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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.


Radial neighbor-joining phylogenetic trees of nuclear and mitochondrial diversity within B. cinerea. (A) Unrooted genomic phylogeny determined based on pairwise SNP differences in the alignments of 17 B. cinerea strains to the reference T4 (including T4 reference and three replicate lineages independently propagated from the Grape isolate). Branch lengths are proportional to the number of segregating sites that differentiate each pair of isolates. (B) Unrooted mitochondrial phylogeny determined based on pairwise SNP differences to B05.10 in the alignments of 17 B. cinerea strains (including BO5.10 reference and three replicate lineages independently propagated from the Grape isolate). Branch lengths are based on very few polymorphisms and are proportional to the number of segregating sites that differentiate each pair of isolates.
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Figure 2: Radial neighbor-joining phylogenetic trees of nuclear and mitochondrial diversity within B. cinerea. (A) Unrooted genomic phylogeny determined based on pairwise SNP differences in the alignments of 17 B. cinerea strains to the reference T4 (including T4 reference and three replicate lineages independently propagated from the Grape isolate). Branch lengths are proportional to the number of segregating sites that differentiate each pair of isolates. (B) Unrooted mitochondrial phylogeny determined based on pairwise SNP differences to B05.10 in the alignments of 17 B. cinerea strains (including BO5.10 reference and three replicate lineages independently propagated from the Grape isolate). Branch lengths are based on very few polymorphisms and are proportional to the number of segregating sites that differentiate each pair of isolates.

Mentions: To assess the genomic relationships amongst this collection of isolates, we used the genome wide diversity to plot the relationships of the isolates via a Neighbor-joining phylogenetic tree (Figure 2A). This was done using pairwise SNP differences to T4 to generate the alignments. The un-rooted radial phylogeny of the 17 isolates (including the reference T4) showed no statistically supported evidence of clustering indicating that there is no genetic isolation amongst the isolates. Of the isolates sampled, Katie Tomato showed the fewest and A517 the most SNP differences to the reference T4. The only genomes that were significantly associated were those from the repeated resequencing of independently propagated Grape isolate clones (Figure 2A).


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)

Radial neighbor-joining phylogenetic trees of nuclear and mitochondrial diversity within B. cinerea. (A) Unrooted genomic phylogeny determined based on pairwise SNP differences in the alignments of 17 B. cinerea strains to the reference T4 (including T4 reference and three replicate lineages independently propagated from the Grape isolate). Branch lengths are proportional to the number of segregating sites that differentiate each pair of isolates. (B) Unrooted mitochondrial phylogeny determined based on pairwise SNP differences to B05.10 in the alignments of 17 B. cinerea strains (including BO5.10 reference and three replicate lineages independently propagated from the Grape isolate). Branch lengths are based on very few polymorphisms and are proportional to the number of segregating sites that differentiate each pair of isolates.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Radial neighbor-joining phylogenetic trees of nuclear and mitochondrial diversity within B. cinerea. (A) Unrooted genomic phylogeny determined based on pairwise SNP differences in the alignments of 17 B. cinerea strains to the reference T4 (including T4 reference and three replicate lineages independently propagated from the Grape isolate). Branch lengths are proportional to the number of segregating sites that differentiate each pair of isolates. (B) Unrooted mitochondrial phylogeny determined based on pairwise SNP differences to B05.10 in the alignments of 17 B. cinerea strains (including BO5.10 reference and three replicate lineages independently propagated from the Grape isolate). Branch lengths are based on very few polymorphisms and are proportional to the number of segregating sites that differentiate each pair of isolates.
Mentions: To assess the genomic relationships amongst this collection of isolates, we used the genome wide diversity to plot the relationships of the isolates via a Neighbor-joining phylogenetic tree (Figure 2A). This was done using pairwise SNP differences to T4 to generate the alignments. The un-rooted radial phylogeny of the 17 isolates (including the reference T4) showed no statistically supported evidence of clustering indicating that there is no genetic isolation amongst the isolates. Of the isolates sampled, Katie Tomato showed the fewest and A517 the most SNP differences to the reference T4. The only genomes that were significantly associated were those from the repeated resequencing of independently propagated Grape isolate clones (Figure 2A).

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.