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Title: Cell type-specific transcriptomic analyses of immunity in Arabidopsis thaliana roots
Author: Rich, Charlotte
ISNI:       0000 0004 8497 7256
Awarding Body: University of Warwick
Current Institution: University of Warwick
Date of Award: 2018
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Plant roots represent a complex organ consisting of different cell types with highly varied functions. Thus, the response of plant roots to environmental stresses, such as pathogen infection, requires the concerted action of many cell-types. Cell type-specific transcriptomic studies are essential to understand stress resistance signalling in such a complex organ. In this thesis, the transcriptomic response to immunity elicitation is examined at the resolution of tissues and individual cell types in two large scale RNA-seq experiments. Firstly, Fluorescence-Activated Cell Sorting combined with RNA-seq was used to produce the first high-resolution gene expression atlas of plant root immunity. The resulting data set encompassed the transcriptomes of three root cell types which had been treated by two immunity elicitors. Differential gene expression analysis revealed that both immunity elicitors induced a largely cell-type specific response with a comparatively small set of genes differentially expressed in all three cell types. This strong specificity indicates that cell identity is a strong driver of the transcriptomic immune response. Secondly, gene expression in root tips was analysed using the single cell technique Drop-seq. Clustering methods were used to identify cells from three developmental stages and multiple cell types, and the immune responses were characterised in these tissues. In an effort to interpret and predict immunity network regulation in different cell types, a novel tool entitled the Paired Motif Enrichment Tool (PMET) was developed to investigate gene regulation by combinatorial transcription factor groups. The tool identifies enriched pairs of known regulatory motifs within immune responsive gene sets and revealed that each cell type/immune response combination has a largely unique regulatory landscape. Furthermore, PMET has predicted new roles of transcription factors within immunity networks.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: QK Botany