Genera of phytopathogenic fungi: GOPHY 4

Chen, Q.; Bakhshi, Mounes; Balcì, Y.; Broders, Kirk; Cheewangkoon, R.; Chen, S.F.; Xie, Fan; Gramaje, David; Halleen, F.; Jung, Marília Horta; Jiang, Ning; Jung, Thomas S.; Májek, Tomáš; Marincowitz, Seonju; Milenković, Ivan; Mostert, Lizel; Nakashima, Chiharu; Faziha, I Nurul; Pan, Meng; Raza, Mubashar; Scanu, Bruno; Spies, Christoffel F J; Suhaizan, L.; Suzuki, Hiroyuki; Tian, Cheng; Tomšovský, Michal; Úrbez-Torres, J. R.; Wang, W.; Wingfield, Brenda D.; Wingfield, Michael J.; Yang, Qingyong; Yang, Xiangli; Zare, Rasoul; Zhao, Pengbo; Groenewald, J.Z.; Cai, Lei; Crous, Pedro W.

doi:10.3114/sim.2022.101.06

Cited by 41 publications

(21 citation statements)

References 340 publications

(172 reference statements)

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“…Pathogenicity testing revealed they are both pathogenic to Vitis vinifera. In the multilocus phylogenetic analyses of a comprehensive dataset, including all currently known Cadophora species, all species were well-supported as independent phylogenetic lineages, except for two taxa: Cadophora vinaceae CBS 146263 (Chen et al, 2022), which clustered with strong support with the type isolate of Cadophora ferruginea CBS 146363, and Cadophora sabaouae (Aigoun-Mouhous et al, 2021), which was nested with strong support with the type isolate of Cadophora luteo-olivacea CBS 141.41. Cadophora vinaceae CBS 146263 was described as phylogenetically related to Cadophora ferruginea CBS 146363 with slight differences in culture growth rate and color, and 17 nucleotide differences in their TEF-1a sequences.…”

Section: Discussionmentioning

confidence: 94%

“…In these cases, sequences with high similarity from ex-type and non-type isolates were included for phylogenetic reference utilizing the BLASTn function in NCBI and extensive literature review. Accordingly, relevant reference sequences were retrieved from recent and comprehensive phylogenetic studies for isolates in the genus Cadophora [ (Travadon et al, 2015;Linnakoski et al, 2018;Walsh et al, 2018;Bien and Damm, 2020;Macia-Vicente et al, 2020;Aigoun-Mouhous et al, 2021;Chen et al, 2022;Koukol and Macia-Vicente, 2022); Supplementary Table 2], Cytospora [ (Lawrence et al, 2018a;Pan et al, 2020;Shang et al, 2020;Pan et al, 2021); v. 3.10 (Maddison and Maddison 2016).…”

Section: Fungal Identificationmentioning

confidence: 99%

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Fungal species associated with grapevine trunk diseases in Washington wine grapes and California table grapes, with novelties in the genera Cadophora, Cytospora, and Sporocadus

Travadon

Lawrence

Moyer

et al. 2022

Front. Fungal Biol.

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Grapevine trunk diseases cause serious economic losses to grape growers worldwide. The identification of the causal fungi is critical to implementing appropriate management strategies. Through a culture-based approach, we identified the fungal species composition associated with symptomatic grapevines from wine grapes in southeastern Washington and table grapes in the southern San Joaquin Valley of California, two regions with contrasting winter climates. Species were confirmed through molecular identification, sequencing two to six gene regions per isolate. Multilocus phylogenetic analyses were used to identify novel species. We identified 36 species from 112 isolates, with a combination of species that are new to science, are known causal fungi of grapevine trunk diseases, or are known causal fungi of diseases of other woody plants. The novel species Cadophora columbiana, Cytospora macropycnidia, Cytospora yakimana, and Sporocadus incarnatus are formally described and introduced, six species are newly reported from North America, and grape is reported as a new host for three species. Six species were shared between the two regions: Cytospora viticola, Diatrype stigma, Diplodia seriata, Kalmusia variispora, Phaeoacremonium minimum, and Phaeomoniella chlamydospora. Dominating the fungal community in Washington wine grape vineyards were species in the fungal families Diatrypaceae, Cytosporaceae and Sporocadaceae, whereas in California table grape vineyards, the dominant species were in the families Diatrypaceae, Togniniaceae, Phaeomoniellaceae and Hymenochaetaceae. Pathogenicity tests demonstrated that 10 isolates caused wood discoloration similar to symptomatic wood from which they were originally isolated. Growth rates at temperatures from 5 to 35°C of 10 isolates per region, suggest that adaptation to local climate might explain their distribution.

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Section: Discussionmentioning

confidence: 94%

Section: Fungal Identificationmentioning

confidence: 99%

Fungal species associated with grapevine trunk diseases in Washington wine grapes and California table grapes, with novelties in the genera Cadophora, Cytospora, and Sporocadus

Travadon

Lawrence

Moyer

et al. 2022

Front. Fungal Biol.

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“…Additionally, both sites rely on ITS -based trees, which are often not detailed enough to provide accurate species placements. Recently, the Phytophthora genus was included in the fourth edition of the “Genera of phytopathogenic fungi” series (GOPHY4) (70). This included a whole genus tree of 192 species.…”

Section: Discussionmentioning

confidence: 99%

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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“…In 2000, a phylogeny of 50 Phytophthora species was developed by Cooke and colleagues based on ITS sequence data [ 25 ]. Since then, expanded phylogenies with additional species and loci have been developed as both the genus and sequencing resources have grown [ 14 , 26 – 31 ]. Yang and colleagues presented a robust phylogeny for the genus, including many newly described species and isolates that have since been described as individual species [ 14 ].…”

Section: Introductionmentioning

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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Genera of phytopathogenic fungi: GOPHY 4

Cited by 41 publications

References 340 publications

Fungal species associated with grapevine trunk diseases in Washington wine grapes and California table grapes, with novelties in the genera Cadophora, Cytospora, and Sporocadus

Fungal species associated with grapevine trunk diseases in Washington wine grapes and California table grapes, with novelties in the genera Cadophora, Cytospora, and Sporocadus

An open-access T-BAS phylogeny for EmergingPhytophthoraspecies

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

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