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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.


Pairwise Vegetative Incompatibility. All pairwise crosses were tested in at least triplicate and the incompatibility was scored as compatible (C), weakly incompatible (W), and incompatible (I) and results are shown above. χ2 was used to test if there was a difference in incompatibility when crossing within or between the Major Effect Haplotypes (χ2 = 4.9, P = 0.02, N = 66, df = 2).
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Figure 4: Pairwise Vegetative Incompatibility. All pairwise crosses were tested in at least triplicate and the incompatibility was scored as compatible (C), weakly incompatible (W), and incompatible (I) and results are shown above. χ2 was used to test if there was a difference in incompatibility when crossing within or between the Major Effect Haplotypes (χ2 = 4.9, P = 0.02, N = 66, df = 2).

Mentions: To test if the major effect allelic diversity of the heterokaryon incompatible loci located within the major effect clusters could be controlling variation in vegetative incompatibility; the isolates were grouped based on their haplotypes at these loci (Figure 4 and replication information is provided in Table S6). We then conducted vegetative incompatibility assays between all pairs of isolates to test if the heterokaryon haplotype modulated vegetative fusion. In these tests, the incompatibility was significantly stronger when vegetative fusion was tested between isolates with different haplotypes than when they shared a haplotype (χ2 = 4.9, P = 0.02, N = 66, df = 2). All strong incompatibilities were found when vegetative fusion was tested between isolates that represent different haplotypes at the major effect clusters (Figure 4). In contrast, when vegetative fusion was tested within a haplotype group, there were no strong incompatibilities (Figure 4). This suggests that while we have likely identified some components controlling diversity in the vegetative fusion process, there are other vegetative incompatibility loci remaining to be identified potentially via sequencing a larger collection of isolates.


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)

Pairwise Vegetative Incompatibility. All pairwise crosses were tested in at least triplicate and the incompatibility was scored as compatible (C), weakly incompatible (W), and incompatible (I) and results are shown above. χ2 was used to test if there was a difference in incompatibility when crossing within or between the Major Effect Haplotypes (χ2 = 4.9, P = 0.02, N = 66, df = 2).
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: Pairwise Vegetative Incompatibility. All pairwise crosses were tested in at least triplicate and the incompatibility was scored as compatible (C), weakly incompatible (W), and incompatible (I) and results are shown above. χ2 was used to test if there was a difference in incompatibility when crossing within or between the Major Effect Haplotypes (χ2 = 4.9, P = 0.02, N = 66, df = 2).
Mentions: To test if the major effect allelic diversity of the heterokaryon incompatible loci located within the major effect clusters could be controlling variation in vegetative incompatibility; the isolates were grouped based on their haplotypes at these loci (Figure 4 and replication information is provided in Table S6). We then conducted vegetative incompatibility assays between all pairs of isolates to test if the heterokaryon haplotype modulated vegetative fusion. In these tests, the incompatibility was significantly stronger when vegetative fusion was tested between isolates with different haplotypes than when they shared a haplotype (χ2 = 4.9, P = 0.02, N = 66, df = 2). All strong incompatibilities were found when vegetative fusion was tested between isolates that represent different haplotypes at the major effect clusters (Figure 4). In contrast, when vegetative fusion was tested within a haplotype group, there were no strong incompatibilities (Figure 4). This suggests that while we have likely identified some components controlling diversity in the vegetative fusion process, there are other vegetative incompatibility loci remaining to be identified potentially via sequencing a larger collection of isolates.

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.