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Phylogenetic data for: High diversity of new and known Phytophthora species from phylogenetic Clade 10 in natural ecosystems of Asia, Europe and the Americas

Cite this dataset

Jung, Thomas et al. (2022). Phylogenetic data for: High diversity of new and known Phytophthora species from phylogenetic Clade 10 in natural ecosystems of Asia, Europe and the Americas [Dataset]. Dryad. https://doi.org/10.5061/dryad.41ns1rngw

Abstract

During extensive surveys of Phytophthora diversity, 14 new species were detected in natural ecosystems in Chile, Louisiana, Sweden, Ukraine, Vietnam and Indonesia. Multigene phylogeny based on the nuclear LSU, rpl10, ITS, ßtub, enl, hsp90, tef-1α, ras-ypt1 and tigA and the mitochondrial cox1, nadh1 and rps10 gene sequences demonstrated that they belong to phylogenetic Clade 10 which is structured into three subclades. Subclades 10a and 10b comprise soil- and waterborne species with nonpapillate sporangia and variable breeding systems, including the known P. afrocarpa, P. gallica and P. intercalaris and the new P. ludoviciana, P. procera, P. pseudogallica, P. scandinavica, P. subarctica, P. tenuimura, P. tonkinensis and P. ukrainensis. In contrast, all species in Subclade 10c are airborne with papillate sporangia and homothallic breeding system, including the known P. boehmeriae, P. kernoviae and P. morindae and the new P. celebensis, P. chilensis, P. javanensis, P. multiglobulosa, P. pseudochilensis and P. pseudokernoviae. All new species differed from each other and from related species by a unique combination of morphological characters, the breeding system, cardinal temperatures and growth rates. The biogeography and evolutionary history of Clade 10 are discussed and the hypothesis put forward that the extant subclades originate from early divergences of pre-Gondwanan ancestors (>175 Mya) into water-/soilborne and airborne lineages which during their global spread experienced multiple allopatric and sympatric radiations.

Methods

For phylogenetic analyses, the sequences obtained in this study were complemented with publicly available sequences of isolates from Phytophthora Clade10 sourced from the GenBank Nucleotide Collection and GenBank Whole-Genome Shotgun contigs.

For the informally designated Clade 10 taxa P. sp. canthium and P. sp. Maryland 6 and several isolates of P. boehmeriae and P. gallica, only sequences from the ITS and partly a few other gene regions were available at GenBank, so they could not be included in the multigene phylogenetic analyses of this study. To assess the phylogenetic positions of P. sp. canthium and P. sp. Maryland 6 within Clade 10 and to confirm the identity of a geographically representative range of isolates designated at GenBank as P. boehmeriae and P. gallica, respectively, a 892-character ITS-dataset was analysed. It included 74 isolates of the 14 new Phytophthora species, 53 isolates belonging to the seven described species and three informally designated taxa of Clade 10, and two isolates of the Clade 9 species P. constricta (CBS 125801) and P. fallax (CBS 119109) as outgroup taxa.

The relative phylogenetic positions of the 14 new and eight described or informally designated Phytophthora species from Clade 10 were assessed with a 12-partition (LSU, ITS, βtub, hsp90, tigA, rpl10, tef-1α, enl, ras-ypt1, cox1, nadh1, rps10) dataset (11,259 characters), which included 88 Clade 10 isolates representative of genetic variation and geographic distribution and P. constricta (CBS 125801) and P. fallax as outgroup taxa. For P. fallax, sequences from two isolates (CBS 119109 and ICMP 17563) were combined since for neither of them all 12 loci were available at GenBank (the two isolates shared an identical cox1 sequence). The 90-isolates datasets of the 12 loci were also analysed separately.

Briefly, the sequences of all loci used in the analyses were aligned using the MAFFT v. 7. Bayesian Inference (BI) analyses were performed using BEAST 2 and Maximum-Likelihood (ML) analyses were carried out using IQ-TREE. Detailed methodology can be found on the official publication "High diversity of new and known Phytophthora species from phylogenetic Clade 10 in natural ecosystems of Asia, Europe and the Americas".

Usage notes

Data supplied:

  • Table for identification of species, isolates and sequences used on the phylogenetic analyses;
  • MAFFT sequence alignments (fasta files, used as input files in BEAST 2 and IQ-TREE).
  • Trees obtained from BI and ML analyses (50% majority-rule consensus trees).

Funding

Fundação para a Ciência e Tecnologia, Award: BIODIVERSA/0002/2012

European Union Horizon 2020 Research and Innovation Programme, Award: 63564

Ministry of Education Youth and Sports, Award: CZ.02.1.01/0.0/0.0/15_003/0000453

European Commission, Award: CZ.02.1.01/0.0/0.0/15_003/0000453