DOI: 10.5061/dryad.gf1vhhmr2
title: Phylogenetic data for the description eight new Halophytophthora species and an updated phylogeny for the genus

description: 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.
description: To provide an updated
 phylogenetic structure of the genus <i>Halophytophthora</i>
 sensu stricto and resolve the phylogenetic positions of the ten new
 <i>Halophytophthora</i> 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 <i>Aphanomyces euteiches</i> (CBS 156.73)
 used as outgroup taxon (dataset: 59 isolates and 1 289 characters). In the
 ITS analysis <i>Phytophthora castanetorum</i> (CBS 142.299)
 and <i>P.</i> ×<i>cambivora</i> (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
 <i>Halophytophthora</i> taxa from Portugal for which isolates
 were available and related <i>Halophytophthora</i> species,
 i.e. <i>H. avicennae</i>, <i>H. fluviatilis</i>
 and <i>H. polymorphica</i>, (iii) a full 9-partition dataset
 (9 loci:
 ITS-LSU-<i>rpl10</i>-<i>Btub</i>-<i>hsp90</i>-<i>tigA</i>-<i>cox1</i>-<i>nadh1</i>-<i>rps10</i>) was analysed with <i>P. castanetorum</i> (CBS 142.299) and <i>P.</i> ×<i>cambivora</i> (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 <i>"H. porrigovesica"</i> and representative species from all phylogenetic clades of <i>Halophytophthora </i>and<i> Phytophthora</i>, and other genera in the Peronosporaceae, Pythiaceae and Salisapiliaceae were perfomed to clarify the status of <i>"H. porrigovesica</i>". 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 "<b>Eight new <i>Halophytophthora</i> species from marine and brackish water ecosystems in Portugal and an updated phylogeny for the genus</b>".
description: 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<strong>;</strong>