Pathogen Genetic Control of Transcriptome Variation in the Arabidopsis thaliana – Botrytis cinerea Pathosystem

In plant–pathogen relations, disease symptoms arise from the interaction of the host and pathogen genomes. Host–pathogen functional gene interactions are well described, whereas little is known about how the pathogen genetic variation modulates both organisms’ transcriptomes. To model and generate hypotheses on a generalist pathogen control of gene expression regulation, we used the Arabidopsis thaliana–Botrytis cinerea pathosystem and the genetic diversity of a collection of 96 B. cinerea isolates. We performed expression-based genome-wide association (eGWA) for each of 23,947 measurable transcripts in Arabidopsis (host), and 9267 measurable transcripts in B. cinerea (pathogen). Unlike other eGWA studies, we detected a relative absence of locally acting expression quantitative trait loci (cis-eQTL), partly caused by structural variants and allelic heterogeneity hindering their identification. This study identified several distantly acting trans-eQTL linked to eQTL hotspots dispersed across Botrytis genome that altered only Botrytis transcripts, only Arabidopsis transcripts, or transcripts from both species. Gene membership in the trans-eQTL hotspots suggests links between gene expression regulation and both known and novel virulence mechanisms in this pathosystem. Genes annotated to these hotspots provide potential targets for blocking manipulation of the host response by this ubiquitous generalist necrotrophic pathogen.

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The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana

Bioinformatics ◽

10.1093/bioinformatics/bty1053 ◽

2018 ◽

Vol 35 (16) ◽

pp. 2718-2723 ◽

Cited By ~ 3

Author(s):

Tamir Tuller ◽

Alon Diament ◽

Avital Yahalom ◽

Assaf Zemach ◽

Shimshi Atar ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Arabidopsis Thaliana ◽

Gene Expression Regulation ◽

Developmental Pathways ◽

Cop9 Signalosome ◽

Supplementary Information ◽

Loss Of Function ◽

Genome Wide ◽

High Level

Abstract Motivation The COP9 signalosome is a highly conserved multi-protein complex consisting of eight subunits, which influences key developmental pathways through its regulation of protein stability and transcription. In Arabidopsis thaliana, mutations in the COP9 signalosome exhibit a number of diverse pleiotropic phenotypes. Total or partial loss of COP9 signalosome function in Arabidopsis leads to misregulation of a number of genes involved in DNA methylation, suggesting that part of the pleiotropic phenotype is due to global effects on DNA methylation. Results We determined and analyzed the methylomes and transcriptomes of both partial- and total-loss-of-function Arabidopsis mutants of the COP9 signalosome. Our results support the hypothesis that the COP9 signalosome has a global genome-wide effect on methylation and that this effect is at least partially encoded in the DNA. Our analyses suggest that COP9 signalosome-dependent methylation is related to gene expression regulation in various ways. Differentially methylated regions tend to be closer in the 3D conformation of the genome to differentially expressed genes. These results suggest that the COP9 signalosome has a more comprehensive effect on gene expression than thought before, and this is partially related to regulation of methylation. The high level of COP9 signalosome conservation among eukaryotes may also suggest that COP9 signalosome regulates methylation not only in plants but also in other eukaryotes, including humans. Supplementary information Supplementary data are available at Bioinformatics online.

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Genome wide gene expression regulation by HIP1 Protein Interactor, HIPPI: Prediction and validation

BMC Genomics ◽

10.1186/1471-2164-12-463 ◽

2011 ◽

Vol 12 (1) ◽

Cited By ~ 11

Author(s):

Moumita Datta ◽

Ananyo Choudhury ◽

Ansuman Lahiri ◽

Nitai P Bhattacharyya

Keyword(s):

Gene Expression ◽

Gene Expression Regulation ◽

Expression Regulation ◽

Genome Wide ◽

Genome Wide Gene Expression

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Pathogen genetic control of transcriptome variation in the Arabidopsis thaliana – Botrytis cinerea pathosystem

10.1101/577585 ◽

2019 ◽

Cited By ~ 1

Author(s):

Nicole E. Soltis ◽

Wei Zhang ◽

Jason A. Corwin ◽

Susanna Atwell ◽

Daniel J. Kliebenstein

Keyword(s):

Arabidopsis Thaliana ◽

Botrytis Cinerea ◽

Genetic Control ◽

Genomic Variation ◽

Disease Symptoms ◽

Complex Interactions ◽

Genome Wide ◽

Pathogen Variation ◽

Transcriptome Variation ◽

Plant Pathogen Interaction

ABSTRACTDisease symptoms arise from the interaction of the host and pathogen genomes. However, little is known about how genetic variation in the interaction modulates both organisms’ transcriptomes, especially in complex interactions like those between generalist pathogens and their plant hosts. To begin mapping how polygenic pathogen variation influences both organisms’ transcriptomes, we used the Botrytis cinerea - Arabidopsis thaliana pathosystem. We measured the co-transcriptome across a genetically diverse collection of 96 B. cinerea isolates infected on the Arabidopsis wildtype, Col-0. Using the B. cinerea genomic variation, we performed genome-wide association (GWA) for each of 23,947 measurable transcripts in the host, and 9,267 measurable transcripts in the pathogen. Unlike other eGWA studies, there was a relative absence of cis-eQTL that is likely explained by structural variants and allelic heterogeneity within the pathogen’s genome. This analysis identified mostly trans-eQTL in the pathogen with eQTL hotspots dispersed across the pathogen genome that altered the pathogen’s transcripts, the host’s transcripts, or both the pathogen and the host. Gene membership in the trans-eQTL hotspots suggests links to several known and many novel virulence mechanisms in the plant-pathogen interaction. Genes annotated to these hotspots provide potential targets for blocking manipulation of the host response by this ubiquitous generalist pathogen. This shows that genetic control over the co-transcriptome is polygenic, similar to the virulence outcome in the interaction of Botrytis cinerea on Arabidopsis thaliana.

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