title: Oogonial biometry and phylogenetic analyses of the Pythium vexans species group from woody agricultural hosts in South Africa reveal distinct groups within this taxon.
abstract: Pythium vexans fits into the internal transcribed spacer (ITS) clade K sensu Lévesque & De Cock (2004). Within clade K, P. vexans forms a distinct clade containing two enigmatic species, Pythium indigoferae and Pythium cucurbitacearum of which no ex-type strains are available. In South Africa, as well as in other regions of the world, P. vexans isolates are known to be heterogeneous in their ITS sequences and may consist of more than one species. This study aimed to investigate the diversity of South African P. vexans isolates, mainly from grapevines, but also citrus and apple using (i) phylogenetic analyses of the ITS, cytochrome c oxidase (cox) I, cox II, and β-tubulin regions and (ii) seven biometric oogonial parameters. Each of the phylogenies clustered P. vexans isolates into a single well-supported clade, distinct from other clade K species. The β-tubulin region was phylogenetically uninformative regarding the P. vexans group. The ITS phylogeny and combined cox I and II phylogenies, although each revealing several P. vexans subclades, were incongruent. One of the most striking incongruences was the presence of one cox subclade that contained two distinct ITS subclades (Ib and IV). Three groups (A-C) were subjectively identified among South African P. vexans isolates using (i) phylogenetic clades (ITS and cox), (ii) univariate analysis of oogonial diameters, and (iii) multivariate analyses of biometric oogonial parameters. Group A is considered to be P. vexans s. str. since it contained the P. vexans CBS reference strain from Van der Plaats-Niterink (1981). This group had significantly smaller oogonial diameters than group B and C isolates. Group B contained the isolates from ITS subclades Ib and IV, which formed a single cox subclade. The ITS subclade IV isolates were all sexually sterile or produced mainly abortive oospores, as opposed to the sexually fertile subclade Ib isolates, and may thus represent a distinct assemblage within group B. Although ITS subclade Ib included the P. indigoferae ex-type sequence, this group was considered to be P. vexans since South African isolates in this clade produced globose sporangia. Group C contained four apple isolates that were related to, but distinct from P. cucurbitacearum. Although P. vexans groups A-C might be distinct species, they are not described here as such due to (i) these groups only representing some of the known diversity in P. vexans, (ii) conflicting gene tree phylogenies preventing phylogenetic species identification, and (iii) sexually sterile isolates preventing the broad application of biometrical data.
authors.affiliation: Department of Plant Pathology, University of Stellenbosch, Matieland 7602, South Africa. cspies@sun.ac.za
authors.forename: Christoffel F J
authors.initials: CF
authors.lastname: Spies
authors.forename: Mark
authors.initials: M
authors.lastname: Mazzola
authors.forename: Wilhelm J
authors.initials: WJ
authors.lastname: Botha
authors.forename: Marieta
authors.initials: M
authors.lastname: Van Der Rijst
authors.forename: Lizel
authors.initials: L
authors.lastname: Mostert
authors.forename: Adéle
authors.initials: A
authors.lastname: Mcleod
mesh_terms: D001699:Biometry; D018556:Crops, Agricultural / Q000382:microbiology*; D004271:DNA, Fungal / Q000235:genetics; D005656:Fungal Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D011775:Pythium / Q000737:chemistry / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D013019:South Africa; D013172:Spores, Fungal / Q000737:chemistry / Q000145:classification / Q000235:genetics / Q000302:isolation & purification
chemical_list: D004271:DNA, Fungal; D005656:Fungal Proteins