A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

Abstract Background Pathogens of the genus Phytophthora are the etiological agents of many devastating diseases in several high-value crops and forestry species such as potato, tomato, cocoa, and oak, among many others. Phytophthora betacei is a recently described species that causes late blight alm...

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Autores principales:	David A. Ayala-Usma, Martha Cárdenas, Romain Guyot, Maryam Chaib De Mares, Adriana Bernal, Alejandro Reyes Muñoz, Silvia Restrepo
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/982beb7b3ba742e097106c17ed1d74e9
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spelling	oai:doaj.org-article:982beb7b3ba742e097106c17ed1d74e92021-11-08T10:57:33ZA whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans10.1186/s12864-021-08079-y1471-2164https://doaj.org/article/982beb7b3ba742e097106c17ed1d74e92021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08079-yhttps://doaj.org/toc/1471-2164Abstract Background Pathogens of the genus Phytophthora are the etiological agents of many devastating diseases in several high-value crops and forestry species such as potato, tomato, cocoa, and oak, among many others. Phytophthora betacei is a recently described species that causes late blight almost exclusively in tree tomatoes, and it is closely related to Phytophthora infestans that causes the disease in potato crops and other Solanaceae. This study reports the assembly and annotation of the genomes of P. betacei P8084, the first of its species, and P. infestans RC1-10, a Colombian strain from the EC-1 lineage, using long-read SMRT sequencing technology. Results Our results show that P. betacei has the largest sequenced genome size of the Phytophthora genus so far with 270 Mb. A moderate transposable element invasion and a whole genome duplication likely explain its genome size expansion when compared to P. infestans, whereas P. infestans RC1-10 has expanded its genome under the activity of transposable elements. The high diversity and abundance (in terms of copy number) of classified and unclassified transposable elements in P. infestans RC1-10 relative to P. betacei bears testimony of the power of long-read technologies to discover novel repetitive elements in the genomes of organisms. Our data also provides support for the phylogenetic placement of P. betacei as a standalone species and as a sister group of P. infestans. Finally, we found no evidence to support the idea that the genome of P. betacei P8084 follows the same gene-dense/gense-sparse architecture proposed for P. infestans and other filamentous plant pathogens. Conclusions This study provides the first genome-wide picture of P. betacei and expands the genomic resources available for P. infestans. This is a contribution towards the understanding of the genome biology and evolutionary history of Phytophthora species belonging to the subclade 1c.David A. Ayala-UsmaMartha CárdenasRomain GuyotMaryam Chaib De MaresAdriana BernalAlejandro Reyes MuñozSilvia RestrepoBMCarticleBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-21 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Biotechnology TP248.13-248.65 Genetics QH426-470 David A. Ayala-Usma Martha Cárdenas Romain Guyot Maryam Chaib De Mares Adriana Bernal Alejandro Reyes Muñoz Silvia Restrepo A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans
description	Abstract Background Pathogens of the genus Phytophthora are the etiological agents of many devastating diseases in several high-value crops and forestry species such as potato, tomato, cocoa, and oak, among many others. Phytophthora betacei is a recently described species that causes late blight almost exclusively in tree tomatoes, and it is closely related to Phytophthora infestans that causes the disease in potato crops and other Solanaceae. This study reports the assembly and annotation of the genomes of P. betacei P8084, the first of its species, and P. infestans RC1-10, a Colombian strain from the EC-1 lineage, using long-read SMRT sequencing technology. Results Our results show that P. betacei has the largest sequenced genome size of the Phytophthora genus so far with 270 Mb. A moderate transposable element invasion and a whole genome duplication likely explain its genome size expansion when compared to P. infestans, whereas P. infestans RC1-10 has expanded its genome under the activity of transposable elements. The high diversity and abundance (in terms of copy number) of classified and unclassified transposable elements in P. infestans RC1-10 relative to P. betacei bears testimony of the power of long-read technologies to discover novel repetitive elements in the genomes of organisms. Our data also provides support for the phylogenetic placement of P. betacei as a standalone species and as a sister group of P. infestans. Finally, we found no evidence to support the idea that the genome of P. betacei P8084 follows the same gene-dense/gense-sparse architecture proposed for P. infestans and other filamentous plant pathogens. Conclusions This study provides the first genome-wide picture of P. betacei and expands the genomic resources available for P. infestans. This is a contribution towards the understanding of the genome biology and evolutionary history of Phytophthora species belonging to the subclade 1c.
format	article
author	David A. Ayala-Usma Martha Cárdenas Romain Guyot Maryam Chaib De Mares Adriana Bernal Alejandro Reyes Muñoz Silvia Restrepo
author_facet	David A. Ayala-Usma Martha Cárdenas Romain Guyot Maryam Chaib De Mares Adriana Bernal Alejandro Reyes Muñoz Silvia Restrepo
author_sort	David A. Ayala-Usma
title	A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans
title_short	A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans
title_full	A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans
title_fullStr	A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans
title_full_unstemmed	A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans
title_sort	whole genome duplication drives the genome evolution of phytophthora betacei, a closely related species to phytophthora infestans
publisher	BMC
publishDate	2021
url	https://doaj.org/article/982beb7b3ba742e097106c17ed1d74e9
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A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

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