Final Report Summary - ALBUGON (Genomics and effectoromics to understand defence suppression and disease resistance in Arabidopsis-Albugo candida interactions)
The project has dramatically advanced our understanding of the white rust pathogens of Brassicaceae, Albugo candida and A. laibachii. We had three goals.
1- We aimed to define genome sequences for multiple strains of Albugo. This was achieved; we determined sequences for 7 races of A. candida, and 6 races of A. laibachii.
2- We aimed to define the Albugo effector repertoire in order to better understand the remarkable capacity of Albugo to impose enhanced disease susceptibility. The risky method in the proposal (delivery of 100s of effector candidates from Pseudomonas) was unsuccessful, and we adopted a slower strategy to define Albugo effectors, by finding Albugo genes recognized by White Rust Resistance (WRR) genes.
3- We aimed to reveal the basis of non-host Resistance (NHR) in Arabidopsis to Brassica-infecting races of Albugo. The Pseudomonas delivery method did not work, so we used a different but slower method, and cloned three new Arabidopsis NHR genes for Albugo resistance.
1, 2- ALBUGO GENOMICS and EFFECTOROMICS. We were among the first to use Illumina sequencing to define a pathogen genome, and reported the analysis of two A. laibachii genomes, revealing a novel class of effectors, the CHxCs (later renamed CCGs).
(i) We then compared multiple A. laibachii races, and correlated variable secreted proteins with the capacity to trigger resistance in >400 Arabidopsis natural accessions, and by association genomics we predicted recognized effectors. Transient assays verified a specific effector is recognized in accession HR-5. We also defined the corresponding WRR gene.
(ii) We used a similar approach to correlate the secretome of multiple A. candida races with growth on different Arabidopsis and Brassica genotypes. We thus predicted CCG “non-host avirulence” effectors, and showed that CCG28 is recognized by WRR4. Unlike other fungal and oomycete effectors, the N terminus of CCG28 is recognized by WRR4.
(iii) Different A. candida races colonize different hosts. We compared multiple A. candida races and revealed mosaic genomes, with haplotypes that show recent exchange of blocks of sequences between races. By sequential infections, we showed defence suppression by an adapted race enables subsequent colonization by a non-adapted race, enabling sexual exchange, effector repertoire shuffling and the creation of new races that can then colonize and asexually expand on new hosts. This explains the strong immuno-suppression ability of Albugo sp.
3- NON-HOST RESISTANCE IN ARABIDOPSIS TO BRASSICA-INFECTING A. CANDIDA RACES. We aimed to use Pseudomonas delivery to identify effectors from Brassica-infecting Albugo races that are recognized in Arabidopsis; this proved unsuccessful. Instead, we hypothesised that WRR genes in Arabidopsis confer NHR, but that different accessions carry different sets of WRR genes. In inbred lines from inter-accession crosses, transgressive segregation for these WRR loci results in rare susceptible segregants. We crossed such rare susceptible lines to resistant parents and analysed their F2 generations for new WRR loci. Most accessions carry resistance at the WRR4 locus, and we defined an additional Resistance (R) gene, WRR4B, in this cluster. WRR4B confers A. candida resistance in Brassica. We also cloned WRR8 and WRR9; these are both being transformed into Brassica. WRR4, WRR4B, WRR8 and WRR9 are TIR-NB-LRR resistance and NHR genes. We predict that “stacking” of these NHR R genes from Arabidopsis in transgenic Brassica lines will confer durable control of A. candida, which will greatly benefit Brassica oilseed farmers.
The success of the project enabled follow-up BBSRC grants to fund 3 postdocs over the next 3 years to advance the analysis initiated in ALBUGON.
1- We aimed to define genome sequences for multiple strains of Albugo. This was achieved; we determined sequences for 7 races of A. candida, and 6 races of A. laibachii.
2- We aimed to define the Albugo effector repertoire in order to better understand the remarkable capacity of Albugo to impose enhanced disease susceptibility. The risky method in the proposal (delivery of 100s of effector candidates from Pseudomonas) was unsuccessful, and we adopted a slower strategy to define Albugo effectors, by finding Albugo genes recognized by White Rust Resistance (WRR) genes.
3- We aimed to reveal the basis of non-host Resistance (NHR) in Arabidopsis to Brassica-infecting races of Albugo. The Pseudomonas delivery method did not work, so we used a different but slower method, and cloned three new Arabidopsis NHR genes for Albugo resistance.
1, 2- ALBUGO GENOMICS and EFFECTOROMICS. We were among the first to use Illumina sequencing to define a pathogen genome, and reported the analysis of two A. laibachii genomes, revealing a novel class of effectors, the CHxCs (later renamed CCGs).
(i) We then compared multiple A. laibachii races, and correlated variable secreted proteins with the capacity to trigger resistance in >400 Arabidopsis natural accessions, and by association genomics we predicted recognized effectors. Transient assays verified a specific effector is recognized in accession HR-5. We also defined the corresponding WRR gene.
(ii) We used a similar approach to correlate the secretome of multiple A. candida races with growth on different Arabidopsis and Brassica genotypes. We thus predicted CCG “non-host avirulence” effectors, and showed that CCG28 is recognized by WRR4. Unlike other fungal and oomycete effectors, the N terminus of CCG28 is recognized by WRR4.
(iii) Different A. candida races colonize different hosts. We compared multiple A. candida races and revealed mosaic genomes, with haplotypes that show recent exchange of blocks of sequences between races. By sequential infections, we showed defence suppression by an adapted race enables subsequent colonization by a non-adapted race, enabling sexual exchange, effector repertoire shuffling and the creation of new races that can then colonize and asexually expand on new hosts. This explains the strong immuno-suppression ability of Albugo sp.
3- NON-HOST RESISTANCE IN ARABIDOPSIS TO BRASSICA-INFECTING A. CANDIDA RACES. We aimed to use Pseudomonas delivery to identify effectors from Brassica-infecting Albugo races that are recognized in Arabidopsis; this proved unsuccessful. Instead, we hypothesised that WRR genes in Arabidopsis confer NHR, but that different accessions carry different sets of WRR genes. In inbred lines from inter-accession crosses, transgressive segregation for these WRR loci results in rare susceptible segregants. We crossed such rare susceptible lines to resistant parents and analysed their F2 generations for new WRR loci. Most accessions carry resistance at the WRR4 locus, and we defined an additional Resistance (R) gene, WRR4B, in this cluster. WRR4B confers A. candida resistance in Brassica. We also cloned WRR8 and WRR9; these are both being transformed into Brassica. WRR4, WRR4B, WRR8 and WRR9 are TIR-NB-LRR resistance and NHR genes. We predict that “stacking” of these NHR R genes from Arabidopsis in transgenic Brassica lines will confer durable control of A. candida, which will greatly benefit Brassica oilseed farmers.
The success of the project enabled follow-up BBSRC grants to fund 3 postdocs over the next 3 years to advance the analysis initiated in ALBUGON.