Phytophthora pseudopolonica sp. nov., a new species recovered from stream water in subtropical forests of China

Li, Wenwen; Zhao, Wenxia; Huai, Wenxia

doi:10.1099/ijsem.0.002254

Cited by 6 publications

(4 citation statements)

References 47 publications

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“…P. cacuminis was strongly supported as part of Clade 9b (62). P. pseudopolonica , which was previously classified as clade 9, grouped closely with P. polonica in clade 9a3 (63). New species P. prodigiosa also clustered in clade 9a3, despite being classified as clade 9b by previous ITS-based phylogenies (27, 64).…”

Section: Discussionmentioning

confidence: 87%

An open-access T-BAS phylogeny for EmergingPhytophthoraspecies

Coomber

Saville

Carbone

et al. 2022

Preprint

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Phytophthora species cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1875, it has expanded to comprise over 190 formally described species. There is a need for an open access bioinformatic tool that centralizes diverse streams of sequence data and metadata to facilitate research and identification of Phytophthora species. We used the Tree-Based Alignment Selector Toolkit (T-BAS) to develop a phylogeny of 192 formally described species and 33 informal taxa in the genus Phytophthora using sequences of eight nuclear genes. The phylogenetic tree was inferred using the RAxML maximum likelihood method. A search engine was also developed to identify genotypes of P. infestans based on genetic distance to known lineages. The T-BAS tool provides a visualization framework allowing users to place unknown isolates on a curated phylogeny of all Phytophthora species. Critically, this resource can be updated in real-time to keep pace with new species descriptions. The tool contains metadata such as clade, host species, substrate, sexual characteristics, distribution, and reference literature, which can be visualized on the tree and downloaded for other uses. This phylogenetic resource will allow data sharing among research groups and the database will enable the global Phytophthora community to upload sequences and determine the phylogenetic placement of an isolate within the larger phylogeny and to download sequence data and metadata. The database will be curated by a community of Phytophthora researchers and housed on the T-BAS web portal in the Center for Integrated Fungal Research at NC State. The T-BAS web tool can be leveraged to create similar metadata enhanced phylogenies for diverse populations of pathogens.

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Section: Discussionmentioning

confidence: 87%

An open-access T-BAS phylogeny for EmergingPhytophthoraspecies

Coomber

Saville

Carbone

et al. 2022

Preprint

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“…Phytophthora pseudopolonica , which was previously classified as clade 9, grouped closely with P . polonica in clade 9a3 [ 90 ]. The new species P .…”

Section: Discussionmentioning

confidence: 99%

An open-access T-BAS phylogeny for emerging Phytophthora species

et al. 2023

View full text Add to dashboard Cite

Phytophthora species cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1876, it has expanded to comprise over 190 formally described species. There is a need for an open access phylogenetic tool that centralizes diverse streams of sequence data and metadata to facilitate research and identification of Phytophthora species. We used the Tree-Based Alignment Selector Toolkit (T-BAS) to develop a phylogeny of 192 formally described species and 33 informal taxa in the genus Phytophthora using sequences of eight nuclear genes. The phylogenetic tree was inferred using the RAxML maximum likelihood program. A search engine was also developed to identify microsatellite genotypes of P. infestans based on genetic distance to known lineages. The T-BAS tool provides a visualization framework allowing users to place unknown isolates on a curated phylogeny of all Phytophthora species. Critically, the tree can be updated in real-time as new species are described. The tool contains metadata including clade, host species, substrate, sexual characteristics, distribution, and reference literature, which can be visualized on the tree and downloaded for other uses. This phylogenetic resource will allow data sharing among research groups and the database will enable the global Phytophthora community to upload sequences and determine the phylogenetic placement of an isolate within the larger phylogeny and to download sequence data and metadata. The database will be curated by a community of Phytophthora researchers and housed on the T-BAS web portal in the Center for Integrated Fungal Research at NC State. The T-BAS web tool can be leveraged to create similar metadata enhanced phylogenies for other Oomycete, bacterial or fungal pathogens.

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“…Pieces of approximately 2 mm 2 were cut from the margins of the brown spots and plated in CARP+. Colonies of suspected Phytophthora species growing from plated baits were transferred to CARP (CARP+ without Benlate and hymexazol) to confirm purity and then to CMA for characterization and storage [23].…”

Section: Sampling and Phytophthora Isolationmentioning

confidence: 99%

Phytophthora Species from Xinjiang Wild Apple Forests in China

Huai

Hamiti³

et al. 2019

Forests

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Phytophthora species are well-known destructive forest pathogens, especially in natural ecosystems. The wild apple (Malus sieversii (Ledeb.) Roem.) is the primary ancestor of M. domestica (Borkh.) and important germplasm resource for apple breeding and improvement. During the period from 2016 to 2018, a survey of Phytophthora diversity was performed at four wild apple forest plots (Xin Yuan (XY), Ba Lian (BL), Ku Erdening (KE), and Jin Qikesai (JQ)) on the northern slopes of Tianshan Mountain in Xinjiang, China. Phytophthora species were isolated from baiting leaves from stream, canopy drip, and soil samples and were identified based on morphological observations and the rDNA internal transcribed spacer (ITS) sequence analysis. This is the first comprehensive study from Xinjiang to examine the Phytophthora communities in wild apple forests The 621 resulting Phytophthora isolates were found to reside in 10 different Phytophthora species: eight known species (P. lacustris being the most frequent, followed by P. gonapodyides, P. plurivora, P. gregata, P. chlamydospora, P. inundata, P. virginiana, and P. cactorum) and two previously unrecognized species (P. sp. CYP74 and P. sp. forestsoil-like). The highest species richness of Phytophthora occurred at BL, followed by XY. P. lacustris was the dominant species at BL, XY, and JQ, while P. gonapodyides was the most common at KE. In the present paper, the possible reasons for their distribution, associated implications, and associated diseases are discussed.

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Phytophthora pseudopolonica sp. nov., a new species recovered from stream water in subtropical forests of China

Cited by 6 publications

References 47 publications

An open-access T-BAS phylogeny for EmergingPhytophthoraspecies

An open-access T-BAS phylogeny for EmergingPhytophthoraspecies

An open-access T-BAS phylogeny for emerging Phytophthora species

Phytophthora Species from Xinjiang Wild Apple Forests in China

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