Whole-genome DNA similarity and population structure of Plasmodiophora brassicae strains from Canada

- population structure of Plasmodiophora brassicae strains from Canada.
- Information on genetic similarity among pathogen populations across Canada could be useful in estimating the genetic variation in pathogen populations, predicting the effect of subsequent selection pressure on changes in the pathogen population over time, and even in identifying the origin of the initial pathogen introduction to canola in Alberta..
- Similarly, at one site in central Canada where resistance had broken down, about half of the genes differed (based on SNPs) between strains before and after the breakdown..
- Keywords: Genetic diversity, Plasmodiophora brassicae , Clubroot, DNA sequencing, Population genetics, Balancing selection, Host shift.
- Clubroot, caused by Plasmodiophora brassicae Woronin, is an increasingly important constraint to canola ( Bras- sica napus L.) production in Canada [1].
- 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0.
- Full list of author information is available at the end of the article.
- The source of the initial infection on canola has never been determined.
- brassicae have been sequenced to date [28–30], study of the gen- omics and population genetics of P.
- Analysis of the single-spore isolate e3 from Europe estimated the total genome size of P.
- In a study of the genome sequence of pathotypes 3 and 6, the total size of each genome was 24.2 Mb [27].
- The main objectives of the study were to compare the genomic structure of P.
- brassicae populations from dif- ferent locations and hosts to assess the genetic variation present in the pathogen population across Canada, and if possible, to obtain insights into the origin of the ori- ginal source of infection on canola in Alberta.
- rapa were estab- lished on Murashiga and Skoog (MS) medium for about 50% of the strains assessed.
- White callus cells grew from the edges of the root tissue after 2 weeks.
- Twenty of the 52 P.
- Multiple stages of the P.
- included in the analysis.
- The variant type and distribution were as follow: 58% of the variants iden- tified in genic regions occurred in coding regions (exons) and 42% in non-coding regions (introns).
- of the SNPs were homozygous (Additional file 1: Figure S1), but 25–75% of SNPs were heterozygous in one col- lection from Alberta (AB9-C-P5)..
- 2b) of the 43 P.
- brassicae strains were used to determine the composition of the population and the number of the clades.
- in genic and intergenic regions of 43 strains of Plasmodiophora brassicae.
- Clade 1 consisted of the strains from British Colombia, Newfoundland, Ontario, and Quebec, mainly from vege- table brassicas (Fig.
- Three of the five strains from China clustered together in Clade 3..
- Clade 4 consisted of the new, virulent pathotypes from Alberta (AB13-C-P5X and AB14-C-P5X), a single recent collection (SK3-C) from Saskatchewan, and col- lection AB9-C-P5 from Alberta.
- Most of the strains from canola in Saskatchewan and Manitoba, which represent a recent expansion of the geographic distribution of the pathogen, clustered together with the older strains from canola in Alberta in Clade 5, along with strains from vegetables in Ontario and British Columbia.
- 2 Three assessments of genetic diversity in the sequenced strains of Plasmodiophora brassicae , with strains of the same clade represented by the same color: a principal component analysis of 43 Canadian strains.
- b population structure analysis of all 43 strains, where each vertical column represents one strain, each color represents a clade (1 – 5) and admixtures are represented by two colors, and (c) a neighbor-joining tree of the 43 strains.
- SNP polymor- phisms were present in more than half of the total 9727 genes in the genome between samples collected before and after the change of pathotype at each site (Fig.
- assess the reproducibility of the sequencing.
- This difference may have been associated with trace amounts of microbial contamination in the sample taken directly from the clubbed root, or inherent variability among strains of the pathogen in a single club..
- 3 SNP-based phylogenetic tree of Plasmodiophora brassicae based on whole-genome alignment of 43 Plasmodiophora brassicae strains from Canada, China, and the USA mapped against e3 from Europe.
- When the evolutionary dis- tance between clades was computed, the distance based on the length of the branch was largest between Clades 1 (Canadian collections from vegetable brassicas) and 3 (collections from China), and smallest between strains from the Prairies (Clades 4 and 5) and Clade 3..
- The decrease of linkage disequi- librium was slower in strains from the Prairies compared with strains from the rest of Canada in the 43 strains (Fig.
- 4 Heat maps of SNPs distribution in Plasmodiophora brassicae .
- The total gene number in the genome is 9727.
- In the current study, the genetic similarity of P.
- Clade 2 was mainly from can- ola outside of the Canadian Prairies at sites where the change in pathotype had been detected.
- Clade 4 consisted of the new, virulent pathotypes from Alberta.
- Most of the strains from can- ola in Saskatchewan and Manitoba, which represent a recent expansion of the geographic distribution of the pathogen, clustered together with the older collections from canola in Alberta and two collections from China in Clade 5..
- In the current study, diversity was high between strains from the Prairies and the rest of Canada.
- 5 Linkage disequilibrium decay ( r 2 ) versus the distance between polymorphic sites in Pop 1 (Clades 1 and 2) and in Pop 2 (Clades 4 and 5) of 43 strains of Plasmodiophora brassicae.
- One approach used to estimate linkage disequilib- rium decay is to find the distance at which half of the maximum linkage disequilibrium has decayed [48, 49]..
- brassicae be- cause of the large populations of long-lived resting spores in soil..
- Prior to the release of the first clubroot-resistant canola cultivar in 2009, all canola cultivars on the Prairies were suscep- tible to pathotype 3.
- Samples of the pathogen that have not been converted to single-spore isolates are referred to as a ‘collections’, and single-spore isolates and collections together as strains.
- McDonald (AB11, AB12) of the University of Guelph, Guelph, ON, from Saskatchewan and Manitoba by Dr.
- Gossen (SK1–SK3, MB1) of the Saskatoon Research and Development Centre of Agriculture and Agri-Food Canada at Saskatoon SK, from Ontario and Quebec by Dr.
- Similarly, the strains from the United States and China were imported under the regulations of the Can- adian Food Inspection Agency of the government of Canada for use in the PPC-2 facility at the Agriculture and Agri-Food Canada Centre at Saskatoon and cannot be distributed without permission of that regulator.
- Each 7-day-old seedling was inoculated at the base of the stem with 5 mL of resting spore suspension (10 6 to 10 8 spores mL − 1 ) of selected strains following the method of Sharma et al.
- Table 1 Origin, names, pathotype (Williams ’ s system) and source of field collections and single-spore isolates (SS) of Plasmodiophora brassicae used for whole-genome sequencing.
- To produce a callus control in the absence of P.
- The ArrayStar program of the Lasergene package was used for analysis of single nucleotide polymorphisms (SNPs).
- The most likely K value was determined by the log probability of the data (LnP(D)) and delta K, based on the rate of change in LnP(D) be- tween successive K values, where model complexity that maximized marginal likelihood = 8 and model compo- nents used to explain structure in data = 5.
- Additional file 1: Figure S1.The ratio of homogenous to heterogeneous SNPs.
- The height of the fusion, presented on the horizontal axis, indicates the dissimilarity between two strains.
- The larger the height of the fusion, the less similar the strains..
- Nucleotide diversity across the genome of 43 strains of Plasmodiophora brassicae .
- The average θπ across all of the strains was 0.00095..
- Nucleotide diversity across the genome of 43 strains of Plasmodiophora brassicae.
- Linkage disequilibrium (LD matrix) in 43 strains of Plasmodiophora brassicae.
- The funding body played no role in the design of the study or in the collection, analysis, interpretation of data or in writing the manuscript..
- brassica from the United States and China were imported into Canada under permit from the Canadian Food Inspection Agency and live strains of the pathogen were studied in a PPC-2 level containment facility at the Agriculture and Agri-Food Canada Re- search and Development Centre.
- Spread of Plasmodiophora brassicae on canola in Canada old pathogen, new home.
- The occurrence and economic impact of Plasmodiophora brassicae and clubroot disease.
- Virulence and pathotype classification of Plasmodiophora brassicae populations collected from clubroot resistant canola ( Brassica napus ) in Canada.
- A system for the determination of races of Plasmodiophora brassicae that infect cabbage and rutabaga.
- Study of physiologic specialization in Plasmodiophora brassicae: proposals for attempted rationalization through an international approach.
- amongst Plasmodiophora brassicae collections from France and derived single-spore isolates.
- Characterization of five molecular markers for pathotype identification of the clubroot pathogen Plasmodiophora brassicae .
- Specific genes identified in Pathotype 4 of the Clubroot pathogen Plasmodiophora brassicae .
- A molecular marker for the specific detection of new pathotype 5-like strains of Plasmodiophora brassicae in canola.
- Detection of Plasmodiophora brassicae in Saskatchewan in 2008.
- Possible gene centers for resistance in the genus Brassica to Plasmodiophora brassicae .
- First report of clubroot on canola caused by Plasmodiophora brassicae in North Dakota.
- The life- cycle of Plasmodiophora brassicae Woron.
- Life cycle of Plasmodiophora brassicae .
- Molecular biology of Plasmodiophora brassicae .
- The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases.
- The compact genome of the plant pathogen Plasmodiophora brassicae is adapted to intracellular interactions with host Brassica spp.
- Genotyping of Plasmodiophora brassicae reveals the presence of distinct populations.
- The enzymatic isolation of secondary vegetative plasmodia of Plasmodiophora brassicae from callus tissue of Brassica campestris .
- Culture of Plasmodiophora brassicae in host callus tissue.
- Proliferation and pathogenicity of Plasmodiophora brassicae in infected callus tissue (studies on the clubroot of cruciferous plant.
- Identification of genes from the obligate intracellular plant pathogen, Plasmodiophora brassicae .
- A shift in the pathotype of Plasmodiophora brassicae at a site in Ontario.
- What can we learn from clubroots: alterations in host roots and hormone homeostasis caused by Plasmodiophora brassicae .
- Studies on the life history of the club root organism, Plasmodiophora brassicae .
- Efficient root infection with single resting spores of Plasmodiophora brassicae .
- Characterization of a single-spore isolate population of Plasmodiophora brassicae resulting from a single club.
- Assessment of biological and molecular variability between and within field isolates of Plasmodiophora brassicae .
- History of oilseed rape cropping and geographic origin affect the genetic structure of Plasmodiophora brassicae populations.
- The relationship between genotypes of three Brassica species and collections of Plasmodiophora brassicae .
- Isolation and variation in virulence of single-spore isolates of Plasmodiophora brassicae from Canada..
- Pathotype classification of Plasmodiophora brassicae and its occurrence in Brassica napus in Alberta, Canada.
- Virulence and spread of Plasmodiophora brassicae (clubroot) in Alberta, Canada.
- Cytology of infection, development and expression of resistance to Plasmodiophora brassicae in canola.
- Emergence of new virulence phenotypes of Plasmodiophora brassicae on canola ( Brassica napus ) in Alberta, Canada.
- Effect of temperature on primary infection by Plasmodiophora brassicae and initiation of clubroot symptoms.

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