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Sequence alignment for 7 gene regions for new Phytophthora species in clade 2a

Citation

Burgess, Treena (2021), Sequence alignment for 7 gene regions for new Phytophthora species in clade 2a , Dryad, Dataset, https://doi.org/10.5061/dryad.02v6wwq22

Abstract

Five new taxa from Phytophthora ITS Clade 2a are described from Cinnamomum cassia plantations and adjacent waterways in Van Yen, Vietnam, and disturbed rainforest in the Hela Province of Papua New Guinea and from disturbed forest on Christmas Island. Phylogenetic analyses were performed using data from nuclear regions (ITS, β-tubulin; Heat shock protein 90) and mitochondrial regions (cytochrome c oxidase subunit 1; cytochrome c oxidase subunit2; NADH dehydrogenase subunit 1; ribosomal protein L10). The molecular data supported recognition of three species: Phytophthora insulinativitatica, P. multibullata and P. x vanyenensis and two informal taxa, P. sp. germisporangia and P. sp. awatangi. P. x vanyenensis appears to be a hybrid between P. sp. mekongensis and an unknown species. P. multibullata and P. sp. germisporangia are phylogenetically close to P. citrophthora, but morphologically distinct. P. insulinativitatica is most closely related to P. botryosa but has different morphology. P. sp. germisporangia and P. sp. awatangi were morphologically distinct and separated in the phylogeny based on mitochondrial sequences, but their nuclear sequences were identical. When comparing the sequences of these new species to that available on GenBank, it became evident that some of these species shared similarity with isolates submitted to GenBank under other species names and a re-evaluation of all P. meadii and P. colocasiae ITS sequence data identified an additional 7 putatively new species all isolated from Asia. The results support the view that many more Phytophthora species remain to be discovered in the Asia-Pacific region.

Methods

To confirm the new species gene regions were amplified and sequenced in both directions; the internal transcribed spacer region (ITS), cytochrome oxidase subunit 1 (cox1), cytochrome c oxidase subunit2 cox2, NADH dehydrogenase subunit 1 (nadh1) ribosomal protein L10 (rps10), β-tubulin and heat shock protein 90 (hsp90)

The sequence data of Phytophthora isolates used in this study were compared with other closely related species (ITS clade 2a) that were either sequenced for this study or taken from GenBank (http://www.ncbi.nlm.nih.gov/) or the Phytophthora database (http://www.phytophthoradb.org/) or the IDphy online resource (http://idtools.org/id/phytophthora/index.php). Sequence data were compiled in Geneious Prime 2019 (Biomatters; available from http://www.geneious.com/). The most appropriate substitution model was determined using jModelTest (Posada 2008). Bayesian analysis with MrBayes (Ronquist et al. 2011) and Maximum Likelihood (ML) analysis using RAxML (Stamatakis 2014) were performed as a plugins within the Geneious software.

Usage Notes

There are seven nexus sequence alignment files that can be directly uploaded