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United States Department of Agriculture

Agricultural Research Service

Research Project: BIOLOGICALLY-BASED SYSTEMS FOR SOILBORNE DISEASE CONTROL IN TREE FRUIT AGRO-ECOSYSTEMS Title: Oogonal biometry and phylogenetic analysis of the Pythium vexans species group from woody agricultural hosts in South Africa reveal distinct groups within this taxon

Authors
item Spies, Christoffel F. -
item Mazzola, Mark
item Wilhelm, J. Botha -
item Van Der Rijst, Marieta -
item Mostert, Lizel -
item Mcleod, Adele -

Submitted to: Fungal Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 20, 2010
Publication Date: February 9, 2011
Citation: Spies, C., Mazzola, M., Wilhelm, J., Van Der Rijst, M., Mostert, L., Mcleod, A. 2011. Oogonal biometry and phylogenetic analysis of the Pythium vexans species group from woody agricultural hosts in South Africa reveal distinct groups within this taxon. Fungal Biology. 115:157-168.

Interpretive Summary: Fungi beloning to the genus Pythium form diverse associations with plants. Sometimes these associations result in damage to plants resulting from infection of the host root system. Pythium spp. have been implicated as pathogens of numerous perennial crops including grape vines and apple, and isolates identified as Pythium vexans are commonly isolated from these crops in South Africa. However, isolates grouped in this species are often diverse and may represent multiple species. Studies were conducted using molecular DNA-based methods (for example internal transcribed spacer [ITS] sequence data) and morphological characteristics to examine the diversity of “P. vexans” recovered from grape vine and apple in South Africa and to determine whether these isolates comprised multiple species. Using these methods three groups (A-C) were identified among the P. vexans isolates studied. These groups are currently not considered as distinct species based upon the data obtained in these studies including the fact that the known ITS DNA sequence diversity in P. vexans is larger than that observed for groups A-C identified here. An important conclusion from results obtained in this study is that two of the three officially described species in the P. vexans ITS groupe, i.e. P. indigoferae and P. cucurbitacearum, should be considered illegitimate until suitable neotype strains for these species can be found.

Technical Abstract: Pythium vexans fits into the internal transcribed spacer (ITS) clade K. 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. Therefore, this study examined 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, and cox II regions and (ii) seven biometric oogonial parameters. Each of the phylogenies clustered the P. vexans isolates into a single well-supported clade, distinct from other clade K species. The ITS phylogeny and combined cox I and II phylogenies, although each revealing several P. vexans sub-clades, were incongruent. One of the most striking incongruences was the presence of one cox sub-clade that contained two distinct ITS sub-clades (Ib and IV). Three groups (A to C) were subjectively identified among South African P. vexans isolates using (i) multivariate analyses of biometric oogonial parameters, (ii) phylogenetic clades (ITS and cox) and (iii) univariate analysis of oogonial diameters. Group A is considered to be P. vexans s.s. since it contained the P. vexans CBS reference strain. Group B contained the isolates from ITS sub-clades Ib and IV, which formed a single cox sub-clade. The ITS sub-clade IV isolates were all sexually sterile or produced mainly abortive oospores, as opposed to the sexually fertile sub-clade Ib isolates, and may thus represent a distinct group within group B. Although ITS sub-clade Ib included the P. indigoferae 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 to 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.

Last Modified: 11/23/2014
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