title: The compact genome of the plant pathogen Plasmodiophora brassicae is adapted to intracellular interactions with host Brassica spp.
abstract: BACKGROUND
  The 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.
  
  
  RESULTS
  To 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Rolfe
authors.affiliation: Department of Agricultural, Food and Nutritional Science, University of Alberta, 410 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada.
authors.forename: Stephen E
authors.initials: SE
authors.lastname: Strelkov
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
authors.forename: Matthew G
authors.initials: MG
authors.lastname: Links
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.|Present address: New York Genome Center, 101 6th Ave, New York, NY, 10013, USA.
authors.forename: Wayne E
authors.initials: WE
authors.lastname: Clarke
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Robinson
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Djavaheri
authors.affiliation: Department of Integrative Plant Biology, Institute of Plant Genetics of the Polish Academy of Sciences, ul. Strzeszynska 34, 60-479 Poznan, Poland.
authors.forename: Robert
authors.initials: R
authors.lastname: Malinowski
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
authors.forename: Parham
authors.initials: P
authors.lastname: Haddadi
authors.affiliation: National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada.
authors.forename: Sateesh
authors.initials: S
authors.lastname: Kagale
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
authors.forename: Isobel A P
authors.initials: IA
authors.lastname: Parkin
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.|Present address: Department of Agricultural and Environmental Sciences, College of Agriculture, Human and Natural Sciences, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN, 37209, USA.
authors.forename: Ali
authors.initials: A
authors.lastname: Taheri
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada. hossein.borhan@agr.gc.ca.
authors.forename: M Hossein
authors.initials: MH
authors.lastname: Borhan
mesh_terms: D017360:Arabidopsis; D001937:Brassica / Q000469:parasitology*; D018556:Crops, Agricultural / Q000469:parasitology; D003583:Cytokinins / Q000378:metabolism; D016054:DNA, Protozoan / Q000235:genetics; D018503:Genome, Protozoan; D058507:Host Specificity; D006790:Host-Parasite Interactions / Q000235:genetics*; D007210:Indoleacetic Acids / Q000378:metabolism; D010935:Plant Diseases / Q000469:parasitology; D056909:Plasmodiophorida / Q000235:genetics*; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D003583:Cytokinins; D016054:DNA, Protozoan; D007210:Indoleacetic Acids
keywords: Biotroph; Brassica napus; Clubroot; Effectors; Plasmodiophora brassicae