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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #388005
Research Project: Management of Pathogens for Strawberry and Vegetable Production Systems

Location: Crop Improvement and Protection Research

Title: Whole genome sequencing and phylogenomic analysis show support for the splitting of genus Pythium

Author
item NGUYEN, HAI - Agriculture And Agri-Food Canada
item DODGE, ANNETTE - Agriculture And Agri-Food Canada
item DADEJ, KASIA - Agriculture And Agri-Food Canada
item RINTOUL, TARA - Agriculture And Agri-Food Canada
item PONOMAREVA, EKATERINA - Agriculture And Agri-Food Canada
item Martin, Frank
item DE COCK, ARTHUR - Fungal Biodiversity
item LEVESQUE, C - Agriculture And Agri-Food Canada
item REDHEAD, SCOTT - Agriculture And Agri-Food Canada
item SPIES, CHRISTOFFEL - Agricultural Research Council Of South Africa

Submitted to: Mycologia
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/18/2022
Publication Date: 5/6/2022
Citation: Nguyen, H.D., Dodge, A., Dadej, K., Rintoul, T.L., Ponomareva, E., Martin, F.N., de Cock, A.W., Levesque, C.A., Redhead, S.A., Spies, C.F. 2022. Whole genome sequencing and phylogenomic analysis show support for the splitting of genus Pythium. Mycologia. 114(3):501-515. https://doi.org/10.1080/00275514.2022.2045116.
DOI: https://doi.org/10.1080/00275514.2022.2045116

Interpretive Summary: The taxonomy of the genus Pythium has needed revision to align with results with recent advances in molecular genetic research. This submission looked at genome assemblies for 119 taxa and extracted 148 genes to use in an analysis of evolutionary relationships among them. The results supported a prior suggestion in the literature to split the genus Pythium into four genera, a proposal that lacked strong support from the data previously used, and to rename the new genera with taxonomically valid names. The analysis provided is in this submission

Technical Abstract: The genus Pythium sensu lato (s.l.), originally described by Pringsheim, comprises hundreds of species including some that are important plant pathogens. Early molecular phylogenetic studies revealed the paraphyletic nature of Pythium, which led to a formal proposal by Uzuhashi et al. for splitting the genus into Pythium sensu stricto (s.s.), Elongisporangium, Globisporangium, and Ovatisporangium (syn. Phytopythium) using morphological characters and phylogenies of the cox2 and 28S regions. Although the split was justified by the delineating morphological characters, there was weakness in the molecular analyses, which created doubt, confusion and reluctance from the scientific community to adopt these new genera for the description of new species in the last decade. In this study, whole genomes of 109 strains of Pythium and close relatives were sequenced, assembled and annotated. These data were combined with 10 genomes sequenced from previous studies, and phylogenomic analyses were performed with 148 single copy genes, represented in at least 90% of the taxa in the dataset. The results show strong support for the division of Pythium (s.l.) as proposed by Uzuhashi et al. Based on our molecular analyses and review of the Pythium generic concepts, we urge the scientific community to adopt the generic names Pythium, Elongisporangium, Globisporangium, and their concepts as proposed by Uzuhashi et al, in their work going forward. In order to consolidate the taxonomy of these genera some of the recently described Pythium spp. are transferred to Elongisporangium and Globisporangium.