DOI: 10.5061/dryad.n2z34tmx3
title: Data from: Whole genome sequencing and phylogenomic analysis show support for the splitting of genus Pythium

description: The genus Pythium (nom. cons.) sensu lato (s.l.) is
 composed of many important species of plant pathogens. Early molecular
 phylogenetic studies suggested paraphyly of Pythium, which led to
 a formal proposal by Uzuhashi and colleagues in 2010 to split the genus
 into Pythium sensu stricto
 (s.s.), Elongisporangium, Globisporangium,
 Ovatisporangium (= Phytopythium),
 and Pilasporangium using morphological characters and
 phylogenies of the mt cytochrome c oxidase subunit 2
 (cox2) and D1–D2 domains of nuc 28S rDNA. Although the split was fairly
 justified by the delineating morphological characters, there were
 weaknesses in the molecular analyses, which created reluctance in the
 scientific community to adopt these new genera for the description of new
 species. In this study, this issue was addressed using phylogenomics.
 Whole genomes of 109 strains of Pythium and close
 relatives were sequenced, assembled, and annotated. These data were
 combined with 10 genomes sequenced in previous studies. Phylogenomic
 analyses were performed with 148 single-copy genes represented in at least
 90% of the taxa in the data set. The results showed support for the
 division of Pythium s.l. The status of alternative
 generic names that have been used for species
 of Pythium in the past (e.g., Artotrogus,
 Cystosiphon, Eupythium, Nematosporangium, Rheosporangium,
 Sphaerosporangium) was investigated. 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 and colleagues in 2010 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.
description: Taken from the Nguyen et al. (2022) paper entitled "Whole
 genome sequencing and phylogenomic analysis show support for the splitting
 of genus <em>Pythium.</em>": Draft
 genome annotation was performed with the funannotate 1.5.2
 (https://github.com/nextgenusfs/funannotate) pipeline following the
 standard procedure outlined in the “Genome assembly only” tutorial
 (https://funannotate.readthedocs.io/en/latest/tutorials.html). Briefly,
 assemblies were repeat-masked with the funannotate mask command, followed
 by ab initio gene prediction with the funannotate predict command. The
 funannotate predict command first uses diamond 0.9.21 (Buchfink et al.
 2021) and exonerate 2.4.0 (Slater and Birney 2005) to map a set of
 pre-downloaded proteins from UniProtKB/Swiss-Prot database (release Feb
 2019) (Bateman 2019) to the input masked genome assembly. It then runs
 GeneMark-ES 4.33 (Borodovsky and Lomsadze 2011) to generate one set of
 gene models, followed by training of Augustus 3.3.1 (Stanke et al. 2008)
 with BUSCO data leading to the generation of a second set of gene models.
 EVidenceModeler (EVM) 1.1.1 (Haas et al. 2008) is used to combine the sets
 of gene models from ab initio gene predictions to give a final set of gene
 models. The funannotate predict command was run with these options:
 –busco_db eukaryota_odb9 –busco_seed_species toxoplasma –organism
 other.
description: The new genera (<em>Globisporangium</em>,
 <em>Elongisporangium</em>) proposed by Uzuhashi et al. (2010)
 have not been used in the file names in this dataset. Please consult with
 Supplementary Table 1 in Nguyen et al. (2022) to see which
 <em>Pythium</em> species (s.l.) are
 in <em>Pythium</em>
 (s.s.), <em>Globisporangium</em>, and
 <em>Elongisporangium</em>. The files can be
 opened with any text editor (e.g. Notepad, BBEdit) or any command line
 program (e.g. cat) that can read text files.