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Evolution of duplicated non-coding RNAs in plants Wang, Sishuo
Abstract
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.
Item Metadata
Title |
Evolution of duplicated non-coding RNAs in plants
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Creator | |
Publisher |
University of British Columbia
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Date Issued |
2017
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Description |
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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Genre | |
Type | |
Language |
eng
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Date Available |
2018-10-31
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Provider |
Vancouver : University of British Columbia Library
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Rights |
Attribution-NonCommercial-NoDerivatives 4.0 International
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DOI |
10.14288/1.0357061
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URI | |
Degree | |
Program | |
Affiliation | |
Degree Grantor |
University of British Columbia
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Graduation Date |
2017-11
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Campus | |
Scholarly Level |
Graduate
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Rights URI | |
Aggregated Source Repository |
DSpace
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Attribution-NonCommercial-NoDerivatives 4.0 International