利用基因组学方法分析二穗短柄草转录组和蛋白质组多样性的关键调控因子——可变剪接

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

作者信息

Irigoyen Sonia, Bedre Renesh H, Scholthof Karen-Beth G, Mandadi Kranthi K

机构信息

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

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

出版信息

Methods Mol Biol. 2018;1667:73-85. doi: 10.1007/978-1-4939-7278-4_7.

DOI:10.1007/978-1-4939-7278-4_7

PMID:29039005

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.

摘要

可变剪接（AS）促进了植物转录组和蛋白质组的多样性，这影响着植物的生长发育以及宿主对胁迫的响应。新一代测序技术、生物信息学和计算生物学工具的进步，使得生物学家能够在全基因组范围内研究多种植物物种的可变剪接情况。此外，短柄草作为禾本科植物的模式系统，其发展促进了禾本科内部可变剪接的比较研究。这些分析揭示了多个生物学过程中大量发生可变剪接的基因，并鉴定出了单子叶和双子叶植物之间保守的可变剪接模式。在本章中，我们以短柄草 - 病毒互作体系作为研究模板，概述了可用于研究植物组成型剪接和可变剪接的基因组及生物信息学工具。