The compact genome of the plant pathogen Plasmodiophora brassicae is adapted to intracellular interactions with host Brassica spp

Abstract

BackgroundThe protist Plasmodiophora brassicae is a soil-borne pathogen of cruciferous species and the causal agent of clubroot disease of Brassicas including agriculturally important crops such as canola/rapeseed (Brassica napus). P. brassicae has remained an enigmatic plant pathogen and is a rare example of an obligate biotroph that resides entirely inside the host plant cell. The pathogen is the cause of severe yield losses and can render infested fields unsuitable for Brassica crop growth due to the persistence of resting spores in the soil for up to 20 years.ResultsTo provide insight into the biology of the pathogen and its interaction with its primary host B. napus, we produced a draft genome of P. brassicae pathotypes 3 and 6 (Pb3 and Pb6) that differ in their host range. Pb3 is highly virulent on B. napus (but also infects other Brassica species) while Pb6 infects only vegetable Brassica crops. Both the Pb3 and Pb6 genomes are highly compact, each with a total size of 24.2 Mb, and contain less than 2 % repetitive DNA. Clustering of genome-wide single nucleotide polymorphisms (SNP) of Pb3, Pb6 and three additional re-sequenced pathotypes (Pb2, Pb5 and Pb8) shows a high degree of correlation of cluster grouping with host range. The Pb3 genome features significant reduction of intergenic space with multiple examples of overlapping untranslated regions (UTRs). Dependency on the host for essential nutrients is evident from the loss of genes for the biosynthesis of thiamine and some amino acids and the presence of a wide range of transport proteins, including some unique to P. brassicae. The annotated genes of Pb3 include those with a potential role in the regulation of the plant growth hormones cytokinin and auxin. The expression profile of Pb3 genes, including putative effectors, during infection and their potential role in manipulation of host defence is discussed.ConclusionThe P. brassicae genome sequence reveals a compact genome, a dependency of the pathogen on its host for some essential nutrients and a potential role in the regulation of host plant cytokinin and auxin. Genome annotation supported by RNA sequencing reveals significant reduction in intergenic space which, in addition to low repeat content, has likely contributed to the P. brassicae compact genome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2597-2) contains supplementary material, which is available to authorized users.

Identification of Plasmodiophora brassicae effectors — A challenging goal

“…This was precisely the strategy followed by Schwelm et al [20]. and Rolfe et al [21]. to identify putative effectors released by P. brassicae during the infection process.…”

“…to identify putative effectors released by P. brassicae during the infection process. However, the obligate parasitic nature of P. brassicae has made it impossible to obtain a complete genome, with six draft genomes barely annotated for five Canadian pathotypes and one European pathotype [20,21]. Transcriptomes of P. brassicae infecting B. napus and Arabidopsis thaliana in the Canadian study, and infecting B. rapa, B. napus , and B. oleracea var.…”

“…Transcriptomes of P. brassicae infecting B. napus and Arabidopsis thaliana in the Canadian study, and infecting B. rapa, B. napus , and B. oleracea var. capitata in the European study, have identified some candidate effectors [20,21]. However, while the information obtained in both studies is a good start, the effectors specifically responsible for P. brassicae infection and subsequent disease progression have still to be identified.…”

“…A common finding in both studies was the over-expression of a benzoic acid/salicylic acid methyltransferase-encoding gene [PBRA_T000444 in P. brassicae European pathotype 3(Pbe3), PbPT3Sc00026_A_1.308_1 in P. brassicae pathotype 3 (Pb3) draft genomes; Genbank accession number AFK13134] during the second week of infection, with expression peaking three and four weeks after infection [20,21,36]. Salicylic acid (SA) is essential for the activation of plant defence [37].…”

“…This pathogen life style is the reason why key knowledge pertaining to the identification of effector proteins mediating infection and subsequent disease progression is still unavailable. The recent draft genomes for European and North American P. brassicae pathotypes have provided the opportunity for the identification of putative effector proteins through comparative genomics [20,21]. However, low levels of similarity to known sequences at either the nucleotide and/or amino acid level has meant that annotating P. brassicae genes has proven to be extremely difficult.…”