1
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Shift from morphological to recent advanced molecular approaches for the identification of nematodes. Genomics 2022; 114:110295. [DOI: 10.1016/j.ygeno.2022.110295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 01/08/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022]
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2
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Nguyen VC, Khallouk S, Polidori J, Truch J, Portier U, Lafargue M, Tandonnet JP, Ollat N, Van Ghelder C, Banora MY, Esmenjaud D. Evidence of Sexual Reproduction Events in the Dagger Nematode Xiphinema index in Grapevine Resistance Experiments Under Controlled Conditions. PLANT DISEASE 2021; 105:2664-2669. [PMID: 33320044 DOI: 10.1094/pdis-06-20-1409-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The dagger nematode Xiphinema index has a major economic impact because of its transmission of Grapevine fanleaf virus to grapevines. This vector nematode, which was introduced into Western countries from the Middle East together with the domesticated grapevine, mostly reproduces by meiotic parthenogenesis, but microsatellite multilocus genotype (MLG) analysis has revealed the occurrence of rare sexual reproduction events in field conditions. In a previous 6-year study under controlled conditions, we evaluated the durability of resistance to X. index in accessions derived from a muscadine resistance source and reference accessions. In this previous study, we used an equal-proportion mixture of four lines (from Spain, Italy, Greece, and Iran) representative of X. index diversity as the inoculum, and we collected random samples in 3-, 4-, 5-, and 6-year-old vines. Here, we genotyped the individuals from these samples using the MLG technique, and we analyzed the changes in line frequency and the occurrence of sexual reproduction events between lines over time. The nematode lines differed in aggressiveness and hybrids between lines were detected at a low, but apparently increasing rate. Hybridization events were recovered in all accessions, regardless of resistance status and propagation type. Finally, our data provide the first evidence of sexual reproduction in the nematode X. index under controlled conditions.
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Affiliation(s)
- Van Chung Nguyen
- INRAE, Université Côte d'Azur, CNRS, ISA, 06903 Sophia Antipolis, France
| | | | - Joël Polidori
- INRAE, Université Côte d'Azur, CNRS, ISA, 06903 Sophia Antipolis, France
| | - Julia Truch
- INRAE, Université Côte d'Azur, CNRS, ISA, 06903 Sophia Antipolis, France
| | - Ulysse Portier
- INRAE, Université Côte d'Azur, CNRS, ISA, 06903 Sophia Antipolis, France
| | - Maria Lafargue
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, 33882 Villenave d'Ornon, France
| | - Jean-Pascal Tandonnet
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, 33882 Villenave d'Ornon, France
| | - Nathalie Ollat
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, 33882 Villenave d'Ornon, France
| | - Cyril Van Ghelder
- INRAE, Université Côte d'Azur, CNRS, ISA, 06903 Sophia Antipolis, France
| | - Mohamed Youssef Banora
- Ain Shams University, Faculty of Agriculture, Department of Plant Pathology, 11241 Hadayek Shoubra, Cairo, Egypt
| | - Daniel Esmenjaud
- INRAE, Université Côte d'Azur, CNRS, ISA, 06903 Sophia Antipolis, France
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3
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Stoeckel S, Arnaud-Haond S, Krueger-Hadfield SA. The Combined Effect of Haplodiplonty and Partial Clonality on Genotypic and Genetic Diversity in a Finite Mutating Population. J Hered 2021; 112:78-91. [PMID: 33710350 DOI: 10.1093/jhered/esaa062] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 12/17/2020] [Indexed: 02/03/2023] Open
Abstract
Partial clonality is known to affect the genetic composition and evolutionary trajectory of diplontic (single, free-living diploid stage) populations. However, many partially clonal eukaryotes exhibit life cycles in which somatic development occurs in both haploid and diploid individuals (haplodiplontic life cycles). Here, we studied how haplodiplontic life cycles and partial clonality structurally constrain, as immutable parameters, the reshuffling of genetic diversity and its dynamics in populations over generations. We assessed the distribution of common population genetic indices at different proportions of haploids, rates of clonality, mutation rates, and sampling efforts. Our results showed that haplodiplontic life cycles alone in finite populations affect effective population sizes and the ranges of distributions of population genetic indices. With nonoverlapping generations, haplodiplonty allowed the evolution of 2 temporal genetic pools that may diverge in sympatry due to genetic drift under full sexuality and clonality. Partial clonality in these life cycles acted as a homogenizing force between those 2 pools. Moreover, the combined effects of proportion of haploids, rate of clonality, and the relative strength of mutation versus genetic drift impacts the distributions of population genetics indices, rendering it difficult to transpose and use knowledge accumulated from diplontic or haplontic species. Finally, we conclude by providing recommendations for sampling and analyzing the population genetics of partially clonal haplodiplontic taxa.
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Affiliation(s)
- Solenn Stoeckel
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, F-35650 Le Rheu, France
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4
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Krueger-Hadfield SA, Guillemin ML, Destombe C, Valero M, Stoeckel S. Exploring the Genetic Consequences of Clonality in Haplodiplontic Taxa. J Hered 2021; 112:92-107. [PMID: 33511982 DOI: 10.1093/jhered/esaa063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/18/2020] [Indexed: 11/15/2022] Open
Abstract
Partially clonality is an incredibly common reproductive mode found across all the major eukaryotic lineages. Yet, population genetic theory is based on exclusive sexuality or exclusive asexuality, and partial clonality is often ignored. This is particularly true in haplodiplontic eukaryotes, including algae, ferns, mosses, and fungi, where somatic development occurs in both the haploid and diploid stages. Haplodiplontic life cycles are predicted to be correlated with asexuality, but tests of this prediction are rare. Moreover, there are unique consequences of having long-lived haploid and diploid stages in the same life cycle. For example, clonal processes uncouple the life cycle such that the repetition of the diploid stage via clonality leads to the loss of the haploid stage. Here, we surveyed the literature to find studies that had genotyped both haploid and diploid stages and recalculated population genetic summary metrics for seven red algae, one green alga, three brown algae, and three mosses. We compared these data to recent simulations that explicitly addressed the population genetic consequences of partial clonality in haplodiplontic life cycles. Not only was partial clonality found to act as a homogenizing force, but the combined effects of proportion of haploids, rate of clonality, and the relative strength of mutation versus genetic drift impacts the distributions of population genetic indices. We found remarkably similar patterns across commonly used population genetic metrics between our empirical and recent theoretical expectations. To facilitate future studies, we provide some recommendations for sampling and analyzing population genetic parameters for haplodiplontic taxa.
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Affiliation(s)
| | - Marie-Laure Guillemin
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Station Biologique de Roscoff, Roscoff, France
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla, Valdivia, Chile
| | - Christophe Destombe
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Station Biologique de Roscoff, Roscoff, France
| | - Myriam Valero
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Station Biologique de Roscoff, Roscoff, France
| | - Solenn Stoeckel
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
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5
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Stoeckel S, Porro B, Arnaud-Haond S. The discernible and hidden effects of clonality on the genotypic and genetic states of populations: Improving our estimation of clonal rates. Mol Ecol Resour 2021; 21:1068-1084. [PMID: 33386695 DOI: 10.1111/1755-0998.13316] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 11/05/2020] [Accepted: 12/21/2020] [Indexed: 11/29/2022]
Abstract
Partial clonality is widespread across the tree of life, but most population genetic models are designed for exclusively clonal or sexual organisms. This gap hampers our understanding of the influence of clonality on evolutionary trajectories and the interpretation of population genetic data. We performed forward simulations of diploid populations at increasing rates of clonality (c), analysed their relationships with genotypic (clonal richness, R, and distribution of clonal sizes, Pareto β) and genetic (FIS and linkage disequilibrium) indices, and tested predictions of c from population genetic data through supervised machine learning. Two complementary behaviours emerged from the probability distributions of genotypic and genetic indices with increasing c. While the impact of c on R and Pareto β was easily described by simple mathematical equations, its effects on genetic indices were noticeable only at the highest levels (c > 0.95). Consequently, genotypic indices allowed reliable estimates of c, while genetic descriptors led to poorer performances when c < 0.95. These results provide clear baseline expectations for genotypic and genetic diversity and dynamics under partial clonality. Worryingly, however, the use of realistic sample sizes to acquire empirical data systematically led to gross underestimates (often of one to two orders of magnitude) of c, suggesting that many interpretations hitherto proposed in the literature, mostly based on genotypic richness, should be reappraised. We propose future avenues to derive realistic confidence intervals for c and show that, although still approximate, a supervised learning method would greatly improve the estimation of c from population genetic data.
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Affiliation(s)
- Solenn Stoeckel
- Institute for Genetics, Environment and Plant Protection, INRAE, Le Rheu, France
| | - Barbara Porro
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France.,MARBEC - Marine Biodiversity Exploitation and Conservation, University of Montpellier, CNRS, Ifremer, IRD, MARBEC, Sète, France
| | - Sophie Arnaud-Haond
- MARBEC - Marine Biodiversity Exploitation and Conservation, University of Montpellier, CNRS, Ifremer, IRD, MARBEC, Sète, France
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6
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Rasmussen DA, Grünwald NJ. Phylogeographic Approaches to Characterize the Emergence of Plant Pathogens. PHYTOPATHOLOGY 2021; 111:68-77. [PMID: 33021879 DOI: 10.1094/phyto-07-20-0319-fi] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Phylogeography combines geographic information with phylogenetic and population genomic approaches to infer the evolutionary history of a species or population in a geographic context. This approach has been instrumental in understanding the emergence, spread, and evolution of a range of plant pathogens. In particular, phylogeography can address questions about where a pathogen originated, whether it is native or introduced, and when and how often introductions occurred. We review the theory, methods, and approaches underpinning phylogeographic inference and highlight applications providing novel insights into the emergence and spread of select pathogens. We hope that this review will be useful in assessing the power, pitfalls, and opportunities presented by various phylogeographic approaches.
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Affiliation(s)
- David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC
| | - Niklaus J Grünwald
- Horticultural Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR
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7
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Winkler DE, Chapin KJ, Garmon JD, Gaut BS, Huxman TE. Sahara mustard as a major threat to desert biodiversity in the southwest United States and the need to integrate contemporary methods to understand its biology. Ecol Evol 2020; 10:14453-14455. [PMID: 33391728 PMCID: PMC7771142 DOI: 10.1002/ece3.6936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 11/18/2022] Open
Affiliation(s)
- Daniel E. Winkler
- Department of Ecology & Evolutionary BiologyUniversity of CaliforniaIrvineCAUSA
- Present address:
U.S. Geological SurveySouthwest Biological Science CenterMoabUTUSA
| | - Kenneth J. Chapin
- Department of Ecology & Evolutionary BiologyUniversity of CaliforniaLos AngelesUSA
- Department of Ecology & Evolutionary BiologyUniversity of ArizonaTucsonUSA
| | | | - Brandon S. Gaut
- Department of Ecology & Evolutionary BiologyUniversity of CaliforniaIrvineCAUSA
| | - Travis E. Huxman
- Department of Ecology & Evolutionary BiologyUniversity of CaliforniaIrvineCAUSA
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8
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Nguyen VC, Tandonnet JP, Khallouk S, Van Ghelder C, Portier U, Lafargue M, Banora MY, Ollat N, Esmenjaud D. Grapevine Resistance to the Nematode Xiphinema index Is Durable in Muscadine-Derived Plants Obtained from Hardwood Cuttings but Not from In Vitro. PHYTOPATHOLOGY 2020; 110:1565-1571. [PMID: 32378451 DOI: 10.1094/phyto-01-20-0008-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Breeding for varieties carrying natural resistance (R) against plant-parasitic nematodes is a promising alternative to nematicide ban. In perennial crops, the long plant-nematode interaction increases the risk for R breaking and R durability is a real challenge. In grapevine, the nematode Xiphinema index has a high economic impact by transmitting Grapevine fanleaf virus (GFLV) and, to delay GFLV transmission, rootstocks resistant to this vector are being selected, using Muscadinia rotundifolia in particular as an R source. To optimize in fine this strategy, the durability has been studied under controlled conditions in F1 and BC1 muscadine-derived resistant accessions previously obtained from either hardwood-cutting or in vitro propagation. After inoculation with a mix, in equal proportions, of four lines representative of the X. index diversity, multiplication on plants has been monitored 3 to 6 years. The nematode reproduction factor remained lower than 1 in resistant plants obtained from hardwood cuttings while it increased at values far beyond 1 in resistant plants of in vitro origin. Data for nematode numbers per gram of roots mostly paralleled those obtained for the reproduction factor. The effect of the propagation type on resistance over years was also evaluated for the ratio female/juvenile and the frequency of males. Altogether our results illustrate that the muscadine-derived resistance based on hardwood cuttings is durable. By contrast, in resistant and reference accessions obtained from in vitro, our data suggest that the increased nematode multiplication might be mainly due to the modification of root architecture consecutive to this propagation method.
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Affiliation(s)
- Van Chung Nguyen
- INRAE, Université Côte d'Azur, CNRS, ISA, 06903 Sophia Antipolis, France
| | - Jean-Pascal Tandonnet
- University of Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, EGFV, 33882 Villenave d'Ornon, France
| | - Samira Khallouk
- Service de la Protection du Patrimoine Végétal, ONSSA, Rabat, Morocco
| | - Cyril Van Ghelder
- INRAE, Université Côte d'Azur, CNRS, ISA, 06903 Sophia Antipolis, France
| | - Ulysse Portier
- INRAE, Université Côte d'Azur, CNRS, ISA, 06903 Sophia Antipolis, France
| | - Maria Lafargue
- University of Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, EGFV, 33882 Villenave d'Ornon, France
| | | | - Nathalie Ollat
- University of Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, EGFV, 33882 Villenave d'Ornon, France
| | - Daniel Esmenjaud
- INRAE, Université Côte d'Azur, CNRS, ISA, 06903 Sophia Antipolis, France
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9
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Nguyen VC, Villate L, Gutierrez-Gutierrez C, Castillo P, Van Ghelder C, Plantard O, Esmenjaud D. Phylogeography of the soil-borne vector nematode Xiphinema index highly suggests Eastern origin and dissemination with domesticated grapevine. Sci Rep 2019; 9:7313. [PMID: 31086246 PMCID: PMC6513855 DOI: 10.1038/s41598-019-43812-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 04/27/2019] [Indexed: 11/10/2022] Open
Abstract
The soil-borne nematode Xiphinema index is closely linked to its main host, the grapevine, and presents a major threat to vineyards worldwide due to its ability to transmit Grapevine fanleaf virus (GFLV). The phylogeography of X. index has been studied using mitochondrial and microsatellite markers in samples from most regions of its worldwide distribution to reveal its genetic diversity. We first used the mitochondrial marker CytB and illustrated the low intraspecific divergence of this mainly meiotic parthenogenetic species. To generate a higher polymorphism level, we then concatenated the sequences of CytB and three mitochondrial markers, ATP6, CO1 and ND4, to obtain a 3044-bp fragment. We differentiated two clades, which each contained two well-supported subclades. Samples from the eastern Mediterranean and the Near and Middle East were grouped into three of these subclades, whereas the samples from the western Mediterranean, Europe and the Americas all belonged to the fourth subclade. The highest polymorphism level was found in the samples of one of the Middle and Near East subclades, strongly suggesting that this region contained the native area of the nematode. An east-to-west nematode dissemination hypothesis appeared to match the routes of the domesticated grapevine during Antiquity, presumably mainly dispersed by the Greeks and the Romans. Surprisingly, the samples of the western subclade comprised only two highly similar mitochondrial haplotypes. The first haplotype, from southern Iberian Peninsula, Bordeaux and Provence vineyards, exhibited a high microsatellite polymorphism level that suggests introductions dating from Antiquity. The second haplotype contained a highly predominant microsatellite genotype widespread in distant western countries that may be a consequence of the massive grapevine replanting following the 19th-century phylloxera crisis. Finally, our study enabled us to draw a first scaffold of X. index diversity at the global scale.
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Affiliation(s)
- Van Chung Nguyen
- INRA, Université Nice Côte d'Azur, CNRS, ISA, Sophia Antipolis, 06903, France. .,Plant Protection Research Institute (PPRI), Hanoi, Vietnam.
| | - Laure Villate
- UMR1202 BIOGECO, INRA, University of Bordeaux, Pessac, 33615, France
| | - Carlos Gutierrez-Gutierrez
- NemaLab/ICAAM, Instituto de Ciencias Agrarias e Ambientais Mediterranicas & Dept. de Biologia, Universidade de Evora, Evora, 7002-554, Portugal
| | - Pablo Castillo
- Institute for Sustainable Agriculture (IAS), CSIC, Cordoba, 14004, Spain
| | - Cyril Van Ghelder
- INRA, Université Nice Côte d'Azur, CNRS, ISA, Sophia Antipolis, 06903, France
| | | | - Daniel Esmenjaud
- INRA, Université Nice Côte d'Azur, CNRS, ISA, Sophia Antipolis, 06903, France.
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10
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Danchin EGJ, Perfus-Barbeoch L, Rancurel C, Thorpe P, Da Rocha M, Bajew S, Neilson R, Guzeeva ES, Da Silva C, Guy J, Labadie K, Esmenjaud D, Helder J, Jones JT, den Akker SEV. 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; 8:genes8100287. [PMID: 29065523 PMCID: PMC5664137 DOI: 10.3390/genes8100287] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 11/16/2022] Open
Abstract
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, Xiphinema index and Longidorus elongatus, 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 X. index and L. elongatus, 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 X. index 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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Affiliation(s)
- Etienne G J Danchin
- INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis Cedex, France.
| | | | - Corinne Rancurel
- INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis Cedex, France.
| | - Peter Thorpe
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
| | - Martine Da Rocha
- INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis Cedex, France.
| | - Simon Bajew
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
| | - Roy Neilson
- Ecological Sciences Group, IPM@Hutton, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
| | - Elena Sokolova Guzeeva
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
- Centre of Parasitology of the A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii Prospect 33, Moscow 119071, Russia.
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, 92057, Evry, France.
| | - Julie Guy
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, 92057, Evry, France.
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, 92057, Evry, France.
| | - Daniel Esmenjaud
- INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis Cedex, France.
| | - Johannes Helder
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - John T Jones
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
- School of Biology, University of St Andrews, North Haugh, St Andrews KY16 9TZ, UK.
| | - Sebastian Eves-van den Akker
- Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
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11
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Becheler R, Masson JP, Arnaud-Haond S, Halkett F, Mariette S, Guillemin ML, Valero M, Destombe C, Stoeckel S. ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps. Mol Ecol Resour 2017; 17:e251-e267. [DOI: 10.1111/1755-0998.12698] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 06/01/2017] [Accepted: 06/22/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Ronan Becheler
- Evolutionary Biology and Ecology of Algae; CNRS; Sorbonne Universités; UPMC; University of Paris VI; UC; UACH; UMI 3614; Roscoff France
| | - Jean-Pierre Masson
- Institute for Genetics; Environment and Plant Protection; INRA; UMR1349; Le Rheu France
| | - Sophie Arnaud-Haond
- Ifremer; MARBEC (Marine Biodiversity, Exploitation and Conservation); Boulevard Jean Monet; 34200 SETE
| | | | | | - Marie-Laure Guillemin
- Evolutionary Biology and Ecology of Algae; CNRS; Sorbonne Universités; UPMC; University of Paris VI; UC; UACH; UMI 3614; Roscoff France
- Facultad de Ciencias; Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Valdivia Chile
| | - Myriam Valero
- Evolutionary Biology and Ecology of Algae; CNRS; Sorbonne Universités; UPMC; University of Paris VI; UC; UACH; UMI 3614; Roscoff France
| | - Christophe Destombe
- Evolutionary Biology and Ecology of Algae; CNRS; Sorbonne Universités; UPMC; University of Paris VI; UC; UACH; UMI 3614; Roscoff France
| | - Solenn Stoeckel
- Institute for Genetics; Environment and Plant Protection; INRA; UMR1349; Le Rheu France
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12
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Gamel S, Letort A, Fouville D, Folcher L, Grenier E. Development and validation of real-time PCR assays based on novel molecular markers for the simultaneous detection and identification of Globodera pallida, G. rostochiensis and Heterodera schachtii. NEMATOLOGY 2017. [DOI: 10.1163/15685411-00003086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Considering the growing trade of seed potato, reliable diagnostic protocols are required for the detection of regulated nematode species. In this study, a specific and sensitive multiplex Taqman-based real-time PCR method was developed in order to detect and identifyGlobodera pallida,G. rostochiensisandHeterodera schachtii. The newly designed primers and probes enabled the detection of all the target populations tested and with no cross-reaction for closely related non-target species (55 populations tested). The limit of detection (LOD) was one juvenile forG. rostochiensisandG. pallidaand five juveniles forH. schachtii. For monitoring potato cyst nematodes, this analytical tool would extend the number of cyst investigated as five juveniles can be detected among 50 cysts in a sample. Furthermore, this multiplex assay detects DNA of the three targeted species in template DNA obtained directly from float material after nematode extraction from soil.
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Affiliation(s)
- Sylvie Gamel
- Anses, Plant Health Laboratory, Nematology unit, Domaine de la Motte au Vicomte, BP35327, 35653 Le Rheu, France
| | - Aude Letort
- Anses, Plant Health Laboratory, Nematology unit, Domaine de la Motte au Vicomte, BP35327, 35653 Le Rheu, France
| | - Didier Fouville
- INRA, UMR1349 IGEPP (Institute of Genetics, Environment and Plant Protection), Domaine de la Motte au Vicomte, BP35327, 35653 Le Rheu, France
| | - Laurent Folcher
- Anses, Plant Health Laboratory, Nematology unit, Domaine de la Motte au Vicomte, BP35327, 35653 Le Rheu, France
| | - Eric Grenier
- INRA, UMR1349 IGEPP (Institute of Genetics, Environment and Plant Protection), Domaine de la Motte au Vicomte, BP35327, 35653 Le Rheu, France
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Gracianne C, Jan P, Fournet S, Olivier E, Arnaud J, Porte C, Bardou‐Valette S, Denis M, Petit EJ. Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 2. Separating the relative effects of gene flow and genetic drift. Evol Appl 2016; 9:1005-16. [PMID: 27606008 PMCID: PMC4999530 DOI: 10.1111/eva.12401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/06/2016] [Indexed: 11/29/2022] Open
Abstract
Studying wild pathogen populations in natural ecosystems offers the opportunity to better understand the evolutionary dynamics of biotic diseases in crops and to enhance pest control strategies. We used simulations and genetic markers to investigate the spatial and temporal population genetic structure of wild populations of the beet cyst nematode Heterodera schachtii on a wild host plant species, the sea beet (Beta vulgaris spp. maritima), the wild ancestor of cultivated beets. Our analysis of the variation of eight microsatellite loci across four study sites showed that (i) wild H. schachtii populations displayed fine-scaled genetic structure with no evidence of substantial levels of gene flow beyond the scale of the host plant, and comparisons with simulations indicated that (ii) genetic drift substantially affected the residual signals of isolation-by-distance processes, leading to departures from migration-drift equilibrium. In contrast to what can be suspected for (crop) field populations, this showed that wild cyst nematodes have very low dispersal capabilities and are strongly disconnected from each other. Our results provide some key elements for designing pest control strategies, such as decreasing passive dispersal events to limit the spread of virulence among field nematode populations.
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Affiliation(s)
- Cécile Gracianne
- IGEPPINRA, Agrocampus OuestUniversité Rennes 1Le RheuFrance
- VetAgro Sup, UMR 1095, GDECClermont UniversitéClermont‐FerrandFrance
| | - Pierre‐Loup Jan
- IGEPPINRA, Agrocampus OuestUniversité Rennes 1Le RheuFrance
- ESE, Ecology and Ecosystems HealthAgrocampus OuestINRARennesFrance
| | | | - Eric Olivier
- IGEPPINRA, Agrocampus OuestUniversité Rennes 1Le RheuFrance
| | - Jean‐François Arnaud
- UMR CNRS 8198 ÉvolutionÉcologie et PaléontologieUniversité Lille 1 ‐ Sciences et TechnologiesVilleneuve d'Ascq CedexFrance
| | | | | | | | - Eric J. Petit
- ESE, Ecology and Ecosystems HealthAgrocampus OuestINRARennesFrance
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14
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Reichel K, Masson JP, Malrieu F, Arnaud-Haond S, Stoeckel S. Rare sex or out of reach equilibrium? The dynamics of F IS in partially clonal organisms. BMC Genet 2016; 17:76. [PMID: 27286682 PMCID: PMC4902967 DOI: 10.1186/s12863-016-0388-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 06/01/2016] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Partially clonal organisms are very common in nature, yet the influence of partial asexuality on the temporal dynamics of genetic diversity remains poorly understood. Mathematical models accounting for clonality predict deviations only for extremely rare sex and only towards mean inbreeding coefficient [Formula: see text]. Yet in partially clonal species, both F IS < 0 and F IS > 0 are frequently observed also in populations where there is evidence for a significant amount of sexual reproduction. Here, we studied the joint effects of partial clonality, mutation and genetic drift with a state-and-time discrete Markov chain model to describe the dynamics of F IS over time under increasing rates of clonality. RESULTS Results of the mathematical model and simulations show that partial clonality slows down the asymptotic convergence to F IS = 0. Thus, although clonality alone does not lead to departures from Hardy-Weinberg expectations once reached the final equilibrium state, both negative and positive F IS values can arise transiently even at intermediate rates of clonality. More importantly, such "transient" departures from Hardy Weinberg proportions may last long as clonality tunes up the temporal variation of F IS and reduces its rate of change over time, leading to a hyperbolic increase of the maximal time needed to reach the final mean [Formula: see text] value expected at equilibrium. CONCLUSION Our results argue for a dynamical interpretation of F IS in clonal populations. Negative values cannot be interpreted as unequivocal evidence for extremely scarce sex but also as intermediate rates of clonality in finite populations. Complementary observations (e.g. frequency distribution of multiloci genotypes, population history) or time series data may help to discriminate between different possible conclusions on the extent of clonality when mean [Formula: see text] values deviating from zero and/or a large variation of F IS over loci are observed.
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Affiliation(s)
- Katja Reichel
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - Jean-Pierre Masson
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - Florent Malrieu
- Université de Tours, CNRS-UMR7350 LMPT, F-37200, Tours, France
| | | | - Solenn Stoeckel
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, 35650, Le Rheu, France.
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15
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Ali S, Soubeyrand S, Gladieux P, Giraud T, Leconte M, Gautier A, Mboup M, Chen W, de Vallavieille-Pope C, Enjalbert J. cloncase: Estimation of sex frequency and effective population size by clonemate resampling in partially clonal organisms. Mol Ecol Resour 2016; 16:845-61. [DOI: 10.1111/1755-0998.12511] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 01/29/2016] [Accepted: 02/02/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Sajid Ali
- UMR1290, BIOGER; INRA-AgroParisTech; BP01 78850 Thiverval-Grignon France
- Institute of Biotechnology and Genetic Engineering; the University of Agriculture, Peshawar; 25000 Peshawar Pakistan
| | - Samuel Soubeyrand
- UR546 Biostatistics and Spatial Processes; INRA; 84914 Avignon France
| | - Pierre Gladieux
- Ecologie Systématique Evolution; CNRS; Univ. Paris-Sud; AgroParisTech; Université Paris-Saclay; 91400 Orsay France
- UMR385 Biologie et Génétique des Interactions Plante-Parasite; CIRAD; INRA; F-34398 Montpellier France
| | - Tatiana Giraud
- Ecologie Systématique Evolution; CNRS; Univ. Paris-Sud; AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - Marc Leconte
- UMR1290, BIOGER; INRA-AgroParisTech; BP01 78850 Thiverval-Grignon France
| | - Angélique Gautier
- UMR1290, BIOGER; INRA-AgroParisTech; BP01 78850 Thiverval-Grignon France
| | - Mamadou Mboup
- DuPont de Nemours (France) SAS Crop Protection - European Research & Development Center; 24, rue du Moulin 68740 Nambsheim France
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests; Institute of Plant Protection; Chinese Academy of Agricultural Sciences; No. 2 Yuanmingyuan West Road Beijing 100193 China
| | | | - Jérôme Enjalbert
- Ecologie Systématique Evolution; CNRS; Univ. Paris-Sud; AgroParisTech; Université Paris-Saclay; 91400 Orsay France
- GQE - Le Moulon; INRA; Univ. Paris-Sud; CNRS; AgroParisTech; Université Paris-Saclay; F-91190 Gif-sur-Yvette France
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16
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Holguin CM, Ma X, Mueller JD, Agudelo P. Distribution of Hoplolaimus Species in Soybean Fields in South Carolina and North Carolina. PLANT DISEASE 2016; 100:149-153. [PMID: 30688569 DOI: 10.1094/pdis-12-14-1332-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Hoplolaimus columbus is an important nematode pest of soybean in South Carolina and North Carolina. Tolerant cultivars are available for the management of this plant-parasitic nematode; however, variation in the response of soybean cultivars to H. columbus populations has been observed. This variation may be due to the presence of different species or high genetic diversity of H. columbus populations. The objective of this study was to identify the Hoplolaimus spp. present in fields representing the main soybean-growing regions in South Carolina and North Carolina and to examine the genetic variability of these populations. In South Carolina, the only species found associated with soybean was H. columbus but, in North Carolina, H. stephanus was the dominant species. The two species were never found together. Genetic variability analyses of a mitochondrial and a nuclear marker showed that only one haplotype was shared by the H. columbus populations. H. stephanus showed higher genetic variability, with private haplotypes per sampling location. Knowledge of the distribution and genetic variability of these two Hoplolaimus spp. is valuable to growers to determine potentially damaging infestations of these plant-parasitic nematodes in soybean fields.
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Affiliation(s)
- Claudia M Holguin
- Department of Agricultural and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - Xinyuan Ma
- Department of Agricultural and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - John D Mueller
- Edisto Research and Education Center, Clemson University, Blackville, SC 29817
| | - Paula Agudelo
- Department of Agricultural and Environmental Sciences, Clemson University, Clemson
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17
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Alenda C, Montarry J, Grenier E. Human influence on the dispersal and genetic structure of French Globodera tabacum populations. INFECTION GENETICS AND EVOLUTION 2014; 27:309-17. [DOI: 10.1016/j.meegid.2014.07.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 07/04/2014] [Accepted: 07/23/2014] [Indexed: 11/28/2022]
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18
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Besnard G, Jühling F, Chapuis É, Zedane L, Lhuillier É, Mateille T, Bellafiore S. Fast assembly of the mitochondrial genome of a plant parasitic nematode (Meloidogyne graminicola) using next generation sequencing. C R Biol 2014; 337:295-301. [PMID: 24841955 DOI: 10.1016/j.crvi.2014.03.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 10/25/2022]
Abstract
Little is known about the variations of nematode mitogenomes (mtDNA). Sequencing a complete mtDNA using a PCR approach remains a challenge due to frequent genome reorganizations and low sequence similarities between divergent nematode lineages. Here, a genome skimming approach based on HiSeq sequencing (shotgun) was used to assemble de novo the first complete mtDNA sequence of a root-knot nematode (Meloidogyne graminicola). An AT-rich genome (84.3%) of 20,030 bp was obtained with a mean sequencing depth superior to 300. Thirty-six genes were identified with a semi-automated approach. A comparison with a gene map of the M. javanica mitochondrial genome indicates that the gene order is conserved within this nematode lineage. However, deep genome rearrangements were observed when comparing with other species of the superfamily Hoplolaimoidea. Repeat elements of 111 bp and 94 bp were found in a long non-coding region of 7.5 kb, as similarly reported in M. javanica and M. hapla. This study points out the power of next generation sequencing to produce complete mitochondrial genomes, even without a reference sequence, and possibly opening new avenues for species/race identification, phylogenetics and population genetics of nematodes.
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Évolution & Diversité biologique), 118, route de Narbonne, 31062 Toulouse, France.
| | - Frank Jühling
- University of Leipzig, Interdisciplinary Center for Bioinformatics, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Élodie Chapuis
- IRD, UMR186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
| | - Loubab Zedane
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Évolution & Diversité biologique), 118, route de Narbonne, 31062 Toulouse, France
| | - Émeline Lhuillier
- INRA, GeT-PlaGe, UAR 1209 Département de génétique animale, INRA Auzeville, 31326 Castanet-Tolosan, France
| | - Thierry Mateille
- IRD, UMR 022 Centre de biologie pour la gestion des populations, campus de Baillarguet, CS30016, 34988 Montferrier-sur-Lez cedex, France
| | - Stéphane Bellafiore
- IRD, UMR186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
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19
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Stoeckel S, Masson JP. The exact distributions of F(IS) under partial asexuality in small finite populations with mutation. PLoS One 2014; 9:e85228. [PMID: 24465510 PMCID: PMC3897417 DOI: 10.1371/journal.pone.0085228] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/18/2013] [Indexed: 11/18/2022] Open
Abstract
Reproductive systems like partial asexuality participate to shape the evolution of genetic diversity within populations, which is often quantified by the inbreeding coefficient FIS. Understanding how those mating systems impact the possible distributions of FIS values in theoretical populations helps to unravel forces shaping the evolution of real populations. We proposed a population genetics model based on genotypic states in a finite population with mutation. For populations with less than 400 individuals, we assessed the impact of the rates of asexuality on the full exact distributions of FIS, the probabilities of positive and negative FIS, the probabilities of fixation and the probabilities to observe changes in the sign of FIS over one generation. After an infinite number of generations, we distinguished three main patterns of effects of the rates of asexuality on genetic diversity that also varied according to the interactions of mutation and genetic drift. Even rare asexual events in mainly sexual populations impacted the balance between negative and positive FIS and the occurrence of extreme values. It also drastically modified the probability to change the sign of FIS value at one locus over one generation. When mutation prevailed over genetic drift, increasing rates of asexuality continuously increased the variance of FIS that reached its highest value in fully asexual populations. In consequence, even ancient asexual populations showed the entire FIS spectrum, including strong positive FIS. The prevalence of heterozygous loci only occurred in full asexual populations when genetic drift dominated.
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Affiliation(s)
- Solenn Stoeckel
- INRA, UMR1349 Institute for Genetics, Environment and Plant Protection, Le Rheu, France
| | - Jean-Pierre Masson
- INRA, UMR1349 Institute for Genetics, Environment and Plant Protection, Le Rheu, France
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20
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Jones JT, Haegeman A, Danchin EGJ, Gaur HS, Helder J, Jones MGK, Kikuchi T, Manzanilla-López R, Palomares-Rius JE, Wesemael WML, Perry RN. Top 10 plant-parasitic nematodes in molecular plant pathology. MOLECULAR PLANT PATHOLOGY 2013; 14:946-61. [PMID: 23809086 PMCID: PMC6638764 DOI: 10.1111/mpp.12057] [Citation(s) in RCA: 805] [Impact Index Per Article: 73.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
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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Affiliation(s)
- John T Jones
- James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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21
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Gilabert A, Wasmuth JD. Unravelling parasitic nematode natural history using population genetics. Trends Parasitol 2013; 29:438-48. [PMID: 23948430 DOI: 10.1016/j.pt.2013.07.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/10/2013] [Accepted: 07/11/2013] [Indexed: 01/01/2023]
Abstract
The health and economic importance of parasitic nematodes cannot be overstated. Moreover, they offer a complex and diverse array of life strategies, raising a multitude of evolutionary questions. Researchers are applying population genetics to parasitic nematodes in order to disentangle some aspects of their life strategies, improve our knowledge about disease epidemiology, and design control strategies. However, population genetics studies of nematodes have been constrained due to the difficulty in sampling nematodes and developing molecular markers. In this context, new computational and sequencing technologies represent promising tools to investigate population genomics of parasitic, non-model, nematode species in an epidemiological context.
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Affiliation(s)
- Aude Gilabert
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, Alberta, T2N 4Z6, Canada
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22
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Derycke S, Backeljau T, Moens T. Dispersal and gene flow in free-living marine nematodes. Front Zool 2013; 10:1. [PMID: 23356547 PMCID: PMC3567977 DOI: 10.1186/1742-9994-10-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 01/21/2013] [Indexed: 11/10/2022] Open
Abstract
Dispersal and gene flow determine connectivity among populations, and can be studied through population genetics and phylogeography. We here review the results of such a framework for free-living marine nematodes. Although field experiments have illustrated substantial dispersal in nematodes at ecological time scales, analysis of the genetic diversity illustrated the importance of priority effects, founder effects and genetic bottlenecks for population structuring between patches <1 km apart. In contrast, only little genetic structuring was observed within an estuary (<50 km), indicating that these small scale fluctuations in genetic differentiation are stabilized over deeper time scales through extensive gene flow. Interestingly, nematode species with contrasting life histories (extreme colonizers vs persisters) or with different habitat preferences (algae vs sediment) show similar, low genetic structuring. Finally, historical events have shaped the genetic pattern of marine nematodes and show that gene flow is restricted at large geographical scales. We also discuss the presence of substantial cryptic diversity in marine nematodes, and end with highlighting future important steps to further unravel nematode evolution and diversity.
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Affiliation(s)
- Sofie Derycke
- Department of Biology, Marine Biology section, Ghent University, Krijgslaan 281, S8, 9000, Ghent, Belgium.
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23
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Gutiérrez-Gutiérrez C, Castillo P, Cantalapiedra-Navarrete C, Landa BB, Derycke S, Palomares-Rius JE. Genetic structure of Xiphinema pachtaicum and X. index populations based on mitochondrial DNA variation. PHYTOPATHOLOGY 2011; 101:1168-1175. [PMID: 21554182 DOI: 10.1094/phyto-07-10-0194] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The dagger nematodes Xiphinema pachtaicum and X. index are two of the most widespread and frequently occurring Xiphinema spp. co-infesting vineyards and other crops and natural habitats worldwide. Sexual reproduction is rare in these species. The primary objective of this study was to determine the genetic structure of X. pachtaicum and X. index populations using eight and seven populations, respectively, from different "wine of denomination of origin (D.O.) zones" in Spain and Sardinia (Italy), by studying mitochondrial (cytochrome oxidase c subunit 1 or COI) and nuclear (D2-D3 expansion segments of 28S rDNA) markers. Both Xiphinema spp. showed low intraspecific divergence among COI sequences, ranging from 0.2% (1 base substitution) to 2.3% (10 substitutions) in X. pachtaicum and from 0.2% (1 base substitution) to 0.4% (2 substitutions) in X. index. Population genetic structure was strong for both species. Nevertheless, molecular differences among grapevine-growing areas were not significant, and intrapopulation diversity was very low. It is hypothesized that this genetic homogeneity in the nematode populations reflects their predominant parthenogenetic reproduction mode and low dispersal abilities. Our results also show that X. pachtaicum populations in Spain have possibly been established from two different populations of origin. Results also demonstrated that the two DNA regions studied are suitable diagnostic markers for X. index and X. pachtaicum.
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Reproductive mode evolution in nematodes: insights from molecular phylogenies and recently discovered species. Mol Phylogenet Evol 2011; 61:584-92. [PMID: 21787872 DOI: 10.1016/j.ympev.2011.07.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 07/06/2011] [Accepted: 07/08/2011] [Indexed: 11/21/2022]
Abstract
The Phylum Nematoda has long been known to contain a great diversity of species that vary in reproductive mode, though our understanding of the evolutionary origins, causes and consequences of nematode reproductive mode change have only recently started to mature. Here we bring together and analyze recent progress on reproductive mode evolution throughout the phylum, resulting from the application of molecular phylogenetic approaches and newly discovered nematode species. Reproductive mode variation is reviewed in multiple free-living, animal-parasitic and plant-parasitic nematode groups. Discussion ranges from the model nematode Caenorhabditis elegans and its close relatives, to the plant-parasitic nematodes of the Meloidogyne genus where there is extreme variation in reproductive mode between and even within species, to the vertebrate-parasitic genus Strongyloides and related genera where reproductive mode varies across generations (heterogony). Multiple evolutionary transitions from dioecous (obligately outcrossing) to hermaphroditism and parthenogenesis in the phylum are discussed, along with one case of an evolutionary transition from hermaphroditism to doioecy in the Oscheius genus. We consider the roles of underlying genetic mechanisms in promoting reproductive plasticity in this phylum, as well as the potential evolutionary forces promoting transitions in reproductive mode.
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25
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XHAARD C, FABRE B, ANDRIEUX A, GLADIEUX P, BARRÈS B, FREY P, HALKETT F. The genetic structure of the plant pathogenic fungus Melampsora larici-populina on its wild host is extensively impacted by host domestication. Mol Ecol 2011; 20:2739-55. [DOI: 10.1111/j.1365-294x.2011.05138.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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26
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Castagnone-Sereno P, Danchin EGJ, Deleury E, Guillemaud T, Malausa T, Abad P. Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita. BMC Genomics 2010; 11:598. [PMID: 20973953 PMCID: PMC3091743 DOI: 10.1186/1471-2164-11-598] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 10/25/2010] [Indexed: 11/13/2022] Open
Abstract
Background Microsatellites are the most popular source of molecular markers for studying population genetic variation in eukaryotes. However, few data are currently available about their genomic distribution and abundance across the phylum Nematoda. The recent completion of the genomes of several nematode species, including Meloidogyne incognita, a major agricultural pest worldwide, now opens the way for a comparative survey and analysis of microsatellites in these organisms. Results Using MsatFinder, the total numbers of 1-6 bp perfect microsatellites detected in the complete genomes of five nematode species (Brugia malayi, Caenorhabditis elegans, M. hapla, M. incognita, Pristionchus pacificus) ranged from 2,842 to 61,547, and covered from 0.09 to 1.20% of the nematode genomes. Under our search criteria, the most common repeat motifs for each length class varied according to the different nematode species considered, with no obvious relation to the AT-richness of their genomes. Overall, (AT)n, (AG)n and (CT)n were the three most frequent dinucleotide microsatellite motifs found in the five genomes considered. Except for two motifs in P. pacificus, all the most frequent trinucleotide motifs were AT-rich, with (AAT)n and (ATT)n being the only common to the five nematode species. A particular attention was paid to the microsatellite content of the plant-parasitic species M. incognita. In this species, a repertoire of 4,880 microsatellite loci was identified, from which 2,183 appeared suitable to design markers for population genetic studies. Interestingly, 1,094 microsatellites were identified in 801 predicted protein-coding regions, 99% of them being trinucleotides. When compared against the InterPro domain database, 497 of these CDS were successfully annotated, and further assigned to Gene Ontology terms. Conclusions Contrasted patterns of microsatellite abundance and diversity were characterized in five nematode genomes, even in the case of two closely related Meloidogyne species. 2,245 di- to hexanucleotide loci were identified in the genome of M. incognita, providing adequate material for the future development of a wide range of microsatellite markers in this major plant parasite.
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