Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops

Rui Fang Gao; Jie Yu Wang; Ke Wei Liu; Kouki Yoshida; Yu Yun Hsiao; Yi Xiang Shi; Kun Chan Tsai; You Yi Chen; Nobutaka Mitsuda; Chieh Kai Liang; Zhi Wen Wang; Ying Wang; Di Yang Zhang; Laiqiang Huang; Xiang Zhao; Wen Ying Zhong; Ying Hui Cheng; Zi De Jiang; Ming He Li; Wei Hong Sun; Xia Yu; Wenqi Hu; Zhuang Zhou; Xiao Fan Zhou; Chuan Ming Yeh; Kazutaka Katoh; Wen Chieh Tsai; Zhong Jian Liu; Francis Martin; Gui Ming Zhang

doi:10.1016/j.heliyon.2021.e06317

Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops

Rui Fang Gao, Jie Yu Wang, Ke Wei Liu, Kouki Yoshida, Yu Yun Hsiao, Yi Xiang Shi, Kun Chan Tsai, You Yi Chen, Nobutaka Mitsuda, Chieh Kai Liang, Zhi Wen Wang, Ying Wang, Di Yang Zhang, Laiqiang Huang, Xiang Zhao, Wen Ying Zhong, Ying Hui Cheng, Zi De Jiang, Ming He Li, Wei Hong SunXia Yu, Wenqi Hu, Zhuang Zhou, Xiao Fan Zhou, Chuan Ming Yeh, Kazutaka Katoh, Wen Chieh Tsai, Zhong Jian Liu, Francis Martin, Gui Ming Zhang

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

6 Citations (Scopus)

Abstract

The oomycete genus Phytophthora includes devastating plant pathogens that are found in almost all ecosystems. We sequenced the genomes of two quarantined Phytophthora species–P. fragariae and P. rubi. Comparing these Phytophthora species and related genera allowed reconstruction of the phylogenetic relationships within the genus Phytophthora and revealed Phytophthora genomic features associated with infection and pathogenicity. We found that several hundred Phytophthora genes are putatively inherited from red algae, but Phytophthora does not have vestigial plastids originating from phototrophs. The horizontally-transferred Phytophthora genes are abundant transposons that “transmit” exogenous gene to Phytophthora species thus bring about the gene recombination possibility. Several expansion events of Phytophthora gene families associated with cell wall biogenesis can be used as mutational targets to elucidate gene function in pathogenic interactions with host plants. This work enhanced the understanding of Phytophthora evolution and will also be helpful for the design of phytopathological control strategies. Phytophthora; Genome; Phylogenetic; Pathogenicity; Horizontally gene transfer.

Original language	English
Article number	e06317
Journal	Heliyon
Volume	7
Issue number	2
DOIs	https://doi.org/10.1016/j.heliyon.2021.e06317
Publication status	Published - 2021 Feb

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Gao, R. F., Wang, J. Y., Liu, K. W., Yoshida, K., Hsiao, Y. Y., Shi, Y. X., Tsai, K. C., Chen, Y. Y., Mitsuda, N., Liang, C. K., Wang, Z. W., Wang, Y., Zhang, D. Y., Huang, L., Zhao, X., Zhong, W. Y., Cheng, Y. H., Jiang, Z. D., Li, M. H., ... Zhang, G. M. (2021). Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops. Heliyon, 7(2), Article e06317. https://doi.org/10.1016/j.heliyon.2021.e06317

@article{322a9ade8ff44d5782f5d6d4c14e48bb,

title = "Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops",

abstract = "The oomycete genus Phytophthora includes devastating plant pathogens that are found in almost all ecosystems. We sequenced the genomes of two quarantined Phytophthora species–P. fragariae and P. rubi. Comparing these Phytophthora species and related genera allowed reconstruction of the phylogenetic relationships within the genus Phytophthora and revealed Phytophthora genomic features associated with infection and pathogenicity. We found that several hundred Phytophthora genes are putatively inherited from red algae, but Phytophthora does not have vestigial plastids originating from phototrophs. The horizontally-transferred Phytophthora genes are abundant transposons that “transmit” exogenous gene to Phytophthora species thus bring about the gene recombination possibility. Several expansion events of Phytophthora gene families associated with cell wall biogenesis can be used as mutational targets to elucidate gene function in pathogenic interactions with host plants. This work enhanced the understanding of Phytophthora evolution and will also be helpful for the design of phytopathological control strategies. Phytophthora; Genome; Phylogenetic; Pathogenicity; Horizontally gene transfer.",

author = "Gao, {Rui Fang} and Wang, {Jie Yu} and Liu, {Ke Wei} and Kouki Yoshida and Hsiao, {Yu Yun} and Shi, {Yi Xiang} and Tsai, {Kun Chan} and Chen, {You Yi} and Nobutaka Mitsuda and Liang, {Chieh Kai} and Wang, {Zhi Wen} and Ying Wang and Zhang, {Di Yang} and Laiqiang Huang and Xiang Zhao and Zhong, {Wen Ying} and Cheng, {Ying Hui} and Jiang, {Zi De} and Li, {Ming He} and Sun, {Wei Hong} and Xia Yu and Wenqi Hu and Zhuang Zhou and Zhou, {Xiao Fan} and Yeh, {Chuan Ming} and Kazutaka Katoh and Tsai, {Wen Chieh} and Liu, {Zhong Jian} and Francis Martin and Zhang, {Gui Ming}",

note = "Publisher Copyright: {\textcopyright} 2021",

year = "2021",

month = feb,

doi = "10.1016/j.heliyon.2021.e06317",

language = "English",

volume = "7",

journal = "Heliyon",

issn = "2405-8440",

publisher = "Elsevier BV",

number = "2",

}

Gao, RF, Wang, JY, Liu, KW, Yoshida, K, Hsiao, YY, Shi, YX, Tsai, KC, Chen, YY, Mitsuda, N, Liang, CK, Wang, ZW, Wang, Y, Zhang, DY, Huang, L, Zhao, X, Zhong, WY, Cheng, YH, Jiang, ZD, Li, MH, Sun, WH, Yu, X, Hu, W, Zhou, Z, Zhou, XF, Yeh, CM, Katoh, K, Tsai, WC, Liu, ZJ, Martin, F & Zhang, GM 2021, 'Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops', Heliyon, vol. 7, no. 2, e06317. https://doi.org/10.1016/j.heliyon.2021.e06317

TY - JOUR

T1 - Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops

AU - Gao, Rui Fang

AU - Wang, Jie Yu

AU - Liu, Ke Wei

AU - Yoshida, Kouki

AU - Hsiao, Yu Yun

AU - Shi, Yi Xiang

AU - Tsai, Kun Chan

AU - Chen, You Yi

AU - Mitsuda, Nobutaka

AU - Liang, Chieh Kai

AU - Wang, Zhi Wen

AU - Wang, Ying

AU - Zhang, Di Yang

AU - Huang, Laiqiang

AU - Zhao, Xiang

AU - Zhong, Wen Ying

AU - Cheng, Ying Hui

AU - Jiang, Zi De

AU - Li, Ming He

AU - Sun, Wei Hong

AU - Yu, Xia

AU - Hu, Wenqi

AU - Zhou, Zhuang

AU - Zhou, Xiao Fan

AU - Yeh, Chuan Ming

AU - Katoh, Kazutaka

AU - Tsai, Wen Chieh

AU - Liu, Zhong Jian

AU - Martin, Francis

AU - Zhang, Gui Ming

PY - 2021/2

Y1 - 2021/2

N2 - The oomycete genus Phytophthora includes devastating plant pathogens that are found in almost all ecosystems. We sequenced the genomes of two quarantined Phytophthora species–P. fragariae and P. rubi. Comparing these Phytophthora species and related genera allowed reconstruction of the phylogenetic relationships within the genus Phytophthora and revealed Phytophthora genomic features associated with infection and pathogenicity. We found that several hundred Phytophthora genes are putatively inherited from red algae, but Phytophthora does not have vestigial plastids originating from phototrophs. The horizontally-transferred Phytophthora genes are abundant transposons that “transmit” exogenous gene to Phytophthora species thus bring about the gene recombination possibility. Several expansion events of Phytophthora gene families associated with cell wall biogenesis can be used as mutational targets to elucidate gene function in pathogenic interactions with host plants. This work enhanced the understanding of Phytophthora evolution and will also be helpful for the design of phytopathological control strategies. Phytophthora; Genome; Phylogenetic; Pathogenicity; Horizontally gene transfer.

AB - The oomycete genus Phytophthora includes devastating plant pathogens that are found in almost all ecosystems. We sequenced the genomes of two quarantined Phytophthora species–P. fragariae and P. rubi. Comparing these Phytophthora species and related genera allowed reconstruction of the phylogenetic relationships within the genus Phytophthora and revealed Phytophthora genomic features associated with infection and pathogenicity. We found that several hundred Phytophthora genes are putatively inherited from red algae, but Phytophthora does not have vestigial plastids originating from phototrophs. The horizontally-transferred Phytophthora genes are abundant transposons that “transmit” exogenous gene to Phytophthora species thus bring about the gene recombination possibility. Several expansion events of Phytophthora gene families associated with cell wall biogenesis can be used as mutational targets to elucidate gene function in pathogenic interactions with host plants. This work enhanced the understanding of Phytophthora evolution and will also be helpful for the design of phytopathological control strategies. Phytophthora; Genome; Phylogenetic; Pathogenicity; Horizontally gene transfer.

UR - http://www.scopus.com/inward/record.url?scp=85101069708&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85101069708&partnerID=8YFLogxK

U2 - 10.1016/j.heliyon.2021.e06317

DO - 10.1016/j.heliyon.2021.e06317

M3 - Article

AN - SCOPUS:85101069708

SN - 2405-8440

VL - 7

JO - Heliyon

JF - Heliyon

IS - 2

M1 - e06317

ER -

Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops

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