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The expansion of Phytophthora clade 8b: three new species associated with winter grown vegetable crops.

ABSTRACT: Despite its association with important agricultural crops, Phytophthora clade 8b is a poorly studied group of species. The clade currently consists of three officially described species (Phytophthora porri, P. brassicae and P. primulae) that are host-specific pathogens of leek, cabbages and Primula spp., respectively. However, over the past few decades, several other clade 8b-like Phytophthoras have been found on a variety of different host plants that were all grown at low temperatures in winter seasons. In this study, a collection of 30 of these isolates was subjected to a phylogenetic study using two loci (the rDNA ITS region and the mitochondrial cox1 gene). This analysis revealed a clear clustering of isolates according to their host plants. To verify whether these isolates belong to separate species, a detailed morphological study was conducted. On the basis of genetic and morphological differences and host specificity, we now present the official description of three new species in clade 8b: Phytophthora cichorii sp. nov., P. dauci sp. nov. and P. lactucae sp. nov. Two other groups of isolates (Phytophthora taxon castitis and Phytophthora taxon parsley) might also represent new species but the data available at this time are insufficient for an official description. This brings Phytophthora clade 8b to a group of six species that are all host-specific, slow-growing and specifically infect herbaceous crops at low temperatures.

SUBMITTER: Bertier L

PROVIDER: S-EPMC3904053 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

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The expansion of Phytophthora clade 8b: three new species associated with winter grown vegetable crops.

Bertier L L Brouwer H H de Cock A W A M AW Cooke D E L DE Olsson C H B CH Höfte M M

Persoonia 20130514

Despite its association with important agricultural crops, Phytophthora clade 8b is a poorly studied group of species. The clade currently consists of three officially described species (Phytophthora porri, P. brassicae and P. primulae) that are host-specific pathogens of leek, cabbages and Primula spp., respectively. However, over the past few decades, several other clade 8b-like Phytophthoras have been found on a variety of different host plants that were all grown at low temperatures in winte ...[more]

PMID: 24761035

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Project description:BackgroundPhytophthora species are oomycete plant pathogens with such major social and economic impact that genome sequences have been determined for Phytophthora infestans, P. sojae and P. ramorum. Pepsin-like aspartic proteinases (APs) are produced in a wide variety of species (from bacteria to humans) and contain conserved motifs and landmark residues. APs fulfil critical roles in infectious organisms and their host cells. Annotation of Phytophthora APs would provide invaluable information for studies into their roles in the physiology of Phytophthora species and interactions with their hosts.ResultsGenomes of Phytophthora infestans, P. sojae and P. ramorum contain 11-12 genes encoding APs. Nine of the original gene models in the P. infestans database and several in P. sojae and P. ramorum (three and four, respectively) were erroneous. Gene models were corrected on the basis of EST data, consistent positioning of introns between orthologues and conservation of hallmark motifs. Phylogenetic analysis resolved the Phytophthora APs into 5 clades. Of the 12 sub-families, several contained an unconventional architecture, as they either lacked a signal peptide or a propart region. Remarkably, almost all APs are predicted to be membrane-bound.ConclusionsOne of the twelve Phytophthora APs is an unprecedented fusion protein with a putative G-protein coupled receptor as the C-terminal partner. The others appear to be related to well-documented enzymes from other species, including a vacuolar enzyme that is encoded in every fungal genome sequenced to date. Unexpectedly, however, the oomycetes were found to have both active and probably-inactive forms of an AP similar to vertebrate BACE, the enzyme responsible for initiating the processing cascade that generates the Aβ peptide central to Alzheimer's Disease. The oomycetes also encode enzymes similar to plasmepsin V, a membrane-bound AP that cleaves effector proteins of the malaria parasite Plasmodium falciparum during their translocation into the host red blood cell. Since the translocation of Phytophthora effector proteins is currently a topic of intense research activity, the identification in Phytophthora of potential functional homologues of plasmepsin V would appear worthy of investigation. Indeed, elucidation of the physiological roles of the APs identified here offers areas for future study. The significant revision of gene models and detailed annotation presented here should significantly facilitate experimental design.

Project description:Domesticated grain crops evolved from wild plants under human cultivation, losing natural dispersal mechanisms to become dependent upon humans, and showing changes in a suite of other traits, including increasing seed size. There is tendency for seed enlargement during domestication to be viewed as the result of deliberate selection for large seeds by early farmers. However, like some other domestication traits, large seeds may have evolved through natural selection from the activities of people as they gathered plants from the wild, or brought them into cultivation in anthropogenic settings. Alternatively, larger seeds could have arisen via pleiotropic effects or genetic linkage, without foresight from early farmers, and driven by selection that acted on other organs or favored larger plants. We have separated these unconscious selection effects on seed enlargement from those of deliberate selection, by comparing the wild and domesticated forms of vegetable crops. Vegetables are propagated by planting seeds, cuttings, or tubers, but harvested for their edible leaves, stems, or roots, so that seed size is not a direct determinant of yield. We find that landrace varieties of seven vegetable crops have seeds that are 20% to 2.5-times larger than those of their closest wild relatives. These domestication effect sizes fall completely within the equivalent range of 14% to 15.2-times for grain crops, although domestication had a significantly larger overall effect in grain than vegetable crops. Seed enlargement in vegetable crops that are propagated vegetatively must arise from natural selection for larger seeds on the occasions when plants recruit from seed and are integrated into the crop gene pool, or via a genetic link to selection for larger plants or organs. If similar mechanisms operate across all species, then unconscious selection during domestication could have exerted stronger effects on the seed size of our staple crops than previously realized.

Project description:The genus Phytophthora contains many destructive and globally important plant pathogens. In the last decade, targeted sampling efforts have resulted in a dramatic increase in the number of known species, as well as a better understanding of their global distribution. Routine activities undertaken in botanical gardens, combined with great numbers of local and international visitors, place botanical gardens at risk to the accidental introduction and establishment of pathogens such as Phytophthora spp. In this study, the occurrence of Phytophthora was investigated in two botanical gardens in the KwaZulu-Natal Province of South Africa. Symptomatic collar and stem tissues were collected, and root and rhizosphere soil samples were taken from trees exhibiting symptoms of decline. Standard baiting techniques and direct plating of symptomatic tissues revealed the presence of seven species of Phytophthora residing in four phylogenetic clades. Five of these species, P. cinnamomi, P. citrophthora, P. multivora, P. parvispora and the informally designated taxon Phytophthora sp. stellaris were known to be present in South Africa and P. aquimorbida was recorded for the first time. Of these, P. citrophthora represented a novel host-pathogen association causing bleeding cankers on indigenous Celtis africana. A multilocus phylogenetic analysis based on ITS, βtub, cox1 and hsp90 sequences showed the presence of an undescribed species belonging to the Phytophthora ITS Clade 5. This species is described here as Phytophthora mammiformis sp. nov. This study highlights the importance of monitoring botanical gardens for the detection and discovery of pathogens and emphasises their value as sites for the discovery of novel host-pathogen associations. Citation: Paap T, Balocchi F, Burgess TI, Bose T, Wingfield MJ (2024). A diverse range of Phytophthora species from botanical gardens in South Africa, including the novel Clade 5 species, Phytophthora mammiformis sp. nov. Fungal Systematics and Evolution 13: 111-122. doi: 10.3114/fuse.2024.13.05.

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The expansion of Phytophthora clade 8b: three new species associated with winter grown vegetable crops.

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The expansion of Phytophthora clade 8b: three new species associated with winter grown vegetable crops.

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