ralph

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Irigoyen, S., Bedre, R.H., Scholthof, KB.G., Mandadi, K.K. (2018). Genomic Approaches to Analyze Alternative Splicing, A Key Regulator of Transcriptome and Proteome Diversity in Brachypodium distachyon . In: Sablok, G., Budak, H., Ralph, P. (eds) Brachypodium Genomics. Methods in Molecular Biology, vol 1667. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7278-4_7

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  • DOI: https://doi.org/10.1007/978-1-4939-7278-4_7

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7276-0

  • Online ISBN: 978-1-4939-7278-4

  • eBook Packages: Springer Protocols

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