Publications by authors named "John T Jones"

58 Publications

Resisting Potato Cyst Nematodes With Resistance.

Front Plant Sci 2021 25;12:661194. Epub 2021 Mar 25.

Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom.

Potato cyst nematodes (PCN) are economically important pests with a worldwide distribution in all temperate regions where potatoes are grown. Because above ground symptoms are non-specific, and detection of cysts in the soil is determined by the intensity of sampling, infestations are frequently spread before they are recognised. PCN cysts are resilient and persistent; their cargo of eggs can remain viable for over two decades, and thus once introduced PCN are very difficult to eradicate. Various control methods have been proposed, with resistant varieties being a key environmentally friendly and effective component of an integrated management programme. Wild and landrace relatives of cultivated potato have provided a source of PCN resistance genes that have been used in breeding programmes with varying levels of success. Producing a PCN resistant variety requires concerted effort over many years before it reaches what can be the biggest hurdle-commercial acceptance. Recent advances in potato genomics have provided tools to rapidly map resistance genes and to develop molecular markers to aid selection during breeding. This review will focus on the translation of these opportunities into durably PCN resistant varieties.
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http://dx.doi.org/10.3389/fpls.2021.661194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8027921PMC
March 2021

Potato cyst nematodes Globodera rostochiensis and G. pallida.

Mol Plant Pathol 2021 May 11;22(5):495-507. Epub 2021 Mar 11.

School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK.

Taxonomy: Phylum Nematoda; class Chromadorea; order Rhabditida; suborder Tylenchina; infraorder Tylenchomorpha; superfamily Tylenchoidea; family Heteroderidae; subfamily Heteroderinae; Genus Globodera.

Biology: Potato cyst nematodes (PCN) are biotrophic, sedentary endoparasitic nematodes. Invasive (second) stage juveniles (J2) hatch from eggs in response to the presence of host root exudates and subsequently locate and invade the host. The nematodes induce the formation of a large, multinucleate syncytium in host roots, formed by fusion of up to 300 root cell protoplasts. The nematodes rely on this single syncytium for the nutrients required to develop through a further three moults to the adult male or female stage. This extended period of biotrophy-between 4 and 6 weeks in total-is almost unparalleled in plant-pathogen interactions. Females remain at the root while adult males revert to the vermiform body plan of the J2 and leave the root to locate and fertilize the female nematodes. The female body forms a cyst that contains the next generation of eggs.

Host Range: The host range of PCN is limited to plants of the Solanaceae family. While the most economically important hosts are potato (Solanum tuberosum), tomato (Solanum lycopersicum), and aubergine (Solanum melongena), over 170 species of Solanaceae are thought to be potential hosts for PCN (Sullivan et al., 2007).

Disease Symptoms: Symptoms are similar to those associated with nutrient deficiency, such as stunted growth, yellowing of leaves and reduced yields. This absence of specific symptoms reduces awareness of the disease among growers.

Disease Control: Resistance genes (where available in suitable cultivars), application of nematicides, crop rotation. Great effort is put into reducing the spread of PCN through quarantine measures and use of certified seed stocks.

Useful Websites: Genomic information for PCN is accessible through WormBase ParaSite.
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http://dx.doi.org/10.1111/mpp.13047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8035638PMC
May 2021

The Genomic Impact of Selection for Virulence against Resistance in the Potato Cyst Nematode, .

Genes (Basel) 2020 Nov 28;11(12). Epub 2020 Nov 28.

Cellular and Molecular Sciences Group, James Hutton Institute, Dundee DD2 5DA, UK.

Although the use of natural resistance is the most effective management approach against the potato cyst nematode (PCN) , the existence of pathotypes with different virulence characteristics constitutes a constraint towards this goal. Two resistance sources, (from ) and from ssp. CPC2802 (from the Commonwealth Potato Collection) are widely used in potato breeding programmes in European potato industry. However, the use of resistant cultivars may drive strong selection towards virulence, which allows the increase in frequency of virulent alleles in the population and therefore, the emergence of highly virulent nematode lineages. This study aimed to identify () genes in populations selected for virulence on the above resistance sources, and the genomic impact of selection processes on the nematode. The selection drive in the populations was found to be specific to their genetic background. At the genomic level, 11 genes were found that represent candidate genes. Most of the variant calls determining selection were associated with -selected populations, while many of them seem to be organised in genomic islands facilitating selection evolution. These phenotypic and genomic findings combined with histological studies performed revealed potential mechanisms underlying selection in .
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http://dx.doi.org/10.3390/genes11121429DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7760817PMC
November 2020

Signatures of adaptation to a monocot host in the plant-parasitic cyst nematode Heterodera sacchari.

Plant J 2020 08 22;103(4):1263-1274. Epub 2020 Jul 22.

The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.

Interactions between plant-parasitic nematodes and their hosts are mediated by effectors, i.e. secreted proteins that manipulate the plant to the benefit of the pathogen. To understand the role of effectors in host adaptation in nematodes, we analysed the transcriptome of Heterodera sacchari, a cyst nematode parasite of rice (Oryza sativa) and sugarcane (Saccharum officinarum). A multi-gene phylogenetic analysis showed that H. sacchari and the cereal cyst nematode Heterodera avenae share a common evolutionary origin and that they evolved to parasitise monocot plants from a common dicot-parasitic ancestor. We compared the effector repertoires of H. sacchari with those of the dicot parasites Heterodera glycines and Globodera rostochiensis to understand the consequences of this transition. While, in general, effector repertoires are similar between the species, comparing effectors and non-effectors of H. sacchari and G. rostochiensis shows that effectors have accumulated more mutations than non-effectors. Although most effectors show conserved spatiotemporal expression profiles and likely function, some H. sacchari effectors are adapted to monocots. This is exemplified by the plant-peptide hormone mimics, the CLAVATA3/EMBRYO SURROUNDING REGION-like (CLE) effectors. Peptide hormones encoded by H. sacchari CLE effectors are more similar to those from rice than those from other plants, or those from other plant-parasitic nematodes. We experimentally validated the functional significance of these observations by demonstrating that CLE peptides encoded by H. sacchari induce a short root phenotype in rice, whereas those from a related dicot parasite do not. These data provide a functional example of effector evolution that co-occurred with the transition from a dicot-parasitic to a monocot-parasitic lifestyle.
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http://dx.doi.org/10.1111/tpj.14910DOI Listing
August 2020

A comparison of 4-year total medical care costs, adverse outcomes, and opioid/prescription analgesic use for 3 knee osteoarthritis pain treatments: Intra-articular hyaluronic acid, intra-articular corticosteroids, and knee arthroplasty.

Semin Arthritis Rheum 2020 12 17;50(6):1525-1534. Epub 2020 Jan 17.

Department of Orthopaedics, Louisiana State University School of Medicine, 1542 Tulane Ave, Box T6-7, New Orleans, LA 70112, United States.

Objectives: To compare the medical costs associated with treatments for knee osteoarthritis (OA): intra-articular corticosteroids (ICS) and intra-articular hyaluronic acid (IHA) primarily, and ICS/IHA vs knee arthroplasty (TKA) secondarily.

Methods: This was a retrospective analysis of an insurance claims database. Eligible members had diagnosed OA and no claims for ICS, IHA, or TKA during the 6-18-month look-back period. Cohorts of interest over the 4-year observation period were: patients who received ICS only, those who received IHA only, and those who received TKA only. Outcomes assessed included: (1) total allowed medical costs, (2) claims for pre-specified, treatment-related adverse outcomes and costs, and (3) opioid and/or prescription analgesic use and costs. Data extraction began on the date of the first ICS, IHA, or TKA in 2013 until December 31, 2017.

Results: Of the 260,828 patients who qualified, 126,831 were taking monotherapy (IHA=3703, ICS=117,588, TKA = 5540). Adjusted 4-year per patient per month (PPPM) costs were lowest in the IHA cohort ($733); PPPM costs were $1230 in the ICS cohort and $1548 in the TKA cohort. A smaller percentage of patients in the IHA (7.1%) vs ICS (8.4%) or TKA cohort (11.8%) experienced any of the pre-specified adverse outcomes. Adverse outcome-related costs in the IHA cohort were lower ($19.91) than costs in the ICS ($32.18) and TKA cohorts ($31.12). Per-patient opioid and analgesic prescriptions were consistently and significantly lower in the IHA (range, 0.70-0.96) vs ICS cohort (range, 2.0-2.26) for Years 1 through 4. Usage rates were significantly lower in the IHA cohort vs TKA cohort in Year 1 (0.96 vs 4.77) and not different in Years 2 through 4 (TKA range, 0.76-1.08). In Year 1, opioid and prescription analgesic costs were significantly lower in the IHA vs ICS and TKA cohorts ($3.45 vs $11.14 and $12.82). After Year 1, opioid and prescription analgesic costs were significantly higher in the ICS (range, $13.83-15.96) vs IHA (range, $3.02-3.87) and TKA cohorts (range, $3.43-4.97).

Conclusions: Patients in the IHA cohort had lower total medical care costs, fewer adverse outcomes, and lower use/costs of opioids and prescription analgesics vs patients in the ICS and TKA cohorts. Reducing total medical care costs and minimizing opioid/analgesic use should be a treatment goal when selecting therapies for patients with knee OA.
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http://dx.doi.org/10.1016/j.semarthrit.2020.01.003DOI Listing
December 2020

Correction to: STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plantparasitic nematode Bursaphelenchus xylophilus.

BMC Genomics 2018 08 10;19(1):603. Epub 2018 Aug 10.

Cell and Molecular Sciences Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.

Following publication of the original article [1], the authors reported that one of the authors' names was erroneously changed during proofing and published incorrectly. In this Correction the incorrect and correct author name are shown. The original publication of this article has been corrected.
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http://dx.doi.org/10.1186/s12864-018-4990-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6085758PMC
August 2018

STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus.

BMC Genomics 2018 Jul 27;19(1):553. Epub 2018 Jul 27.

Cell and Molecular Sciences Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.

Background: Plant-parasitic nematodes cause severe damage to a wide range of crop and forest species worldwide. The migratory endoparasitic nematode, Bursaphelenchus xylophilus, (pinewood nematode) is a quarantine pathogen that infects pine trees and has a hugely detrimental economic impact on the forestry industry. Under certain environmental conditions large areas of infected trees can be destroyed, leading to damage on an ecological scale. The interactions of B. xylophilus with plants are mediated by secreted effector proteins produced in the pharyngeal gland cells. Identification of effectors is important to understand mechanisms of parasitism and to develop new control measures for the pathogens.

Results: Using an approach pioneered in cyst nematodes, we have analysed the promoter regions of a small panel of previously validated pharyngeal gland cell effectors from B. xylophilus to identify an associated putative regulatory promoter motif: STATAWAARS. The presence of STATAWAARS in the promoter region of an uncharacterized gene is a predictor that the corresponding gene encodes a putatively secreted protein, consistent with effector function. Furthermore, we are able to experimentally validate that a subset of STATAWAARS-containing genes are specifically expressed in the pharyngeal glands. Finally, we independently validate the association of STATAWAARS with tissue-specific expression by directly sequencing the mRNA of pharyngeal gland cells. We combine a series of criteria, including STATAWAARS predictions and abundance in the gland cell transcriptome, to generate a comprehensive effector repertoire for B. xylophilus. The genes highlighted by this approach include many previously described effectors and a series of novel "pioneer" effectors.

Conclusions: We provide a major scientific advance in the area of effector regulation. We identify a novel promoter motif (STATAWAARS) associated with expression in the pharyngeal gland cells. Our data, coupled with those from previous studies, suggest that lineage-specific promoter motifs are a theme of effector regulation in the phylum Nematoda.
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http://dx.doi.org/10.1186/s12864-018-4908-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6062891PMC
July 2018

The SPRYSEC Effector SPRY-414-2 That Suppresses Plant Defenses Targets a Regulatory Component of the Dynamic Microtubule Network.

Front Plant Sci 2018 12;9:1019. Epub 2018 Jul 12.

Dundee Effector Consortium, Cell and Molecular Sciences Group, The James Hutton Institute, Dundee, United Kingdom.

The white potato cyst nematode, , is an obligate biotrophic pathogen of a limited number of Solanaceous plants. Like other plant pathogens, deploys effectors into its host that manipulate the plant to the benefit of the nematode. Genome analysis has led to the identification of large numbers of candidate effectors from this nematode, including the cyst nematode-specific SPRYSEC proteins. These are a secreted subset of a hugely expanded gene family encoding SPRY domain-containing proteins, many of which remain to be characterized. We investigated the function of one of these SPRYSEC effector candidates, SPRY-414-2. Expression of the gene encoding SPRY-414-2 is restricted to the dorsal pharyngeal gland cell and reducing its expression in infective second stage juveniles using RNA interference causes a reduction in parasitic success on potato. Transient expression assays in indicated that SPRY-414-2 disrupts plant defenses. It specifically suppresses effector-triggered immunity (ETI) induced by co-expression of the resistance gene and its cognate avirulence factor . It also causes a reduction in the production of reactive oxygen species triggered by exposure of plants to the bacterial flagellin epitope flg22. Yeast two-hybrid screening identified a potato cytoplasmic linker protein (CLIP)-associated protein (CLASP) as a host target of SPRY-414-2. The two proteins co-localize at the microtubules. CLASPs are members of a conserved class of microtubule-associated proteins that contribute to microtubule stability and growth. However, disruption of the microtubule network does not prevent suppression of ETI by SPRY-414-2 nor the interaction of the effector with its host target. Besides, SPRY-414-2 stabilizes its target while effector dimerization and the formation of high molecular weight protein complexes including SPRY-414-2 are prompted in the presence of the CLASP. These data indicate that the nematode effector SPRY-414-2 targets the microtubules to facilitate infection.
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http://dx.doi.org/10.3389/fpls.2018.01019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6052128PMC
July 2018

Sex: Not all that it's cracked up to be?

PLoS Genet 2018 02 22;14(2):e1007160. Epub 2018 Feb 22.

Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1007160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5823364PMC
February 2018

The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes.

Genes (Basel) 2017 Oct 23;8(10). Epub 2017 Oct 23.

Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.

Nematodes have evolved the ability to parasitize plants on at least four independent occasions, with plant parasites present in Clades 1, 2, 10 and 12 of the phylum. In the case of Clades 10 and 12, horizontal gene transfer of plant cell wall degrading enzymes from bacteria and fungi has been implicated in the evolution of plant parasitism. We have used ribonucleic acid sequencing (RNAseq) to generate reference transcriptomes for two economically important nematode species, and , representative of two genera within the early-branching Clade 2 of the phylum Nematoda. We used a transcriptome-wide analysis to identify putative horizontal gene transfer events. This represents the first in-depth transcriptome analysis from any plant-parasitic nematode of this clade. For each species, we assembled ~30 million Illumina reads into a reference transcriptome. We identified 62 and 104 transcripts, from and , respectively, that were putatively acquired via horizontal gene transfer. By cross-referencing horizontal gene transfer prediction with a phylum-wide analysis of Pfam domains, we identified Clade 2-specific events. Of these, a GH12 cellulase from was analysed phylogenetically and biochemically, revealing a likely bacterial origin and canonical enzymatic function. Horizontal gene transfer was previously shown to be a phenomenon that has contributed to the evolution of plant parasitism among nematodes. Our findings underline the importance and the extensiveness of this phenomenon in the evolution of plant-parasitic life styles in this speciose and widespread animal phylum.
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http://dx.doi.org/10.3390/genes8100287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5664137PMC
October 2017

Genome Evolution of Plant-Parasitic Nematodes.

Annu Rev Phytopathol 2017 08 7;55:333-354. Epub 2017 Jun 7.

Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom.

Plant parasitism has evolved independently on at least four separate occasions in the phylum Nematoda. The application of next-generation sequencing (NGS) to plant-parasitic nematodes has allowed a wide range of genome- or transcriptome-level comparisons, and these have identified genome adaptations that enable parasitism of plants. Current genome data suggest that horizontal gene transfer, gene family expansions, evolution of new genes that mediate interactions with the host, and parasitism-specific gene regulation are important adaptations that allow nematodes to parasitize plants. Sequencing of a larger number of nematode genomes, including plant parasites that show different modes of parasitism or that have evolved in currently unsampled clades, and using free-living taxa as comparators would allow more detailed analysis and a better understanding of the organization of key genes within the genomes. This would facilitate a more complete understanding of the way in which parasitism has shaped the genomes of plant-parasitic nematodes.
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http://dx.doi.org/10.1146/annurev-phyto-080516-035434DOI Listing
August 2017

Design evolution enhances patient compliance for low-intensity pulsed ultrasound device usage.

Med Devices (Auckl) 2016 30;9:423-427. Epub 2016 Nov 30.

Bioventus LLC, Durham, NC, USA.

Poor patient compliance or nonadherence with prescribed treatments can have a significant unfavorable impact on medical costs and clinical outcomes. In the current study, voice-of-the-customer research was conducted to aid in the development of a next-generation low-intensity pulsed ultrasound (LIPUS) bone healing product. An opportunity to improve patient compliance reporting was identified, resulting in the incorporation into the next-generation device of a visual calendar that provides direct feedback to the patient, indicating days for which they successfully completed treatment. Further investigation was done on whether inclusion of the visual calendar improved patient adherence to the prescribed therapy (20 minutes of daily treatment) over a 6-month period. Thus, 12,984 data files were analyzed from patients prescribed either the earlier- or the next-generation LIPUS device. Over the 6-month period, overall patient compliance was 83.8% with the next-generation LIPUS device, compared with 74.2% for the previous version (<0.0001). Incorporation of the calendar feature resulted in compliance never decreasing below 76% over the analysis period, whereas compliance with the earlier-generation product fell to 51%. A literature review on the LIPUS device shows a correlation between clinical effectiveness and compliance rates more than 70%. Incorporation of stakeholder feedback throughout the design and innovation process of a next-generation LIPUS device resulted in a measurable improvement in patient adherence, which may help to optimize clinical outcomes.
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http://dx.doi.org/10.2147/MDER.S119887DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5140031PMC
November 2016

The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence.

Genome Biol 2016 Jun 10;17(1):124. Epub 2016 Jun 10.

USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA.

Background: The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes.

Results: We generate a high quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression through the life cycle focusing on key parasitic transitions and sequence the genomes of eight populations including four additional pathotypes to identify variation. Horizontal gene transfer contributes 3.5 % of the predicted genes, of which approximately 8.5 % are deployed as effectors. Over one-third of all effector genes are clustered in 21 putative 'effector islands' in the genome. We identify a dorsal gland promoter element motif (termed DOG Box) present upstream in representatives from 26 out of 28 dorsal gland effector families, and predict a putative effector superset associated with this motif. We validate gland cell expression in two novel genes by in situ hybridisation and catalogue dorsal gland promoter element-containing effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights correlation with plant resistance-breaking.

Conclusions: These G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. Dorsal gland promoter element-containing effectors are at the front line of the evolutionary arms race between plant and parasite and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action.
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http://dx.doi.org/10.1186/s13059-016-0985-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4901422PMC
June 2016

Functional C-TERMINALLY ENCODED PEPTIDE (CEP) plant hormone domains evolved de novo in the plant parasite Rotylenchulus reniformis.

Mol Plant Pathol 2016 Oct 6;17(8):1265-75. Epub 2016 Jun 6.

Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK.

Sedentary plant-parasitic nematodes (PPNs) induce and maintain an intimate relationship with their host, stimulating cells adjacent to root vascular tissue to re-differentiate into unique and metabolically active 'feeding sites'. The interaction between PPNs and their host is mediated by nematode effectors. We describe the discovery of a large and diverse family of effector genes, encoding C-TERMINALLY ENCODED PEPTIDE (CEP) plant hormone mimics (RrCEPs), in the syncytia-forming plant parasite Rotylenchulus reniformis. The particular attributes of RrCEPs distinguish them from all other CEPs, regardless of origin. Together with the distant phylogenetic relationship of R. reniformis to the only other CEP-encoding nematode genus identified to date (Meloidogyne), this suggests that CEPs probably evolved de novo in R. reniformis. We have characterized the first member of this large gene family (RrCEP1), demonstrating its significant up-regulation during the plant-nematode interaction and expression in the effector-producing pharyngeal gland cell. All internal CEP domains of multi-domain RrCEPs are followed by di-basic residues, suggesting a mechanism for cleavage. A synthetic peptide corresponding to RrCEP1 domain 1 is biologically active and capable of up-regulating plant nitrate transporter (AtNRT2.1) expression, whilst simultaneously reducing primary root elongation. When a non-CEP-containing, syncytia-forming PPN species (Heterodera schachtii) infects Arabidopsis in a CEP-rich environment, a smaller feeding site is produced. We hypothesize that CEPs of R. reniformis represent a two-fold adaptation to sustained biotrophy in this species: (i) increasing host nitrate uptake, whilst (ii) limiting the size of the syncytial feeding site produced.
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http://dx.doi.org/10.1111/mpp.12402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5103176PMC
October 2016

Horizontal Gene Transfer from Bacteria Has Enabled the Plant-Parasitic Nematode Globodera pallida to Feed on Host-Derived Sucrose.

Mol Biol Evol 2016 06 25;33(6):1571-9. Epub 2016 Feb 25.

Dundee Effector Consortium, The James Hutton Institute, Dundee, United Kingdom Biology Department, University of St Andrews, St Andrews, Fife, United Kingdom

The evolution of plant-parasitic nematodes (PPN) is unusual in that these organisms have acquired a range of genes from bacteria via horizontal gene transfer (HGT). The proteins encoded by most of these genes are involved in metabolism of various components of the plant cell wall during invasion of the host. Recent genome sequencing projects for PPN have shown that Glycosyl Hydrolase Family 32 (GH32) sequences are present in several PPN species. These sequences are absent from almost all other animals. Here, we show that the GH32 sequences from an economically important cyst nematode species, Globodera pallida are functional invertases, are expressed during feeding and are restricted in expression to the nematode digestive system. These data are consistent with a role in metabolizing host-derived sucrose. In addition, a detailed phylogenetic analysis shows that the GH32 sequences from PPN and those present in some insect species have distinct bacterial origins and do not therefore derive from a gene present in the last common ancestor of ecdysozoan species. HGT has therefore played at least two critical roles in the evolution of PPN, enabling both invasion of the host and feeding on the main translocation carbohydrate of the plant.
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http://dx.doi.org/10.1093/molbev/msw041DOI Listing
June 2016

Gene expression changes in diapause or quiescent potato cyst nematode, Globodera pallida, eggs after hydration or exposure to tomato root diffusate.

PeerJ 2016 4;4:e1654. Epub 2016 Feb 4.

Cell and Molecular Sciences, The James Hutton Institute , Dundee , United Kingdom.

Plant-parasitic nematodes (PPN) need to be adapted to survive in the absence of a suitable host or in hostile environmental conditions. Various forms of developmental arrest including hatching inhibition and dauer stages are used by PPN in order to survive these conditions and spread to other areas. Potato cyst nematodes (PCN) (Globodera pallida and G. rostochiensis) are frequently in an anhydrobiotic state, with unhatched nematode persisting for extended periods of time inside the cyst in the absence of the host. This paper shows fundamental changes in the response of quiescent and diapaused eggs of G. pallida to hydration and following exposure to tomato root diffusate (RD) using microarray gene expression analysis encompassing a broad set of genes. For the quiescent eggs, 547 genes showed differential expression following hydration vs. hydratation and RD (H-RD) treatment whereas 708 genes showed differential regulation for the diapaused eggs following these treatments. The comparison between hydrated quiescent and diapaused eggs showed marked differences, with 2,380 genes that were differentially regulated compared with 987 genes following H-RD. Hydrated quiescent and diapaused eggs were markedly different indicating differences in adaptation for long-term survival. Transport activity is highly up-regulated following H-RD and few genes were coincident between both kinds of eggs. With the quiescent eggs, the majority of genes were related to ion transport (mainly sodium), while the diapaused eggs showed a major diversity of transporters (amino acid transport, ion transport, acetylcholine or other molecules).
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http://dx.doi.org/10.7717/peerj.1654DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748719PMC
February 2016

A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual.

Mol Ecol 2015 Dec;24(23):5842-51

Cell and Molecular Sciences Group, Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.

Distinct populations of the potato cyst nematode (PCN) Globodera pallida exist in the UK that differ in their ability to overcome various sources of resistance. An efficient method for distinguishing between populations would enable pathogen-informed cultivar choice in the field. Science and Advice for Scottish Agriculture (SASA) annually undertake national DNA diagnostic tests to determine the presence of PCN in potato seed and ware land by extracting DNA from soil floats. These DNA samples provide a unique resource for monitoring the distribution of PCN and further interrogation of the diversity within species. We identify a region of mitochondrial DNA descriptive of three main groups of G. pallida present in the UK and adopt a metagenetic approach to the sequencing and analysis of all SASA samples simultaneously. Using this approach, we describe the distribution of G. pallida mitotypes across Scotland with field-scale resolution. Most fields contain a single mitotype, one-fifth contain a mix of mitotypes, and less than 3% contain all three mitotypes. Within mixed fields, we were able to quantify the relative abundance of each mitotype across an order of magnitude. Local areas within mixed fields are dominated by certain mitotypes and indicate towards a complex underlying 'pathoscape'. Finally, we assess mitotype distribution at the level of the individual cyst and provide evidence of 'hybrids'. This study provides a method for accurate, quantitative and high-throughput typing of up to one thousand fields simultaneously, while revealing novel insights into the national genetic variability of an economically important plant parasite.
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http://dx.doi.org/10.1111/mec.13434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4981918PMC
December 2015

Identification and characterization of parasitism genes from the pinewood nematode Bursaphelenchus xylophilus reveals a multilayered detoxification strategy.

Mol Plant Pathol 2016 Feb 16;17(2):286-95. Epub 2015 Jun 16.

Cell and Molecular Sciences Group/Information and Computer Sciences Group (PJAC), The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.

The migratory endoparasitic nematode Bursaphelenchus xylophilus, which is the causal agent of pine wilt disease, has phytophagous and mycetophagous phases during its life cycle. This highly unusual feature distinguishes it from other plant-parasitic nematodes and requires profound changes in biology between modes. During the phytophagous stage, the nematode migrates within pine trees, feeding on the contents of parenchymal cells. Like other plant pathogens, B. xylophilus secretes effectors from pharyngeal gland cells into the host during infection. We provide the first description of changes in the morphology of these gland cells between juvenile and adult life stages. Using a comparative transcriptomics approach and an effector identification pipeline, we identify numerous novel parasitism genes which may be important for the mediation of interactions of B. xylophilus with its host. In-depth characterization of all parasitism genes using in situ hybridization reveals two major categories of detoxification proteins, those specifically expressed in either the pharyngeal gland cells or the digestive system. These data suggest that B. xylophilus incorporates effectors in a multilayer detoxification strategy in order to protect itself from host defence responses during phytophagy.
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http://dx.doi.org/10.1111/mpp.12280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6638532PMC
February 2016

Transcriptional and morphological changes in the transition from mycetophagous to phytophagous phase in the plant-parasitic nematode Bursaphelenchus xylophilus.

Mol Plant Pathol 2016 Jan 7;17(1):77-83. Epub 2015 May 7.

Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan.

Drastic physiological and morphological changes in parasites are crucial for the establishment of a successful infection. The nematode Bursaphelenchus xylophilus is the pathogenic agent of pine wilt disease, and little is known about the physiology and morphology in this nematode at the initial stage of infection. In this study, we devised an infection system using pine stem cuttings that allowed us to observe transcriptional and morphological changes in the host-infecting phytophagous phase. We found that 60 genes enriched in xenobiotic detoxification were up-regulated in two independent post-inoculation events, whereas down-regulation was observed in multiple members of collagen gene families. After 48 h of inoculation, the tails in some of the adult females exposed to the host changed in morphology. These results suggest that B. xylophilus may change its physiology and morphology to protect itself and to adapt to the host pine wood environment.
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http://dx.doi.org/10.1111/mpp.12261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6638504PMC
January 2016

Ancient and novel small RNA pathways compensate for the loss of piRNAs in multiple independent nematode lineages.

PLoS Biol 2015 Feb 10;13(2):e1002061. Epub 2015 Feb 10.

Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, United Kingdom.

Small RNA pathways act at the front line of defence against transposable elements across the Eukaryota. In animals, Piwi interacting small RNAs (piRNAs) are a crucial arm of this defence. However, the evolutionary relationships among piRNAs and other small RNA pathways targeting transposable elements are poorly resolved. To address this question we sequenced small RNAs from multiple, diverse nematode species, producing the first phylum-wide analysis of how small RNA pathways evolve. Surprisingly, despite their prominence in Caenorhabditis elegans and closely related nematodes, piRNAs are absent in all other nematode lineages. We found that there are at least two evolutionarily distinct mechanisms that compensate for the absence of piRNAs, both involving RNA-dependent RNA polymerases (RdRPs). Whilst one pathway is unique to nematodes, the second involves Dicer-dependent RNA-directed DNA methylation, hitherto unknown in animals, and bears striking similarity to transposon-control mechanisms in fungi and plants. Our results highlight the rapid, context-dependent evolution of small RNA pathways and suggest piRNAs in animals may have replaced an ancient eukaryotic RNA-dependent RNA polymerase pathway to control transposable elements.
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http://dx.doi.org/10.1371/journal.pbio.1002061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4323106PMC
February 2015

Signatures of adaptation to plant parasitism in nematode genomes.

Parasitology 2015 Feb;142 Suppl 1:S71-84

INRA, UMR 1355, Institut Sophia Agrobiotech,F-06903, Sophia-Antipolis,France.

Plant-parasitic nematodes cause considerable damage to global agriculture. The ability to parasitize plants is a derived character that appears to have independently emerged several times in the phylum Nematoda. Morphological convergence to feeding style has been observed, but whether this is emergent from molecular convergence is less obvious. To address this, we assess whether genomic signatures can be associated with plant parasitism by nematodes. In this review, we report genomic features and characteristics that appear to be common in plant-parasitic nematodes while absent or rare in animal parasites, predators or free-living species. Candidate horizontal acquisitions of parasitism genes have systematically been found in all plant-parasitic species investigated at the sequence level. Presence of peptides that mimic plant hormones also appears to be a trait of plant-parasitic species. Annotations of the few genomes of plant-parasitic nematodes available to date have revealed a set of apparently species-specific genes on every occasion. Effector genes, important for parasitism are frequently found among those species-specific genes, indicating poor overlap. Overall, nematodes appear to have developed convergent genomic solutions to adapt to plant parasitism.
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http://dx.doi.org/10.1017/S0031182013002163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4413825PMC
February 2015

Genomic characterisation of the effector complement of the potato cyst nematode Globodera pallida.

BMC Genomics 2014 Oct 23;15:923. Epub 2014 Oct 23.

The James Hutton Institute, Dundee Effector Consortium, Invergowrie, Dundee DD2 5DA, UK.

Background: The potato cyst nematode Globodera pallida has biotrophic interactions with its host. The nematode induces a feeding structure - the syncytium - which it keeps alive for the duration of the life cycle and on which it depends for all nutrients required to develop to the adult stage. Interactions of G. pallida with the host are mediated by effectors, which are produced in two sets of gland cells. These effectors suppress host defences, facilitate migration and induce the formation of the syncytium.

Results: The recent completion of the G. pallida genome sequence has allowed us to identify the effector complement from this species. We identify 128 orthologues of effectors from other nematodes as well as 117 novel effector candidates. We have used in situ hybridisation to confirm gland cell expression of a subset of these effectors, demonstrating the validity of our effector identification approach. We have examined the expression profiles of all effector candidates using RNAseq; this analysis shows that the majority of effectors fall into one of three clusters of sequences showing conserved expression characteristics (invasive stage nematode only, parasitic stage only or invasive stage and adult male only). We demonstrate that further diversity in the effector pool is generated by alternative splicing. In addition, we show that effectors target a diverse range of structures in plant cells, including the peroxisome. This is the first identification of effectors from any plant pathogen that target this structure.

Conclusion: This is the first genome scale search for effectors, combined to a life-cycle expression analysis, for any plant-parasitic nematode. We show that, like other phylogenetically unrelated plant pathogens, plant parasitic nematodes deploy hundreds of effectors in order to parasitise plants, with different effectors required for different phases of the infection process.
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http://dx.doi.org/10.1186/1471-2164-15-923DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4213498PMC
October 2014

Identification and characterisation of a hyper-variable apoplastic effector gene family of the potato cyst nematodes.

PLoS Pathog 2014 Sep 25;10(9):e1004391. Epub 2014 Sep 25.

Centre for Plant Sciences, University of Leeds, Leeds, United Kingdom.

Sedentary endoparasitic nematodes are obligate biotrophs that modify host root tissues, using a suite of effector proteins to create and maintain a feeding site that is their sole source of nutrition. Using assumptions about the characteristics of genes involved in plant-nematode biotrophic interactions to inform the identification strategy, we provide a description and characterisation of a novel group of hyper-variable extracellular effectors termed HYP, from the potato cyst nematode Globodera pallida. HYP effectors comprise a large gene family, with a modular structure, and have unparalleled diversity between individuals of the same population: no two nematodes tested had the same genetic complement of HYP effectors. Individuals vary in the number, size, and type of effector subfamilies. HYP effectors are expressed throughout the biotrophic stages in large secretory cells associated with the amphids of parasitic stage nematodes as confirmed by in situ hybridisation. The encoded proteins are secreted into the host roots where they are detectable by immunochemistry in the apoplasm, between the anterior end of the nematode and the feeding site. We have identified HYP effectors in three genera of plant parasitic nematodes capable of infecting a broad range of mono- and dicotyledon crop species. In planta RNAi targeted to all members of the effector family causes a reduction in successful parasitism.
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http://dx.doi.org/10.1371/journal.ppat.1004391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177990PMC
September 2014

The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes.

Genome Biol Evol 2014 Aug 13;6(9):2181-94. Epub 2014 Aug 13.

Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, United Kingdom

Within the phylum Nematoda, plant-parasitism is hypothesized to have arisen independently on at least four occasions. The most economically damaging plant-parasitic nematode species, and consequently the most widely studied, are those that feed as they migrate destructively through host roots causing necrotic lesions (migratory endoparasites) and those that modify host root tissue to create a nutrient sink from which they feed (sedentary endoparasites). The false root-knot nematode Nacobbus aberrans is the only known species to have both migratory endoparasitic and sedentary endoparasitic stages within its life cycle. Moreover, its sedentary stage appears to have characteristics of both the root-knot and the cyst nematodes. We present the first large-scale genetic resource of any false-root knot nematode species. We use RNAseq to describe relative abundance changes in all expressed genes across the life cycle to provide interesting insights into the biology of this nematode as it transitions between modes of parasitism. A multigene phylogenetic analysis of N. aberrans with respect to plant-parasitic nematodes of all groups confirms its proximity to both cyst and root-knot nematodes. We present a transcriptome-wide analysis of both lateral gene transfer events and the effector complement. Comparing parasitism genes of typical root-knot and cyst nematodes to those of N. aberrans has revealed interesting similarities. Importantly, genes that were believed to be either cyst nematode, or root-knot nematode, "specific" have both been identified in N. aberrans. Our results provide insights into the characteristics of a common ancestor and the evolution of sedentary endoparasitism of plants by nematodes.
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http://dx.doi.org/10.1093/gbe/evu171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4202313PMC
August 2014

Distribution and evolution of glycoside hydrolase family 45 cellulases in nematodes and fungi.

BMC Evol Biol 2014 Apr 1;14:69. Epub 2014 Apr 1.

Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan.

Background: Horizontal gene transfer (HGT) has been suggested as the mechanism by which various plant parasitic nematode species have obtained genes important in parasitism. In particular, cellulase genes have been acquired by plant parasitic nematodes that allow them to digest plant cell walls. Unlike the typical glycoside hydrolase (GH) family 5 cellulase genes which are found in several nematode species from the order Tylenchida, members of the GH45 cellulase have only been identified in a cluster including the families Parasitaphelenchidae (with the pinewood nematode Bursaphelenchus xylophilus) and Aphelenchoididae, and their origins remain unknown.

Results: In order to investigate the distribution and evolution of GH45 cellulase genes in nematodes and fungi we performed a wide ranging screen for novel putative GH45 sequences. This revealed that the sequences are widespread mainly in Ascomycetous fungi and have so far been found in a single major nematode lineage. Close relationships between the sequences from nematodes and fungi were found through our phylogenetic analyses. An intron position is shared by sequences from Bursaphelenchus nematodes and several Ascomycetous fungal species.

Conclusions: The close phylogenetic relationships and conserved gene structure between the sequences from nematodes and fungi strongly supports the hypothesis that nematode GH45 cellulase genes were acquired via HGT from fungi. The rapid duplication and turnover of these genes within Bursaphelenchus genomes demonstrate that useful sequences acquired via HGT can become established in the genomes of recipient organisms and may open novel niches for these organisms to exploit.
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http://dx.doi.org/10.1186/1471-2148-14-69DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3997829PMC
April 2014

Functional characterization of nematode effectors in plants.

Methods Mol Biol 2014 ;1127:113-24

Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA,

Secreted effectors represent the molecular interface between the nematode and its host plant. Studies that aimed at deciphering molecular plant-nematode interactions are hampered by technical hurdles that prevent the generation of transgenic nematodes. However, RNA interference (RNAi) has proven to be a valuable tool to specifically knock-down nematode effector genes, both ex planta and in planta. Plant-mediated RNAi of nematode genes not only facilitates functional characterization of effectors but also lends itself to a novel control strategy against plant-parasitic nematodes. Here, we describe currently used methods to silence genes in plant-parasitic cyst and root-knot nematodes.
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http://dx.doi.org/10.1007/978-1-62703-986-4_9DOI Listing
November 2014

Bioinformatic analysis of expression data to identify effector candidates.

Methods Mol Biol 2014 ;1127:17-27

Parasite Genomics, Wellcome Trust Sanger Institute, Genome Campus, Cambridge, CB10 1SA, UK,

Pathogens produce effectors that manipulate the host to the benefit of the pathogen. These effectors are often secreted proteins that are upregulated during the early phases of infection. These properties can be used to identify candidate effectors from genomes and transcriptomes of pathogens. Here we describe commonly used bioinformatic approaches that (1) allow identification of genes encoding predicted secreted proteins within a genome and (2) allow the identification of genes encoding predicted secreted proteins that are upregulated at important stages of the life cycle. Other approaches for bioinformatic identification of effector candidates, including OrthoMCL analysis to identify expanded gene families, are also described.
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http://dx.doi.org/10.1007/978-1-62703-986-4_2DOI Listing
November 2014

The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode.

Genome Biol 2014 Mar 3;15(3):R43. Epub 2014 Mar 3.

Background: Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security.

Results: We present the complete genome sequence of G. pallida, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site. Despite the relatively close phylogenetic relationship with root-knot nematodes, we describe a very different gene family content between the two groups and in particular extensive differences in the repertoire of effectors, including an enormous expansion of the SPRY domain protein family in G. pallida, which includes the SPRYSEC family of effectors. This highlights the distinct biology of cyst nematodes compared to the root-knot nematodes that were, until now, the only sedentary plant parasitic nematodes for which genome information was available. We also present in-depth descriptions of the repertoires of other genes likely to be important in understanding the unique biology of cyst nematodes and of potential drug targets and other targets for their control.

Conclusions: The data and analyses we present will be central in exploiting post-genomic approaches in the development of much-needed novel strategies for the control of G. pallida and related pathogens.
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http://dx.doi.org/10.1186/gb-2014-15-3-r43DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054857PMC
March 2014

The feeding tube of cyst nematodes: characterisation of protein exclusion.

PLoS One 2014 28;9(1):e87289. Epub 2014 Jan 28.

Centre for Plant Sciences, University of Leeds, Leeds, United Kingdom.

Plant parasitic nematodes comprise several groups; the most economically damaging of these are the sedentary endoparasites. Sedentary endoparasitic nematodes are obligate biotrophs and modify host root tissue, using a suite of effector proteins, to create a feeding site that is their sole source of nutrition. They feed by withdrawing host cell assimilate from the feeding site though a structure known as the feeding tube. The function, composition and molecular characteristics of feeding tubes are poorly characterised. It is hypothesised that the feeding tube facilitates uptake of host cell assimilate by acting as a molecular sieve. Several studies, using molecular mass as the sole indicator of protein size, have given contradictory results about the exclusion limits of the cyst nematode feeding tube. In this study we propose a method to predict protein size, based on protein database coordinates in silico. We tested the validity of these predictions using travelling wave ion mobility spectrometry--mass spectrometry, where predictions and measured values were within approximately 6%. We used the predictions, coupled with mass spectrometry, analytical ultracentrifugation and protein electrophoresis, to resolve previous conflicts and define the exclusion characteristics of the cyst nematode feeding tube. Heterogeneity was tested in the liquid, solid and gas phase to provide a comprehensive evaluation of three proteins of particular interest to feeding tube size exclusion, GFP, mRFP and Dual PI. The data and procedures described here could be applied to the design of plant expressed defence compounds intended for uptake into cyst nematodes. We also highlight the need to assess protein heterogeneity when creating novel fusion proteins.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087289PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905015PMC
November 2014

Top 10 plant-parasitic nematodes in molecular plant pathology.

Mol Plant Pathol 2013 Dec 1;14(9):946-61. Epub 2013 Jul 1.

James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.

The aim of this review was to undertake a survey of researchers working with plant-parasitic nematodes in order to determine a 'top 10' list of these pathogens based on scientific and economic importance. Any such list will not be definitive as economic importance will vary depending on the region of the world in which a researcher is based. However, care was taken to include researchers from as many parts of the world as possible when carrying out the survey. The top 10 list emerging from the survey is composed of: (1) root-knot nematodes (Meloidogyne spp.); (2) cyst nematodes (Heterodera and Globodera spp.); (3) root lesion nematodes (Pratylenchus spp.); (4) the burrowing nematode Radopholus similis; (5) Ditylenchus dipsaci; (6) the pine wilt nematode Bursaphelenchus xylophilus; (7) the reniform nematode Rotylenchulus reniformis; (8) Xiphinema index (the only virus vector nematode to make the list); (9) Nacobbus aberrans; and (10) Aphelenchoides besseyi. The biology of each nematode (or nematode group) is reviewed briefly.
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http://dx.doi.org/10.1111/mpp.12057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6638764PMC
December 2013