Secretome characterization and correlation analysis reveal putative pathogenicity mechanisms and identify candidate avirulence genes in the wheat stripe rust fungus Puccinia striiformis f. sp. tritici

Authors: XIA, CHONGJING - Washington State University; WANG, MEINAN - Washington State University; CORNEJO, OMAR - Washington State University; JIWAN, DERICK - Washington State University; See, Deven; Chen, Xianming

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/20/2017
Publication Date: 12/11/2017
Citation: Xia, C., Wang, M., Cornejo, O.E., Jiwan, D.A., See, D.R., Chen, X. 2017. Secretome characterization and correlation analysis reveal putative pathogenicity mechanisms and identify candidate avirulence genes in the wheat stripe rust fungus Puccinia striiformis f. sp. tritici. BMC Genomics. https://doi:10.3389/fmicb.2017.02394.
DOI: https://doi.org/10.3389/fmicb.2017.02394

Interpretive Summary: Stripe rust is one of the most destructive diseases of wheat worldwide. In this study, we re-sequenced 7 stripe rust pathogen isolates and included 7 previously sequenced isolates to represent a balanced virulence/avirulence profile for several avirulence loci. We observed an unevenly distribution of heterozygosity among the isolates and among different genomic regions in each of the isolates, with secreted protein (SP) gene regions more variable, reflecting different evolutionary forces during interacting with host genes. Secretome comparison with other rust fungi identified a large portion of species-specific SPs, suggesting that they may have specific roles when interacting with the wheat host. A total of 32 effectors of were identified from the stripe rust secretome. A class of superoxide dismutase 5-homolog proteins was identified, suggesting that antioxidant defense is a common strategy for the fungus to suppress host basal immunity. We also identified candidates for avirulence genes corresponding to six resistance genes by correlating polymorphisms of effector genes to the virulence/avirulence profiles of the 14 isolates. The putative Avr76 was present in the avirulent isolates, but absent in the virulent isolates, suggesting that deleting the coding region of the avirulence gene has produced races virulent to resistance gene Yr76. The candidate effector genes provide a rich resource for further studies to clone avirulence genes and determine the evolutionary mechanisms of the stripe rust pathogen populations.

Technical Abstract: Background: Stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat worldwide. Planting resistant cultivars is an effective way to control this disease, but race-specific resistance can be overcome quickly due to the rapid evolving Pst population. Studying the pathogenicity mechanisms is critical for understanding how Pst virulence changes and how to develop wheat cultivars with durable resistance to stripe rust. Results: We re-sequenced 7 Pst isolates and included 7 previously sequenced isolates to represent a balanced virulence/avirulence profile for several avirulence loci. We observed an unevenly distribution of heterozygosity among the isolates and among different genomic regions in each of the isolates, with SP gene regions more variable, reflecting different evolutionary forces during interacting with host genes. Secretome comparison of Pst with other rust fungi identified a large portion of species-specific SPs, suggesting that they may have specific roles when interacting with the wheat host. A total of 32 effectors of Pst were identified from its secretome based on the following five characteristics: a) cysteine-rich, b) polymorphic among the 14 isolates, c) predicted by EffectorP, d) haustorial differentially expressed and e) species-specific. A class of superoxide dismutase 5 (SOD5)-homologs proteins was identified by searching the Pst secretome against functionally validated effectors in the PHI-base, suggesting that antioxidant defense is a common strategy for Pst to suppress host basal immunity. We also identified candidates for Avr genes corresponding to six Yr genes by correlating polymorphisms of effector genes to the virulence/avirulence profiles of the 14 Pst isolates. The putative Avr76 was present in the avirulent isolates, but absent in the virulent isolates, suggesting that deleting the coding region of the avirulence gene has produced races virulent to resistance gene Yr76. Conclusions: A large number of SP genes were identified through comparing the secretomes of 14 Pst isolates. Incorporating avirulence/virulence phenotypes into correlation analysis with variations in genomic structure and secretome, particularly presence/absence polymorphisms of effectors, is an efficient way to identify candidate Avr genes in Pst. The candidate effector genes provide a rich resource for further studies to determine the evolutionary history of Pst populations and the co-evolutionary arms race between Pst and wheat. The Avr candidates identified in this study will lead to cloning avirulence genes in Pst, which will enable us to understand molecular mechanisms underlying Pst-wheat interactions, to determine the effectiveness of resistance genes and further to develop durable resistance to stripe rust.