Phylogenetic data for the description eight new Halophytophthora species and an updated phylogeny for the genus
Cite this dataset
Horta Jung, Marília et al. (2022). Phylogenetic data for the description eight new Halophytophthora species and an updated phylogeny for the genus [Dataset]. Dryad. https://doi.org/10.5061/dryad.gf1vhhmr2
Abstract
During an oomycete survey in December 2015 ten previously unknown Halophytophthora taxa were isolated from marine and brackish water of tidal ponds and channels in saltmarshes, lagoon ecosystems and river estuaries at seven sites along the Algarve coast in the South of Portugal. Phylogenetic analyses of LSU and ITS datasets, comprising all described Halophytophthora species, the ten new Halophytophthora taxa from Portugal and all relevant and distinctive sequences available from GenBank, provided an updated phylogeny of the genus Halophytophthora s. str. showing for the first time a structure of ten clades designated as Clades 1–10. Nine of the ten new Halophytophthora taxa resided in Clade 6. Based on differences in morphology and temperature-growth relations and a multigene (LSU, ITS, Btub, hsp90, rpl10, tigA, cox1, nadh1, rps10) phylogeny eight new Halophytophthora taxa from Portugal are described here as H. brevisporangia, H. celeris, H. frigida, H. lateralis, H. lusitanica, H. macrosporangia, H. sinuata and H. thermoambigua. Three species, H. frigida, H. macrosporangia and H. sinuata, have a homothallic breeding system while the remaining five species are sterile. Pathogenicity and litter decomposition tests are underway to clarify their pathological and ecological role in the marine and brackish-water ecosystems. More oomycete surveys in yet undersurveyed regions of the world and populationgenetic or phylogenomic analyses of global populations are needed to clarify the origin of the new Halophytophthora species.
Methods
To provide an updated phylogenetic structure of the genus Halophytophthora sensu stricto and resolve the phylogenetic positions of the ten new Halophytophthora taxa from Portugal within the genus two datasets comprising all relevant and distinctive (i) LSU and (ii) ITS sequences available from GenBank and respective sequences from the new Portuguese taxa were analysed. In the LSU analysis representative species of related genera in the Peronosporaceae, Pythiaceae and Salisapiliaceae were included and Aphanomyces euteiches (CBS 156.73) used as outgroup taxon (dataset: 59 isolates and 1 289 characters). In the ITS analysis Phytophthora castanetorum (CBS 142.299) and P. ×cambivora (CBS 141.218) were used as outgroup taxa (dataset: 63 isolates and 1 254 characters). To study the relative phylogenetic positions of the nine new Halophytophthora taxa from Portugal for which isolates were available and related Halophytophthora species, i.e. H. avicennae, H. fluviatilis and H. polymorphica, (iii) a full 9-partition dataset (9 loci: ITS-LSU-rpl10-Btub-hsp90-tigA-cox1-nadh1-rps10) was analysed with P. castanetorum (CBS 142.299) and P. ×cambivora (CBS 141.218) as outgroup taxa (dataset: 60 isolates and 8 759 characters). In addition, ML and BI analyses using a 1 373 characters dataset including 69 ITS sequences of "H. porrigovesica" and representative species from all phylogenetic clades of Halophytophthora and Phytophthora, and other genera in the Peronosporaceae, Pythiaceae and Salisapiliaceae were perfomed to clarify the status of "H. porrigovesica". The sequences obtained in this study were complemented with publicly available sequences from the GenBank Nucleotide Collection and GenBank Whole-Genome Shotgun contigs.
Briefly, the sequences of the loci used in the analyses were aligned using the online version of MAFFT v. 7. Bayesian Inference (BI) analysis was performed using MrBayes version 3.2.7 and Maximum-Likelihood (ML) analysis was carried out using the raxmlGUI v. 2.0 implementation of RAxML.
Detailed methodology can be found on the official publication "Eight new Halophytophthora species from marine and brackish water ecosystems in Portugal and an updated phylogeny for the genus".
Usage notes
Data supplied:
- Table for identification of species, isolates and sequences used on the phylogenetic analyses;
- Input files used in MrBayes and raxmlGUI;
- Original trees obtained from the BI and ML analyses;
Funding
Universidade do Algarve, Portugal, Award: BiodivERsA project RESIPATH: Responses of European Forests and Society to Invasive Pathogens (BIODIVERSA/0002/2012), financed by Portuguese Science and Technology Foundation.
Mendel University in Brno, Czech Republic, Award: Project "Phytophthora Research Centre" (Reg. No. CZ.02.1.01/0.0/0.0/15_003/0000453) financed by the financed by the Czech Ministry for Education, Youth and Sports and the European Regional Development Fund