UBC Theses and Dissertations
Evolution of duplicated non-coding RNAs in plants Wang, Sishuo
Non-coding RNAs (ncRNAs) consist of microRNAs, lincRNAs (long intergenic non-coding RNA), rRNAs, tRNAs and the RNAs from other types of genes that do not have the potential to be protein-coding. Non-coding RNAs play various roles in cellular processes. Gene duplication is a major force in gene evolution and the evolution of duplicated protein-coding genes has been studied extensively. Whether the same evolutionary principles hold true for ncRNAs, especially lincRNAs, is still poorly understood particularly in plants. I characterized the effects of the change in microRNA binding sites on the divergence of multiple types of duplicated genes in Arabidopsis thaliana and Brassica rapa (Chapter 2). I found that the vast majority of duplicated genes showed divergence in their microRNA binding sites that could be associated with their expression and functional divergence. To better understand the evolutionary dynamics of lincRNAs in plants, I analyzed the sequence evolution of lincRNAs from five species (Arabidopsis thaliana, Oryza sativa ssp. japonica, Zea mays, Medicago truncatula and Solanum lycopersicum) across 55 plant genomes (Chapter 3). My analyses revealed that lincRNAs show more rapid sequence divergence compared with protein-coding genes and microRNAs. I also analyzed the expression conservation of lincRNAs between closely related species and showed rapid expression evolution of lincRNAs. I also identified a considerable number of conserved regions in the sequence of lincRNAs that are under stronger selection constraints than surrounding regions. To investigate the role of gene duplication in the evolution of plant lincRNAs, I identified duplicated lincRNAsiii in several plant species (Chapter 4). I compared the expression patterns between duplicated lincRNAs using RNA-seq data from multiple tissue types and developmental stages, revealing extensive expression divergence of lincRNAs. Finally, I studied the effects of polyploidy and abiotic stress on the expression of lincRNAs in diploid and polyploid Brassica species (Chapter 5). My results showed extensive divergence of the expression of lincRNAs after polyploidy and in response to different stresses. This thesis provides new insights into lincRNA evolution and fates of lincRNAs after duplication in flowering plants.
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