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Access Type

WSU Access

Date of Award

January 2022

Degree Type


Degree Name



Biological Sciences

First Advisor

Chuanzhu Fan


Since 2008, RNA sequencing (RNA-seq) has become an essential tool in transcriptomics research. Though identification of differential gene expression is the main purpose for most of the studies, RNA-seq is a catch-all tool including almost 100 distinct approaches which could be applied to different biological areas. Here, I presented the three applications of RNA-seq in plants: 1. I applied the comparative phylogenetic approaches with five tissues RNA-seq data from three closely related species Arabidopsis thalian, A. lyrata, and Capsella rubella to categorize the evolutionary trajectories of recent duplicate genes in the genus Arabidopsis; 2. I extended the RNA-seq dataset to 2,843 samples, which cover most of the tissues and samples under various treatments, to determine the functional divergence between recent tandem duplicate genes AT5G12950 and AT5G12960 in A. thaliana; 3. I used the RNA-seq data extracted from four tissues of non-native subspecies Phragmites australis (spp. australis) to demonstrate the necessity of de novo transcriptome assembly process by comparing forty-six transcriptomes via different de novo assembly tools and multiple parameter settings. Moreover, the first two works further showed related mechanisms of recent gene duplication, as the first one detected the impact of the retention of recent duplicate genes from associated epigenetic changes on the genome-wide level, and the second one revealed the different phenotypic effects by the distinct function of AT5G12950 and AT5G12960. In the last study, we verified that the optimal transcriptome selected from forty-six transcriptomes is a valuable resource for future P. australis studies. Overall, based on these three studies, RNA-seq will continue to be applied to diverse biological questions by adding new approaches from the development of technology and methodology.

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