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Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity.

Atwell S, Corwin JA, Soltis NE, Subedy A, Denby KJ, Kliebenstein DJ - Front Microbiol (2015)

Bottom Line: A high level of genetic diversity was found within the 13 isolates.This suggests that the vegetative incompatibility loci within B. cinerea are associated with regions of increased genetic diversity.This suggests that B. cinerea does not display an elevated spontaneous mutation rate.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Sciences, University of California, Davis Davis, CA, USA.

ABSTRACT
How standing genetic variation within a pathogen contributes to diversity in host/pathogen interactions is poorly understood, partly because most studied pathogens are host-specific, clonally reproducing organisms which complicates genetic analysis. In contrast, Botrytis cinerea is a sexually reproducing, true haploid ascomycete that can infect a wide range of diverse plant hosts. While previous work had shown significant genomic variation between two isolates, we proceeded to assess the level and frequency of standing variation in a population of B. cinerea. To begin measuring standing genetic variation in B. cinerea, we re-sequenced the genomes of 13 different isolates and aligned them to the previously sequenced T4 reference genome. In addition one of these isolates was resequenced from four independently repeated cultures. A high level of genetic diversity was found within the 13 isolates. Within this variation, we could identify clusters of genes with major effect polymorphisms, i.e., polymorphisms that lead to a predicted functional knockout, that surrounded genes involved in controlling vegetative incompatibility. The genotype at these loci was able to partially predict the interaction of these isolates in vegetative fusion assays showing that these loci control vegetative incompatibility. This suggests that the vegetative incompatibility loci within B. cinerea are associated with regions of increased genetic diversity. The genome re-sequencing of four clones from the one isolate (Grape) that had been independently propagated over 10 years showed no detectable spontaneous mutation. This suggests that B. cinerea does not display an elevated spontaneous mutation rate. Future work will allow us to test if, and how, this diversity may be contributing to the pathogen's broad host range.

No MeSH data available.


Genomic distribution of non-synonymous and synonymous SNPs. Polymorphisms were assigned as non-synonymous or synonymous amongst the 14 isolates (including T4) and then measured in a 10 gene sliding window as the number of segregating sites (S). The top mirrored plot shows the sliding window of non-synonymous polymorphisms while the bottom shows the corresponding synonymous analysis.
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Figure 5: Genomic distribution of non-synonymous and synonymous SNPs. Polymorphisms were assigned as non-synonymous or synonymous amongst the 14 isolates (including T4) and then measured in a 10 gene sliding window as the number of segregating sites (S). The top mirrored plot shows the sliding window of non-synonymous polymorphisms while the bottom shows the corresponding synonymous analysis.

Mentions: To compare the distribution of potentially neutral and non-neutral polymorphisms the genomic diversity in non-synonymous and synonymous polymorphisms was plotted as the number of segregating sites (S) within 10 kb sliding windows (Figure 5). This identified a number of regions with an elevated rate of clustering of non-synonymous SNPs. Notably, non-synonymous SNPs are abundant in the regions of major effect polymorphism (Figures 3, 5). Highly polymorphic regions of non-synonymous and synonymous SNPs appeared to occur in the same 10 kb bins as each other when visualized in a mirrored plot (Figure 5). However, in the majority of these regions of clustered polymorphisms, the rate of non-synonymous SNPs is noticeably higher (Figures 5, 6A). In contrast, there were only three regions of clustered polymorphisms where the synonymous polymorphism level was higher than the non-synonymous rate (one on chromosome 1 and two on chromosome 13). In contrast to the regions of elevated diversity, synonymous SNPs were more abundant overall across the genome in the regions of moderate or lower polymorphism rates (Figure 6B). This suggests that these regions of high non-synonymous polymorphism and major effect polymorphisms are non-random. Fully testing this hypothesis and assessing the potential for diversifying selection will require the sequencing of more isolates to generate a larger sample size.


Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity.

Atwell S, Corwin JA, Soltis NE, Subedy A, Denby KJ, Kliebenstein DJ - Front Microbiol (2015)

Genomic distribution of non-synonymous and synonymous SNPs. Polymorphisms were assigned as non-synonymous or synonymous amongst the 14 isolates (including T4) and then measured in a 10 gene sliding window as the number of segregating sites (S). The top mirrored plot shows the sliding window of non-synonymous polymorphisms while the bottom shows the corresponding synonymous analysis.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585241&req=5

Figure 5: Genomic distribution of non-synonymous and synonymous SNPs. Polymorphisms were assigned as non-synonymous or synonymous amongst the 14 isolates (including T4) and then measured in a 10 gene sliding window as the number of segregating sites (S). The top mirrored plot shows the sliding window of non-synonymous polymorphisms while the bottom shows the corresponding synonymous analysis.
Mentions: To compare the distribution of potentially neutral and non-neutral polymorphisms the genomic diversity in non-synonymous and synonymous polymorphisms was plotted as the number of segregating sites (S) within 10 kb sliding windows (Figure 5). This identified a number of regions with an elevated rate of clustering of non-synonymous SNPs. Notably, non-synonymous SNPs are abundant in the regions of major effect polymorphism (Figures 3, 5). Highly polymorphic regions of non-synonymous and synonymous SNPs appeared to occur in the same 10 kb bins as each other when visualized in a mirrored plot (Figure 5). However, in the majority of these regions of clustered polymorphisms, the rate of non-synonymous SNPs is noticeably higher (Figures 5, 6A). In contrast, there were only three regions of clustered polymorphisms where the synonymous polymorphism level was higher than the non-synonymous rate (one on chromosome 1 and two on chromosome 13). In contrast to the regions of elevated diversity, synonymous SNPs were more abundant overall across the genome in the regions of moderate or lower polymorphism rates (Figure 6B). This suggests that these regions of high non-synonymous polymorphism and major effect polymorphisms are non-random. Fully testing this hypothesis and assessing the potential for diversifying selection will require the sequencing of more isolates to generate a larger sample size.

Bottom Line: A high level of genetic diversity was found within the 13 isolates.This suggests that the vegetative incompatibility loci within B. cinerea are associated with regions of increased genetic diversity.This suggests that B. cinerea does not display an elevated spontaneous mutation rate.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Sciences, University of California, Davis Davis, CA, USA.

ABSTRACT
How standing genetic variation within a pathogen contributes to diversity in host/pathogen interactions is poorly understood, partly because most studied pathogens are host-specific, clonally reproducing organisms which complicates genetic analysis. In contrast, Botrytis cinerea is a sexually reproducing, true haploid ascomycete that can infect a wide range of diverse plant hosts. While previous work had shown significant genomic variation between two isolates, we proceeded to assess the level and frequency of standing variation in a population of B. cinerea. To begin measuring standing genetic variation in B. cinerea, we re-sequenced the genomes of 13 different isolates and aligned them to the previously sequenced T4 reference genome. In addition one of these isolates was resequenced from four independently repeated cultures. A high level of genetic diversity was found within the 13 isolates. Within this variation, we could identify clusters of genes with major effect polymorphisms, i.e., polymorphisms that lead to a predicted functional knockout, that surrounded genes involved in controlling vegetative incompatibility. The genotype at these loci was able to partially predict the interaction of these isolates in vegetative fusion assays showing that these loci control vegetative incompatibility. This suggests that the vegetative incompatibility loci within B. cinerea are associated with regions of increased genetic diversity. The genome re-sequencing of four clones from the one isolate (Grape) that had been independently propagated over 10 years showed no detectable spontaneous mutation. This suggests that B. cinerea does not display an elevated spontaneous mutation rate. Future work will allow us to test if, and how, this diversity may be contributing to the pathogen's broad host range.

No MeSH data available.