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

• DOI: 10.1007/978-1-4939-7278-4_7
• Publication Date: 2017-10-16T06:28:12Z
• Authors: Sonia Irigoyen; Renesh H. Bedre; Karen-Beth G. Sch...; Kranthi K. Mandadi
• Keywords: 2. Zero hunger; Alternative Splicing; Proteome; Gene Expression Regulation, Plant; Sequence Analysis, RNA; Tombusviridae; Genomics; 15. Life on land; Transcriptome; Brachypodium; Plant Diseases; Plant Proteins

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.