Eric B. Holub
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View article: Fork to farm: reverse engineering a food system
Fork to farm: reverse engineering a food system Open
Using two new common ( Phaseolus ) dry bean varieties developed for UK growing conditions, the BeanMeals project explored how to pursue ‘fork to farm’ systemic innovation in the food system to transform institutional catering and home-cook…
View article: The Arabidopsis <scp> <i>WRR4A</i> </scp> and <scp> <i>WRR4B</i> </scp> paralogous <scp>NLR</scp> proteins both confer recognition of multiple <i>Albugo candida</i> effectors
The Arabidopsis <span> <i>WRR4A</i> </span> and <span> <i>WRR4B</i> </span> paralogous <span>NLR</span> proteins both confer recognition of multiple <i>Albugo candida</i> effectors Open
Summary The oomycete Albugo candida causes white blister rust, an important disease of Brassica crops. Distinct races of A. candida are defined by their capacity to infect different host plant species. Each A. candida race encodes secreted…
View article: Evolutionary trade‐offs at the Arabidopsis <i>WRR4A</i> resistance locus underpin alternate <i>Albugo candida</i> race recognition specificities
Evolutionary trade‐offs at the Arabidopsis <i>WRR4A</i> resistance locus underpin alternate <i>Albugo candida</i> race recognition specificities Open
SUMMARY The oomycete Albugo candida causes white rust of Brassicaceae , including vegetable and oilseed crops, and wild relatives such as Arabidopsis thaliana . Novel White Rust Resistance ( WRR ) genes from Arabidopsis enable new insights…
View article: Evolutionary trade-offs at the Arabidopsis<i>WRR4A</i>resistance locus underpin alternate<i>Albugo</i>candida recognition specificities
Evolutionary trade-offs at the Arabidopsis<i>WRR4A</i>resistance locus underpin alternate<i>Albugo</i>candida recognition specificities Open
Summary The oomycete Albugo candida causes white rust of Brassicaceae, including vegetable and oilseed crops, and wild relatives such as Arabidopsis thaliana . Novel White Rust Resistance ( WRR )-genes from Arabidopsis enable new insights …
View article: An improved assembly of the<i>Albugo candida</i>Ac2V genome reveals the expansion of the “CCG” class of effectors
An improved assembly of the<i>Albugo candida</i>Ac2V genome reveals the expansion of the “CCG” class of effectors Open
Albugo candida is an obligate oomycete pathogen that infects many plants in the Brassicaceae family. We re-sequenced the genome of isolate Ac2V using PacBio long reads and constructed an assembly augmented by Illumina reads. The Ac2VPB gen…
View article: The Arabidopsis <i>WRR4A</i> and <i>WRR4B</i> paralogous NLR proteins both confer recognition of multiple <i>Albugo candida</i> effectors
The Arabidopsis <i>WRR4A</i> and <i>WRR4B</i> paralogous NLR proteins both confer recognition of multiple <i>Albugo candida</i> effectors Open
Summary The oomycete Albugo candida causes white blister rust, an important disease of Brassica crops. Distinct races of A. candida are defined by their specificity for infecting different host species. The White Rust Resistance 4 ( WRR4 )…
View article: The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression
The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression Open
Plant NLR-type receptors serve as sensitive triggers of host immunity. Their expression has to be well-balanced, due to their interference with various cellular processes and dose-dependency of their defense-inducing activity. A genetic "a…
View article: Population Genetics of the Highly Polymorphic RPP8 Gene Family
Population Genetics of the Highly Polymorphic RPP8 Gene Family Open
Plant nucleotide-binding domain and leucine-rich repeat containing (NLR) genes provide some of the most extreme examples of polymorphism in eukaryotic genomes, rivalling even the vertebrate major histocompatibility complex. Surprisingly, t…
View article: Population genetics of the highly polymorphic<i>RPP8</i>gene family
Population genetics of the highly polymorphic<i>RPP8</i>gene family Open
Plant NLR resistance genes provide some of the most extreme examples of polymorphism in eukaryotic genomes, rivalling even the vertebrate major histocompatibility complex. Surprisingly, this is also true in Arabidopsis thaliana , a predomi…
View article: Transgressive segregation reveals mechanisms of<i>Arabidopsis</i>immunity to<i>Brassica</i>-infecting races of white rust (<i>Albugo candida</i>)
Transgressive segregation reveals mechanisms of<i>Arabidopsis</i>immunity to<i>Brassica</i>-infecting races of white rust (<i>Albugo candida</i>) Open
Arabidopsis thaliana accessions are universally resistant at the adult leaf stage to white rust ( Albugo candida ) races that infect the crop species Brassica juncea and Brassica oleracea . We used transgressive segregation in recombinant …
View article: The Arabidopsis <scp>RRM</scp> domain protein <scp>EDM</scp>3 mediates race‐specific disease resistance by controlling H3K9me2‐dependent alternative polyadenylation of <i><scp>RPP</scp>7</i> immune receptor transcripts
The Arabidopsis <span>RRM</span> domain protein <span>EDM</span>3 mediates race‐specific disease resistance by controlling H3K9me2‐dependent alternative polyadenylation of <i><span>RPP</span>7</i> immune receptor transcripts Open
Summary The NLR ‐receptor RPP 7 mediates race‐specific immunity in Arabidopsis. Previous screens for enhanced downy mildew ( edm ) mutants identified the co‐chaperone SGT 1b ( EDM 1) and the PHD ‐finger protein EDM 2 as critical regulators…
View article: <i>Albugo candida</i> race diversity, ploidy and host‐associated microbes revealed using DNA sequence capture on diseased plants in the field
<i>Albugo candida</i> race diversity, ploidy and host‐associated microbes revealed using DNA sequence capture on diseased plants in the field Open
Summary Physiological races of the oomycete Albugo candida are biotrophic pathogens of diverse plant species, primarily the Brassicaceae, and cause infections that suppress host immunity to other pathogens. However, A. candida race diversi…
View article: Comparative genomics of <i>Pseudomonas syringae</i> reveals convergent gene gain and loss associated with specialization onto cherry ( <i>Prunus avium</i> )
Comparative genomics of <i>Pseudomonas syringae</i> reveals convergent gene gain and loss associated with specialization onto cherry ( <i>Prunus avium</i> ) Open
Summary Genome‐wide analyses of the effector‐ and toxin‐encoding genes were used to examine the phylogenetics and evolution of pathogenicity amongst diverse strains of Pseudomonas syringae causing bacterial canker of cherry ( Prunus avium …
View article: A Suppressor/Avirulence Gene Combination in Hyaloperonospora arabidopsidis Determines Race Specificity in Arabidopsis thaliana
A Suppressor/Avirulence Gene Combination in Hyaloperonospora arabidopsidis Determines Race Specificity in Arabidopsis thaliana Open
The pathosystem of Arabidopsis thaliana and diploid biotrophic oomycete Hyaloperonospora arabidopsidis (Hpa) has been a model for investigating the molecular basis of Flor's gene-for-gene hypothesis. The isolates Hpa-Noks1 and Hpa-Cala2 ar…
View article: Comparative genomics of<i>Pseudomonas syringae</i>reveals convergent gene gain and loss associated with specialisation onto cherry (<i>Prunus avium</i>)
Comparative genomics of<i>Pseudomonas syringae</i>reveals convergent gene gain and loss associated with specialisation onto cherry (<i>Prunus avium</i>) Open
Summary Genome-wide analyses of the effector- and toxin-encoding genes were used to examine the phylogenetics and evolution of pathogenicity amongst diverse strains of Pseudomonas syringae causing bacterial canker of cherry ( Prunus avium …
View article: Genome-Wide Linkage and Association Mapping of Halo Blight Resistance in Common Bean to Race 6 of the Globally Important Bacterial Pathogen
Genome-Wide Linkage and Association Mapping of Halo Blight Resistance in Common Bean to Race 6 of the Globally Important Bacterial Pathogen Open
Pseudomonas syringae pv. phaseolicola (Psph) Race 6 is a globally prevalent and broadly virulent bacterial pathogen with devastating impact causing halo blight of common bean (Phaseolus vulgaris L.). Common bean lines PI 150414 and CAL 143…
View article: Additional file 24: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana
Additional file 24: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana Open
Data analyzed in Fig. 8. Spreadsheets showing the data analyzed in Fig. 8b. (XLSX 14 kb)
View article: Additional file 17: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana
Additional file 17: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana Open
Data analyzed in Fig. 6. Spreadsheets showing the data analyzed in Fig. 6a and b. (XLSX 17 kb)
View article: Additional file 3: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana
Additional file 3: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana Open
Differentially regulated genes at each time point and overlap between genes regulated by each pathogen. Comparisons of the Arabidopsis genes differentially expressed during infection with AlNc2 and/or AlNc14 over a time course. (XLSX 104 k…
View article: Additional file 13: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana
Additional file 13: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana Open
Data analyzed in Additional files. Spreadsheets showing the data analyzed in Additional files 11, 16 and 20. (XLSX 27 kb)
View article: Additional file 8: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana
Additional file 8: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana Open
Gene ontology (GO) terms within biological processes that are significantly enriched amongst genes down-regulated in the expression profiling. Results of the GO enrichment analysis for down-regulated genes. (XLSX 157 kb)
View article: Additional file 2: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana
Additional file 2: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana Open
Arabidopsis genes differently regulated in expression profiling through randomly sheared cDNA tag sequencing (EXPRSS) data. Lists of the Arabidopsis genes that were differentially expressed in AlNc2 and AlNc14 infected tissue over a time c…
View article: Additional file 19: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana
Additional file 19: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana Open
Data analyzed in Fig. 7. Spreadsheets showing the data analyzed in Fig. 7aâ c. (XLSX 17 kb)
View article: Additional file 25: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana
Additional file 25: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana Open
Data analyzed in Fig. 9. Spreadsheets showing the data analyzed in Fig. 9c and j. (XLSX 16 kb)
View article: Additional file 22: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana
Additional file 22: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana Open
Benzo-(1,2,3)-thiadiazole-7-carbothioic acid (BTH) regulated genes during Albugo infection time course. Spreadsheet showing the expression of Arabidopsis BTH regulated genes during infection with Albugo. (XLSX 346 kb)
View article: Additional file 7: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana
Additional file 7: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana Open
Gene ontology (GO) terms within biological processes that are significantly enriched amongst genes up-regulated in the expression profiling. Results of the GO enrichment analysis for up-regulated genes. (XLSX 328 kb)
View article: Additional file 10: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana
Additional file 10: of Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana Open
Data analyzed in Fig. 4. Spreadsheets showing the data analyzed in Fig. 4aâ d. (XLSX 30 kb)