Genome-Wide Increased Copy Number is Associated with Emergence of Dominant Clones of the Irish Potato Famine Pathogen <named-content content-type="genus-species">Phytophthora infestans</named-content>

ABSTRACT The plant pathogen that caused the Irish potato famine, Phytophthora infestans, continues to reemerge globally. These modern epidemics are caused by clonally reproducing lineages. In contrast, a sexual mode of reproduction is observed at its center of origin in Mexico. We conducted a compar...

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Autores principales:	Brian J. Knaus, Javier F. Tabima, Shankar K. Shakya, Howard S. Judelson, Niklaus J. Grünwald
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	Irish famine Phytophthora copy number variation oomycetes plant pathogen plant pathology Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/f0506aa211534f23ba1c8a973d8b10fc
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spelling	oai:doaj.org-article:f0506aa211534f23ba1c8a973d8b10fc2021-11-15T15:56:46ZGenome-Wide Increased Copy Number is Associated with Emergence of Dominant Clones of the Irish Potato Famine Pathogen <named-content content-type="genus-species">Phytophthora infestans</named-content>10.1128/mBio.00326-202150-7511https://doaj.org/article/f0506aa211534f23ba1c8a973d8b10fc2020-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00326-20https://doaj.org/toc/2150-7511ABSTRACT The plant pathogen that caused the Irish potato famine, Phytophthora infestans, continues to reemerge globally. These modern epidemics are caused by clonally reproducing lineages. In contrast, a sexual mode of reproduction is observed at its center of origin in Mexico. We conducted a comparative genomic analysis of 47 high-coverage genomes to infer changes in genic copy number. We included samples from sexual populations at the center of origin as well as several dominant clonal lineages sampled worldwide. We conclude that sexual populations at the center of origin are diploid, as was the lineage that caused the famine, while modern clonal lineages showed increased copy number (3×). Copy number variation (CNV) was found genome-wide and did not to adhere to the two-speed genome hypothesis. Although previously reported, tetraploidy was not found in any of the genomes evaluated. We propose a model of dominant clone emergence supported by the epidemiological record (e.g., EU_13_A2, US-11, US-23) whereby a higher copy number provides fitness, leading to replacement of prior clonal lineages. IMPORTANCE The plant pathogen implicated in the Irish potato famine, Phytophthora infestans, continues to reemerge globally. Understanding changes in the genome during emergence can provide insights useful for managing this pathogen. Previous work has relied on studying individuals from the United States, South America, Europe, and China reporting that these can occur as diploids, triploids, or tetraploids and are clonal. We studied variation in sexual populations at the pathogen’s center of origin, in Mexico, where it has been reported to reproduce sexually as well as within clonally reproducing, dominant clones from the United States and Europe. Our results newly show that sexual populations at the center of origin are diploid, whereas populations elsewhere are more variable and show genome-wide variation in gene copy number. We propose a model of evolution whereby new pathogen clones emerge predominantly by increasing the gene copy number genome-wide.Brian J. KnausJavier F. TabimaShankar K. ShakyaHoward S. JudelsonNiklaus J. GrünwaldAmerican Society for MicrobiologyarticleIrish faminePhytophthoracopy number variationoomycetesplant pathogenplant pathologyMicrobiologyQR1-502ENmBio, Vol 11, Iss 3 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Irish famine Phytophthora copy number variation oomycetes plant pathogen plant pathology Microbiology QR1-502
spellingShingle	Irish famine Phytophthora copy number variation oomycetes plant pathogen plant pathology Microbiology QR1-502 Brian J. Knaus Javier F. Tabima Shankar K. Shakya Howard S. Judelson Niklaus J. Grünwald Genome-Wide Increased Copy Number is Associated with Emergence of Dominant Clones of the Irish Potato Famine Pathogen <named-content content-type="genus-species">Phytophthora infestans</named-content>
description	ABSTRACT The plant pathogen that caused the Irish potato famine, Phytophthora infestans, continues to reemerge globally. These modern epidemics are caused by clonally reproducing lineages. In contrast, a sexual mode of reproduction is observed at its center of origin in Mexico. We conducted a comparative genomic analysis of 47 high-coverage genomes to infer changes in genic copy number. We included samples from sexual populations at the center of origin as well as several dominant clonal lineages sampled worldwide. We conclude that sexual populations at the center of origin are diploid, as was the lineage that caused the famine, while modern clonal lineages showed increased copy number (3×). Copy number variation (CNV) was found genome-wide and did not to adhere to the two-speed genome hypothesis. Although previously reported, tetraploidy was not found in any of the genomes evaluated. We propose a model of dominant clone emergence supported by the epidemiological record (e.g., EU_13_A2, US-11, US-23) whereby a higher copy number provides fitness, leading to replacement of prior clonal lineages. IMPORTANCE The plant pathogen implicated in the Irish potato famine, Phytophthora infestans, continues to reemerge globally. Understanding changes in the genome during emergence can provide insights useful for managing this pathogen. Previous work has relied on studying individuals from the United States, South America, Europe, and China reporting that these can occur as diploids, triploids, or tetraploids and are clonal. We studied variation in sexual populations at the pathogen’s center of origin, in Mexico, where it has been reported to reproduce sexually as well as within clonally reproducing, dominant clones from the United States and Europe. Our results newly show that sexual populations at the center of origin are diploid, whereas populations elsewhere are more variable and show genome-wide variation in gene copy number. We propose a model of evolution whereby new pathogen clones emerge predominantly by increasing the gene copy number genome-wide.
format	article
author	Brian J. Knaus Javier F. Tabima Shankar K. Shakya Howard S. Judelson Niklaus J. Grünwald
author_facet	Brian J. Knaus Javier F. Tabima Shankar K. Shakya Howard S. Judelson Niklaus J. Grünwald
author_sort	Brian J. Knaus
title	Genome-Wide Increased Copy Number is Associated with Emergence of Dominant Clones of the Irish Potato Famine Pathogen <named-content content-type="genus-species">Phytophthora infestans</named-content>
title_short	Genome-Wide Increased Copy Number is Associated with Emergence of Dominant Clones of the Irish Potato Famine Pathogen <named-content content-type="genus-species">Phytophthora infestans</named-content>
title_full	Genome-Wide Increased Copy Number is Associated with Emergence of Dominant Clones of the Irish Potato Famine Pathogen <named-content content-type="genus-species">Phytophthora infestans</named-content>
title_fullStr	Genome-Wide Increased Copy Number is Associated with Emergence of Dominant Clones of the Irish Potato Famine Pathogen <named-content content-type="genus-species">Phytophthora infestans</named-content>
title_full_unstemmed	Genome-Wide Increased Copy Number is Associated with Emergence of Dominant Clones of the Irish Potato Famine Pathogen <named-content content-type="genus-species">Phytophthora infestans</named-content>
title_sort	genome-wide increased copy number is associated with emergence of dominant clones of the irish potato famine pathogen <named-content content-type="genus-species">phytophthora infestans</named-content>
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/f0506aa211534f23ba1c8a973d8b10fc
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Genome-Wide Increased Copy Number is Associated with Emergence of Dominant Clones of the Irish Potato Famine Pathogen <named-content content-type="genus-species">Phytophthora infestans</named-content>

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