TOOLS-PGR Alternative Splice Isoforms in Plant Genomes: Collection, Characterization and Evolutionary Relationships

University Of Florida, Gainesville FL

Investigators

Abstract

Expressing a eukaryotic gene stimulates transcription, which produces an mRNA transcript. Most often, the mRNA transcript is used as a template for translation into protein molecules. The transcription process produces a pre-messenger RNA, which is extensively processed to yield a mature mRNA ready for translation. Because the structure of most genes in animals and plants is one where the DNA sequence information used to specify protein (exons) is interspersed with stretches of DNA sequences that are non-coding (introns), one of the modifications that pre-mRNA undergo is the splicing out of intron sequence and the joining of the exon sequences. In many cases, this splicing process can be directed to purposefully skip exons, retain introns, and change the exon boundaries. This process, called Alternative Splicing (AS), enables the production of distinctly different messages from a single gene, and this can increase the number of different proteins a gene is able to produce. The extent and roles of AS in plants is not well understood; however, a thorough understanding of AS, especially within crop plants that produce food, industrial and fuel products, is necessary to enable prediction of phenotype from genotype and utilize crop genetic resources to their full potential. The outcomes of this project will be the genome-wide identification and public release of AS isoforms within 42 plant species. Analysis of these data during this project will provide a better understanding of the evolutionary history of AS in plants and provide access to some of the genetic features involved in regulating AS. With regard to outreach and training, this project will develop a course-based undergraduate research experience (CURE) that provides hands-on training for undergraduate life science majors in modern genomics, lab techniques, high performance computing and "big data" OMICS analysis, skill sets that have become increasingly important in research and medicine. An understanding of the extent of AS in plants and the biological processes that AS transcript isoforms impact are not well established. However, it is proposed that alternatively spliced transcripts may play significant roles during growth, development and stress response, and failure to identify these and understand their significance hampers the understanding of gene to phenotype, and slows crop improvement efforts. The long-term goal of this research is to understand the function, regulation and evolution of alternative splicing (AS) in plants. Specifically, the project will address the following questions: 1) What genes produce alternatively spliced transcripts and what processes do they affect? 2) How is AS in plants regulated? 3) What are the evolutionary histories of AS isoforms in plants? To address these questions, this project will identify and characterize AS events broadly from available public data and investigate their ancestral states in plants. Specifically, AS isoforms will be identified across and within 46 genomes representing 42 plant species broadly distributed across the kingdom. Once identified, AS isoforms will be characterized with regard to their conservation and evolutionary history. Finally, evolutionary conserved AS events will be selected to investigate sequence and epigenetic features associated with AS that may play a regulatory role. All data and resources generated in this project will be made available to the public through the project website, as well as long-term through the NCBI's SRA and CyVerse.