Grant de Jong

Grant de Jong

Graduate student studying genomics

Talks and presentations

Transcriptomic response of multiple Brassica species to Sclerotinia sclerotiorum infection

June 09, 2019

Talk, University of Guelph, Plant Canada Conference, Guelph, ON, Canada

To investigate the interplay between polyploid gene expression and biotic stress response, Brassica napus, Brassica oleracea, Brassica rapa, and a synthetic Brassica napus (formed directly from the aforementioned parental species of B. napus) were subjected to the economically devastating fungus Sclerotinia sclerotiorum. RNA-Seq analysis of these pathosystems revealed wide-spread transcriptomic changes involving both constitutive gene expression and alternative splicing. Cross-species comparisons showed a concerted response between all assayed Brassica species characterized by the up-regulation of jasmonic acid signalling pathways, cell-wall defense genes, chitinases, and pathogen responsive genes. Subgenome comparisons also showed considerable non-parental gene expression patterns in the synthetic Brassica napus, in addition to a C-subgenome expression bias, suggesting transcriptome reprogramming occurs relatively quickly following polyploidization.

Evolution of paralog gene expression patterns among paleopolyploid and cytogenetically polyploid plants

April 30, 2019

Exit seminar, University of British Columbia, Department of Botany, Vancouver BC, Canada

Using RNA-Seq data I have surveyed the transcriptomes of root developmental zones and their constituent cell-types in paleopolyploid Arabidopsis thaliana. Incorporating such high-resolution data with further in silico analyses, I have demonstrated near-complete divergence in both gene expression and splicing patterns.

A survey of ancient paralog alternative splicing patterns in Arabidopsis thaliana root cell-types

April 05, 2019

Lightning talk, University of British Columbia, Department of Botany, Vancouver BC, Canada

Whole-genome duplication events have played an extensive role in the evolution of flowering plants. The sudden doubling of genetic material can expedite large scale changes in gene function and expression patterns. Alternative splicing (AS) offers an avenue with which genes duplicated in polyploidy events (homeologs) may contribute to such functional diversity. AS produces multiple transcript isoforms through the differential removal of introns from the primary mRNA transcript. This process contributes to the function complexity of the cell by expanding both proteomic diversity and mechanisms of post-transcriptional regulation. While there is evidence of considerable divergence in alternative splicing between homeologous genes, the extent to which these differences manifest in different tissue-types is less understood. Using RNA-Seq data I have surveyed the transcriptomes of root tissues in paleopolyploid Arabidopsis thaliana. Assessing the distribution of splicing events between homeolog pairs, I am determining the extent of homeologous AS divergence across multiple zones of root development. Consequently, I have identified a high degree of asymmetry in alternative splicing patterns between several gene pairs. These results will hopefully provide insight into how alternative splicing contributes to tissue-specific variation following gene duplication in plants.

Introduction to RNA-Seq informatics

November 01, 2018

Tutorial, University of British Columbia, BIOL430, Vancouver, British Columbia

A multi-session tutorial educating students on the fundamentals of RNA-seq informatics (analytical workflow, pipeline construction, and common tools.