Host adaptation and microbial competition drive Ralstonia solanacearum phylotype I evolution in the Republic of Korea

Abstract

Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) threatens the cultivation of important crops worldwide. We sequenced 30 RSSC phylotype I ( R. pseudosolanacearum ) strains isolated from pepper (Capsicum annuum) and tomato (Solanum lycopersicum) across the Republic of Korea. These isolates span the diversity of phylotype I, have extensive effector repertoires and are subject to frequent recombination. Recombination hotspots among South Korean phylotype I isolates include multiple predicted contact-dependent inhibition loci, suggesting that microbial competition plays a significant role in Ralstonia evolution. Rapid diversification of secreted effectors presents challenges for the development of disease-resistant plant varieties. We identified potential targets for disease resistance breeding by testing for allele-specific host recognition of T3Es present among South Korean phyloype I isolates. The integration of pathogen population genomics and molecular plant pathology contributes to the development of location-specific disease control and development of plant cultivars with durable resistance to relevant threats.

Identification of RipAZ1 as an avirulence determinant of Ralstonia solanacearum in Solanum americanum

“…We hypothesized that an avirulence effector is present in Pe_26 but absent or showing significant sequence polymorphism in To_1. Recently, the genome sequences and T3E repertoires of multiple R. solanacearum phylotype I strains, including Pe_26 and To_1, were reported (Prokchorchik et al, 2020). To identify the candidate avirulence effectors, effector repertoires of Pe_26 and To_1 strains were compared with the following criteria.…”

“…To identify the avirulence effector that induces cell death in S. americanum SP2273 but not SP2275, the 12 selected candidate avirulence effector genes were cloned with a C‐terminal FLAG tag under the control of the constitutive cauliflower mosaic virus (CaMV) 35S promoter. The R. solanacearum GMI1000 allele of the effector RipA1 with the C‐terminal FLAG tag was used as a positive control because it induced robust cell death in all tested S. americanum accessions (data not shown), including SP2273 and SP2275, when transiently expressed (Figures 2a and ), as well as in N. benthamiana (Jeon et al, 2020; Prokchorchik et al, 2020; Sole et al, 2012). C‐terminal FLAG‐tagged yellow fluorescent protein (YFP) was expressed as a negative control.…”

“…Naturally occurring avirulence effectors often show significant sequence polymorphism in pathogen populations (Asai et al, 2018; Dodds et al, 2006). To survey natural sequence polymorphisms of RipAZ1, we used the publicly available database RalstoT3E (https://iant.toulouse.inra.fr/T3E from Peeters et al, 2013) and the R. solanacearum phylotype I strain database from Prokchorchik et al (2020) to identify 21 nonredundant RipAZ1 natural sequence variants (Table and Figure ). Phylogenetic analysis indicated that the RipAZ1 amino acid sequence of R. solanacearum phylotype IV strain SL3022 is the most distantly related to RipAZ1 Pe_26 (Figure ).…”

“…R. solanacearum virulence requires type III secretion system effectors (T3Es) that are translocated into host plant cells during infection (Coll & Valls, 2013; Genin & Denny, 2012). Extensive genomic and transcriptomic studies have uncovered the T3E repertoires in the RSSC (Genin & Denny, 2012; Mukaihara et al, 2010; Occhialini et al, 2005; Peeters et al, 2013; Prokchorchik et al, 2020; Sabbagh et al, 2019; Valls et al, 2006). In addition, several T3Es from R. solanacearum have been reported to trigger disease resistance in plants.…”

“…PopP1 (RipP1) plays a role in avirulence in tobacco and petunia (Chen et al, 2018; Lavie et al, 2002; Poueymiro et al, 2009). Moreover, several R. solanacearum effectors were shown to induce cell death when transiently expressed in plant cells, such as AWR1 (RipA1) (Jeon et al, 2020; Prokchorchik et al, 2020; Sole et al, 2012), AWR2 (RipA2), AWR4 (RipA4), AWR5 (RipA5) (Sole et al, 2012), RipE1 (Jeon et al, 2020; Prokchorchik et al, 2020; Sang et al, 2020), RipI (Zhuo et al, 2020), PopA (RipX) (Arlat et al, 1994; Belbahri et al, 2001; Racape et al, 2005), RipAB (Zheng et al, 2019), RipAT, RipAV (Clarke et al, 2015; Wroblewski et al, 2009) and RipTPS (Poueymiro et al, 2014).…”