High-throughput genomic sequencing of cassava bacterial blight strains identifies conserved effectors to target for durable resistance

Abstract

Cassava bacterial blight (CBB), incited by Xanthomonas axonopodis pv. manihotis ( Xam ), is the most important bacterial disease of cassava, a staple food source for millions of people in developing countries. Here we present a widely applicable strategy for elucidating the virulence components of a pathogen population. We report Illumina-based draft genomes for 65 Xam strains and deduce the phylogenetic relatedness of Xam across the areas where cassava is grown. Using an extensive database of effector proteins from animal and plant pathogens, we identify the effector repertoire for each sequenced strain and use a comparative sequence analysis to deduce the least polymorphic of the conserved effectors. These highly conserved effectors have been maintained over 11 countries, three continents, and 70 y of evolution and as such represent ideal targets for developing resistance strategies.

Positive selection is the main driving force for evolution of citrus canker-causing Xanthomonas

“…As no XacA* genome was publically available, De Novo assembly was conducted for the genome of XacA*270 (Supplementary Table S2) using previously described methodology (Jalan et al, 2011), and the two remaining XacA* strains were reference assembled based on the XacA*270 genome. The comparison of our reads and assemblies (Supplementary Table S3) with other published assemblies for Xanthomonas (Bart et al, 2012) indicated that our assemblies are of high quality. Assembly of all strains was annotated using the IMG/ER annotation pipeline and submitted to GenBank, the results for which are presented in Supplementary Table S1.…”

“…Among all the effectors identified in the strains analyzed as previously described (Bart et al, 2012) ( Supplementary Table S5), 10 common effectors that were shared by all 25 strains were identified in the 2822 core genes. Although none of the 10 effectors was found to have been affected by intragenic recombination as suggested by single breakpoint method result, the maximum likelihood gene trees of all the 10 effectors were found to be incongruent with the maximum likelihood reference tree based on 2822 core genes revealed by ShimodairaHasegawa test (Po0.001; Table 2) (Shimodaira and Hasegawa, 1999).…”

“…Effector prediction was conducted as previously described (Bart et al, 2012). In short, a data set of all known effectors from animal and plant pathogens was obtained and tblastn (Blast+ 2.2.28) was used to identify potential effectors in Xac strains with at least 45% amino acid homology and 80% coverage length.…”

Identification of QTLs controlling resistance to Pseudomonas syringae pv. tomato race 1 strains from the wild tomato, Solanum habrochaites LA1777

“…Next-generation sequencing has made it possible to rapidly analyze pathogen strains from the field for their type III effector repertoires and other virulence components (Baltrus et al 2011;Bart et al 2012). The draft genome sequences of Pst A9 and 407 provide insight into how these field strains can overcome R-gene-mediated resistance in tomato conferred by Pto and Prf (Pedley and Martin 2003).…”

Recognition of Verticillium effector Ave1 by tomato immune receptor Ve1 mediates Verticillium resistance in diverse plant species

“…This is especially powerful as it also allows screening for recognition specificities in plant species that are not hosts for the pathogen for which recognition is sought. Moreover, an effectoromics strategy allows combination with pathogenomics strategies to select the potentially most widespread or invariant effectors to, once identified and deployed, maximize durability of the recognition specificity (Bart et al, 2012). However, the subsequent cloning of immune receptor genes is typically laborious and slow, but functional genomic approaches based on NLR gene enrichment and sequencing (RenSeq), especially when combined with long-read sequencing, can accelerate mapping of functional NLRs in crop plants (Jupe et al, 2013;Witek et al, 2016), as well as in wild relatives (Stam et al, 2016).…”