Lost in the middle of nowhere: the AvrLm1 avirulence gene of the Dothideomycete Leptosphaeria maculans

Abstract

SummaryLeptosphaeria maculans , a Dothideomycete causing stem canker on oilseed rape ( Brassica napus ), develops gene-for-gene interactions with its host plants. To date, nine resistance genes ( Rlm1-9 ) have been identified in Brassica spp. The corresponding nine avirulence genes ( AvrLm1-9 ) in L. maculans have been mapped at four independent loci, thereby revealing two clusters of three and four linked avirulence genes. Here, we report the completion of map-based cloning of AvrLm1 . AvrLm1 was genetically delineated within a 7.3 centimorgan interval corresponding to a 439 kb BAC contig. AvrLm1 is a single copy gene isolated within a 269 kb non-coding, heterochromatin-like region. The region comprised a number of degenerated, nested copies of four long-terminal repeat (LTR) retrotransposons, including Pholy and three novel Gypsy-like retrotransposons. AvrLm1 restored the avirulent phenotype on Rlm1 cultivars following functional complementation of virulent isolates. AvrLm1 homologues were not detected in other Leptosphaeria species or in known fungal genomes including the closely related species Stagonospora nodorum . The predicted AvrLm1 protein is composed of 205 amino acids, of which only one is a cysteine residue. It contains a peptide signal suggesting extracellular localization. Unlike most other fungal avirulence genes, AvrLm1 is constitutively expressed, with a probable increased level of expression upon plant infection, suggesting the absence of tight regulation of AvrLm1 expression.

Population diversity and genomics of the fungal pathogen of canola Leptosphaeria maculans

“…The products of these genes are known as effector proteins, and these carry out functions such as plant defence suppression and host cellwall modifications upon infection (Rouxel et al, 2011). Of the eleven L. maculans Avr genes identified, six (AvrLm1, AvrLm6, AvrLm4-7, AvrLm11, AvrLm2 and AvrLm3) (Fudal et al, 2007;Gout et al, 2006b;Parlange et al, 2009;Balesdent et al, 2013;Ghanbarnia et al, 2014;Plissonneau et al, 2015), have been characterised (Table 1.1). A seventh AvrLm gene, AvrLmJ1, virulent on Brassica juncea cultivars, has also been characterised .…”

“…The region surrounding AvrLm1 is 296 kb long, rich in GC-isochores and long-terminal repeat retrotransposons and gene poor (Gout et al, 2006b). The AvrLm1 protein itself contains a single cysteine residue and is composed of 205 amino acids.…”

“…On the other hand, effectors damaging to pathogen fitness can just as easily be lost. Four of the known effector genes, AvrLm1, AvrLm6, AvrLm4-7 and AvrLm11 are hosted in AT-rich isochores of the blackleg genome (Gout et al, 2006b;Fudal et al, 2007;Parlange et al, 2009;Balesdent et al, 2013;Grandaubert et al, 2014b).…”

“…Previous studies have established that L. maculans possesses a high evolutionary potential and rapidly evolves to overcome host resistance (Chapter 3; Barrins et al, 2004;Rouxel et al, 2011;Travadon et al, 2011;Dilmaghani et al, 2012;Zander et al, 2013;Grandaubert et al, 2014b;Patel et al, 2015). Gene loss via deletion is an effective method of adaptation employed by several fungal pathogens like Magnaporthe oryzae (Couch et al, 2005), Blumeria graminis (Wicker et al, 2013), including L. maculans (Gout et al, 2006b;Fudal et al, 2007). We hypothesised that one of the major causes for gene loss in this pathogen would be deletion in known effector genes and other pathogenicity related or unknown effectors, to overcome host recognition.…”

“…Initially, map-based cloning was used to identify AvrLm1 and AvrLm6 (Gout et al, 2006b;Fudal et al, 2007), which are clustered on SC_6, along with AvrLm2 (Ghanbarnia et al, 2014), in a region affected by RIP mutations. In isolates virulent on cultivars containing Rlm1 and Rlm6, the loci containing AvrLm1…”