Spatiotemporal Transcriptome Diversity and Responses to Salinity Tolerance in the Extremophyte Schrenkiella Parvula
Doctor of Philosophy (PhD)
Schrenkiella parvula is an extremophyte model related to the most widely studied plant model, Arabidopsis thaliana and Brassica crops in the mustard family (Brassicaceae). It can thrive in highly saline environments where the soil is enriched in Na+, K+, Li+, borates, and chlorides. Understanding how this extremophyte can survive high salinity with genomic adaptations can provide insight into developing stress resilient crops in the future. Gene expression of S. parvula in response to salt has been investigated using shoot and root tissue from mature vegetative-phase plants. However, prior studies have not examined the transcript diversity allowing multiple isoforms to be expressed per gene and the spatiotemporal diversity of gene expression across developmental stages and tissues in response to salt. In my research I created two novel transcriptomic resources for S. parvula and studied how specific transcripts per gene and overall expression of genes are modulated in response to salinity changes in a spatiotemporal scale. I used long-read-sequencing to create high quality reference transcripts and short-read-sequencing to quantify gene expression at a high resolution. These datasets were analyzed using computational pipelines I developed together with existing programs and machine learning methods. This study revealed that S. parvula tissues and development stages express distinct sets of isoforms or genes that respond to salinity with minimal overlaps, but their collective functions were enriched for salt stress regulation. My research contributes to the growing body of work that aims to understand how plants adapt to environmental stresses. Also, genes that were differently expressed in response to salt were largely mutually exclusive from those genes that showed differential usage of specific isoforms. With the high resolution expression maps developed into co-expression networks, I was able to identify genes that were associated with known salt-stress regulator genes, but were previously not recognized for their involvement in salt responses.
Wijesinghege, Chathura, "Spatiotemporal Transcriptome Diversity and Responses to Salinity Tolerance in the Extremophyte Schrenkiella Parvula" (2022). LSU Doctoral Dissertations. 6006.
Available for download on Friday, November 03, 2023
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