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

Rolfe SA, Strelkov SE, Links MG, Clarke WE, Robinson SJ, Djavaheri M, Malinowski R, Haddadi P, Kagale S, Parkin IA, Taheri A, Borhan MH - BMC Genomics (2016)

Bottom Line: The Pb3 genome features significant reduction of intergenic space with multiple examples of overlapping untranslated regions (UTRs).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.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.

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.

Conclusion: 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.

No MeSH data available.


Related in: MedlinePlus

Graphical representation of the 89 SNP haplotypes discovered across four re-sequenced pathotypes. Pathotype alleles are coded in green or red for the reference (Pb3) or alternate alleles, respectively. Clustering was performed using the default dist fuction of the stats R package
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Fig1: Graphical representation of the 89 SNP haplotypes discovered across four re-sequenced pathotypes. Pathotype alleles are coded in green or red for the reference (Pb3) or alternate alleles, respectively. Clustering was performed using the default dist fuction of the stats R package

Mentions: Alignment of the Pb3 and Pb6 genomes revealed a close to perfect synteny with rare examples of inversion of small segments of the Pb6 genome (Additional file 5: Figure S4). The majority of predicted Pb6 genes had an orthologue in the Pb3 genome except for 14 genes that were unique to Pb6, with six of these having no homologue in the NCBI non-redundant (nr) protein database and eight that matched hypothetical proteins (E value < 0.001). To gain insight into genome variation and its correlation with host specificity we re-sequenced the genomes of Pb2, Pb5 and Pb8. A total of 173,134 SNPs were discovered by alignment of the genome sequence of Pb6 and the re-sequenced pathotypes against the Pb3 reference. Paired-end Illumina reads generated for Pb3 were also aligned to the Pb3 genome. After filtering (on allele frequency, SNP positions with heterozygous genotypes and indels) 132,429 SNPs remained and were clustered into 90 haplotype blocks. One haplotype block was found to result from a single SNP between the reference genome and Pb3 Illumina reads; investigation of this SNP indicated that it resulted from a sequencing error and this haplotype (hap19) was therefore excluded (Fig. 1). Of the remaining 89 haplotype blocks, 86.5 % contained more than one SNP. Comparison of whole genome SNP profiles revealed that Pb2, 3, 5, 8 were highly similar and clustered as one group, while the SNP profile of Pb6 was more divergent (Fig. 1 and Additional file 6: Table S2). The haplotypes correlate with the host range and geographical distribution of these pathotypes, with Pb2, 3, 5, 8 being virulent on B. napus and present in the prairie provinces and Pb6 failing to cause disease on B. napus and being prevalent in British Columbia and Eastern provinces of Canada (Additional file 7: Table S3). Without access to read data, analyses of the e3 genome could not be completed as with the other pathotypes. However, by direct sequence comparison 48,578 out of the identified 132,429 SNPs were found to differentiate the genome of e3 reported by Schwelm et al. [21] and Pb3. These SNPs were grouped into 58 haplotypes and showed that e3 clustered with Pb6 (Additional file 8: Figure S5 and Additional file 6: Table S2).Fig. 1


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

Rolfe SA, Strelkov SE, Links MG, Clarke WE, Robinson SJ, Djavaheri M, Malinowski R, Haddadi P, Kagale S, Parkin IA, Taheri A, Borhan MH - BMC Genomics (2016)

Graphical representation of the 89 SNP haplotypes discovered across four re-sequenced pathotypes. Pathotype alleles are coded in green or red for the reference (Pb3) or alternate alleles, respectively. Clustering was performed using the default dist fuction of the stats R package
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4815078&req=5

Fig1: Graphical representation of the 89 SNP haplotypes discovered across four re-sequenced pathotypes. Pathotype alleles are coded in green or red for the reference (Pb3) or alternate alleles, respectively. Clustering was performed using the default dist fuction of the stats R package
Mentions: Alignment of the Pb3 and Pb6 genomes revealed a close to perfect synteny with rare examples of inversion of small segments of the Pb6 genome (Additional file 5: Figure S4). The majority of predicted Pb6 genes had an orthologue in the Pb3 genome except for 14 genes that were unique to Pb6, with six of these having no homologue in the NCBI non-redundant (nr) protein database and eight that matched hypothetical proteins (E value < 0.001). To gain insight into genome variation and its correlation with host specificity we re-sequenced the genomes of Pb2, Pb5 and Pb8. A total of 173,134 SNPs were discovered by alignment of the genome sequence of Pb6 and the re-sequenced pathotypes against the Pb3 reference. Paired-end Illumina reads generated for Pb3 were also aligned to the Pb3 genome. After filtering (on allele frequency, SNP positions with heterozygous genotypes and indels) 132,429 SNPs remained and were clustered into 90 haplotype blocks. One haplotype block was found to result from a single SNP between the reference genome and Pb3 Illumina reads; investigation of this SNP indicated that it resulted from a sequencing error and this haplotype (hap19) was therefore excluded (Fig. 1). Of the remaining 89 haplotype blocks, 86.5 % contained more than one SNP. Comparison of whole genome SNP profiles revealed that Pb2, 3, 5, 8 were highly similar and clustered as one group, while the SNP profile of Pb6 was more divergent (Fig. 1 and Additional file 6: Table S2). The haplotypes correlate with the host range and geographical distribution of these pathotypes, with Pb2, 3, 5, 8 being virulent on B. napus and present in the prairie provinces and Pb6 failing to cause disease on B. napus and being prevalent in British Columbia and Eastern provinces of Canada (Additional file 7: Table S3). Without access to read data, analyses of the e3 genome could not be completed as with the other pathotypes. However, by direct sequence comparison 48,578 out of the identified 132,429 SNPs were found to differentiate the genome of e3 reported by Schwelm et al. [21] and Pb3. These SNPs were grouped into 58 haplotypes and showed that e3 clustered with Pb6 (Additional file 8: Figure S5 and Additional file 6: Table S2).Fig. 1

Bottom Line: The Pb3 genome features significant reduction of intergenic space with multiple examples of overlapping untranslated regions (UTRs).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.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.

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.

Conclusion: 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.

No MeSH data available.


Related in: MedlinePlus