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

Susanna Atwell; Jason A. Corwin; Nicole E. Soltis; Anushryia Subedy; Katherine J. Denby; Daniel J. Kliebenstein

doi:10.3389/fmicb.2015.00996

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

Susanna Atwell, Jason A. Corwin, Nicole E. Soltis, Anushryia Subedy, Katherine J. Denby, Daniel J. Kliebenstein^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	00996
Number of pages	14
Journal	Frontiers in Microbiology
Volume	6
DOIs	https://doi.org/10.3389/fmicb.2015.00996
Publication status	Published - 2015

Keywords

Botrytis cinerea
Diversity
Genome resequencing
Standing genetic variation
Vegetative incompatibility loci

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10.3389/fmicb.2015.00996

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title = "Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity",

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.",

keywords = "Botrytis cinerea, Diversity, Genome resequencing, Standing genetic variation, Vegetative incompatibility loci",

author = "Susanna Atwell and Corwin, {Jason A.} and Soltis, {Nicole E.} and Anushryia Subedy and Denby, {Katherine J.} and Kliebenstein, {Daniel J.}",

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AU - Atwell, Susanna

AU - Corwin, Jason A.

AU - Soltis, Nicole E.

AU - Subedy, Anushryia

AU - Denby, Katherine J.

AU - Kliebenstein, Daniel J.

PY - 2015

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AB - 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.

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

Abstract

Keywords

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