Posts by Collection

portfolio

Portfolio item number 1

Short description of portfolio item number 1

Portfolio item number 2

Short description of portfolio item number 2

publications

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

Published in TBD, 2020

While the extent to which AS influences functional or regulatory divergence in ancient paralogs has been previously investigated, such as those derived from the α-WGD event in Arabidopsis thaliana, the manifestation of this divergence in distinct tissues and cell-types is less understood. 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, this demonstrates near-complete divergence in both gene expression and splicing patterns.

Recommended citation: TBD TBD

Analysis of multiple Brassica transcriptomes reveals subgenome dominance in the response of Brassica napus to Sclerotinia sclerotiorum

Published in TBD, 2020

Allopolyploids are organisms which form due to the hybridization between two re- lated parental species, resulting in a whole-genome duplication. This phenomenon is particularly common among agronomically relevant plant species, partly due to the adaptive potential conferred through an influx of genetic material, and corre- spondingly, enhanced genetic diversity. However, these species must reconcile di- vergent parental transcriptomes, which can have profound consequences on global gene expression patterns — especially when confronted with environmental stres- sors. I used RNA-sequencing to investigate not only the response of Brassica na- pus to pathogen stress — elicited by the fungal necrotroph Sclerotinia sclerotio- rum — but also how this response manifested in its parental species, Brassica rapa and Brassica oleracea, and a resynthesized allopolyploid B. napus formed directly from these species. This allowed me to identify a distinct bias to towards the B. oleracea-derived genome in both polyploids, which consequentially influenced the defence response of B. napus.

Recommended citation: TBD TBD

talks

Introduction to RNA-Seq informatics

Published: November 01, 2018

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

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

Published: April 05, 2019

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.

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

Published: April 30, 2019

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.

Transcriptomic response of multiple Brassica species to Sclerotinia sclerotiorum infection

Published: June 09, 2019

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.

Grant de Jong