Winkelmüller, Thomas Maximilian (2018). Comparative transcriptomics within Arabidopsis thaliana accessions and across Brassicaceae species reveal evolutionary conserved and lineage-specific expression signatures in pattern-triggered immunity. PhD thesis, Universität zu Köln.

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Abstract

In nature plants are surrounded by a diverse set of beneficial and harmful microbes. Plants can recognize these microbes by sensing conserved microbe-associated molecular patterns (MAMPs) via cell surface-localized receptors, leading to the activation of pattern-triggered immunity (PTI). PTI protects plants from potential microbial pathogens through induction of a myriad of defence responses including massive transcriptional reprogramming in Arabidopsis thaliana. Despite the significance of PTI responses for the plant adaptation to diverse microbes, we currently do not understand the importance of this massive transcriptional reprogramming, whether PTI responses are conserved, and how they evolved. Here I used comparative transcriptomics to analyse the responses of six A. thaliana accessions and three additional Brassicaceae species to the bacterial MAMP flg22. This analysis revealed that large parts of the transcriptional response to flg22 are conserved among Brassicaceae species, suggesting that these are under purifying selection over the Brassicaceae evolution and that flg22-triggered transcriptional reprogramming during PTI is important. At the same time, I found that a considerable fraction of flg22-responsive genes showed species-specific expression signatures. Moreover, variation in flg22-triggered transcriptional reprogramming was incongruent with the Brassicaceae phylogeny, suggesting that adaptive evolution acts on subsets of flg22-responsive genes. In contrast, flg22-triggered transcriptional responses among genetically and geographically diverse A. thaliana accessions were extremely conserved. Thus, inter-species clearly exceeds intra-species transcriptome variation in response to flg22. This further suggests the adaptive nature of gene expression evolution and points to a small contribution of neutral transcriptome evolution during PTI within Brassicaceae. Regulatory regions of conserved flg22-inducible genes were highly enriched for WRKY transcription factor (TF)-binding motifs throughout all tested species. Interestingly, regulatory regions of genes specifically induced in A. thaliana or Capsella rubella were enriched for WRKY-binding motifs only in A. thaliana or C. rubella, respectively. This indicates that WRKY TFs play an important role in flg22-triggered gene induction and that the gain of WRKY-binding motifs in regulatory regions accounts for some species-specific expression changes. Taken together, this study advances the field of comparative transcriptomics by providing empirical analysis for the evolution of stress-induced transcriptome changes within and across plant species with a defined phylogenetic framework.

Item Type: Thesis (PhD thesis)
Creators:
CreatorsEmailORCIDORCID Put Code
Winkelmüller, Thomas Maximilianthomas.winkelmueller@live.comUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-83207
Date: 19 February 2018
Language: English
Faculty: Faculty of Mathematics and Natural Sciences
Divisions: Außeruniversitäre Forschungseinrichtungen > MPI for Plant Breeding Research
Subjects: Natural sciences and mathematics
Life sciences
Agriculture
Uncontrolled Keywords:
KeywordsLanguage
PTI; Comparative transcriptomics; Brassicaceae; transcriptome evolution; Immunity; plant-microbe interactionUNSPECIFIED
Date of oral exam: 11 April 2018
Referee:
NameAcademic Title
Schulze-Lefert, PaulProf. Dr.
Kopriva, StanislavProf. Dr.
Refereed: Yes
URI: http://kups.ub.uni-koeln.de/id/eprint/8322

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