Dataset Information

Identification of candidate effector genes of Pratylenchus penetrans.

ABSTRACT: Pratylenchus penetrans is one of the most important species of root lesion nematodes (RLNs) because of its detrimental and economic impact in a wide range of crops. Similar to other plant-parasitic nematodes (PPNs), P. penetrans harbours a significant number of secreted proteins that play key roles during parasitism. Here, we combined spatially and temporally resolved next-generation sequencing datasets of P. penetrans to select a list of candidate genes aimed at the identification of a panel of effector genes for this species. We determined the spatial expression of transcripts of 22 candidate effectors within the oesophageal glands of P. penetrans by in situ hybridization. These comprised homologues of known effectors of other PPNs with diverse putative functions, as well as novel pioneer effectors specific to RLNs. It is noteworthy that five of the pioneer effectors encode extremely proline-rich proteins. We then combined in situ localization of effectors with available genomic data to identify a non-coding motif enriched in promoter regions of a subset of P. penetrans effectors, and thus a putative hallmark of spatial expression. Expression profiling analyses of a subset of candidate effectors confirmed their expression during plant infection. Our current results provide the most comprehensive panel of effectors found for RLNs. Considering the damage caused by P. penetrans, this information provides valuable data to elucidate the mode of parasitism of this nematode and offers useful suggestions regarding the potential use of P. penetrans-specific target effector genes to control this important pathogen.

SUBMITTER: Vieira P

PROVIDER: S-EPMC6638058 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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Identification of candidate effector genes of Pratylenchus penetrans.

Vieira Paulo P Maier Thomas R TR Eves-van den Akker Sebastian S Howe Dana K DK Zasada Inga I Baum Thomas J TJ Eisenback Jonathan D JD Kamo Kathryn K

Molecular plant pathology 20180209

Pratylenchus penetrans is one of the most important species of root lesion nematodes (RLNs) because of its detrimental and economic impact in a wide range of crops. Similar to other plant-parasitic nematodes (PPNs), P. penetrans harbours a significant number of secreted proteins that play key roles during parasitism. Here, we combined spatially and temporally resolved next-generation sequencing datasets of P. penetrans to select a list of candidate genes aimed at the identification of a panel of ...[more]

PMID: 29424950

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Project description:Sweet cherry growers are increasingly using semi-dwarfing rootstocks, including the Gisela® series, when replanting orchards. Little is known of the susceptibility of these new cherry rootstocks to Pratylenchus penetrans, a recognized pest of temperate fruit trees worldwide. Two field experiments were planted in 2010, one in the Okanagan Valley of British Columbia and one in the Annapolis Valley of Nova Scotia. Each experiment was a factorial combination of three rootstocks (Gi.3, Gi.5, and Gi.6) × three training systems, with six replicate four-tree plots of each of the nine combinations. Both sites were fumigated prior to planting and population densities of P. penetrans in roots and root-zone soil were subsequently monitored from 2013 through 2017. None of the P. penetrans population parameters (nematodes/kg soil, nematodes/g fine root, and nematodes/kg soil including roots) differed among rootstocks at either site, suggesting that the rootstocks did not differ in their ability to host P. penetrans. At the British Columbia site only there was an inverse relationship between P. penetrans population densities and tree size for Gi.3 trees in four years and for Gi.6 in 2017, suggesting that Gi.3 rootstock is less tolerant than Gi.5 and Gi.6 rootstocks.Sweet cherry growers are increasingly using semi-dwarfing rootstocks, including the Gisela® series, when replanting orchards. Little is known of the susceptibility of these new cherry rootstocks to Pratylenchus penetrans, a recognized pest of temperate fruit trees worldwide. Two field experiments were planted in 2010, one in the Okanagan Valley of British Columbia and one in the Annapolis Valley of Nova Scotia. Each experiment was a factorial combination of three rootstocks (Gi.3, Gi.5, and Gi.6) × three training systems, with six replicate four-tree plots of each of the nine combinations. Both sites were fumigated prior to planting and population densities of P. penetrans in roots and root-zone soil were subsequently monitored from 2013 through 2017. None of the P. penetrans population parameters (nematodes/kg soil, nematodes/g fine root, and nematodes/kg soil including roots) differed among rootstocks at either site, suggesting that the rootstocks did not differ in their ability to host P. penetrans. At the British Columbia site only there was an inverse relationship between P. penetrans population densities and tree size for Gi.3 trees in four years and for Gi.6 in 2017, suggesting that Gi.3 rootstock is less tolerant than Gi.5 and Gi.6 rootstocks.

Project description:Pratylenchus penetrans is a common and important agricultural pest in Wisconsin, a USA state with a diverse agriculture. We compared populations from around the state to each other and to data published for populations around the world to gain insight on the variability of features important for identification of this cosmopolitan species. Thirteen isolates from samples collected in soybean fields in ten Wisconsin counties were established in monoxenic cultures. Analysis of morphological features revealed the least variable feature for all isolates collectively was vulva percentage. Features less variable within than among isolates were body width, lip region height, and stylet length. Some isolates showed only the smooth tail tip phenotype and others had a mix of smooth and annulated tail phenotypes. A suite of features provided sufficient pattern to group isolates into four clusters according to hierarchical agglomerative clustering and canonical discriminative analyses, but not with enough distinction to be useful for classification. Haplotype analysis based on the COI mitochondrial gene of the 13 cultured isolates, 39 Wisconsin field populations, and published sequences representing five additional USA states and six countries revealed 21 haplotypes, 15 of which occurred in Wisconsin. Ten haplotypes represented in Wisconsin were shared with populations from Europe, South America, Africa, or Asia. Five haplotypes were unique to Wisconsin, six were unique to The Netherlands, and one was unique to Japan suggesting that even more COI diversity will be revealed when more COI sequences for P. penetrans become available. The maximum pairwise sequence variation was 6% and the SNPs did not alter amino acids, indicating cryptic biodiversity within the species worldwide. The cosmopolitan to localized scale of distribution of COI haplotypes could be due to frequent and ongoing dispersal events, facilitated by life history traits and the broad host range of P. penetrans. Regions of diverse agriculture, like Wisconsin, show promise for studying this important pest and our study confirms the utility of the COI mtDNA gene for studying variation within a species.

Dataset Information

Identification of candidate effector genes of Pratylenchus penetrans.

Publications

Identification of candidate effector genes of Pratylenchus penetrans.

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