Daniel Esmenjaud

Background: Nematodes constitute a particularly speciose animal phylum, occupying an exceptionally broad range of biomes and encompassing free-living microbe-feeders, predators, and notorious plant or animal parasites. However, the limited availability of genome resources for early-branching nematode clades has constrained our understanding of the molecular determinants underlying these multiple evolutionary adaptations. Results: We present the genome of the plant-parasitic nematode Xiphinema index , constituting the first telomere-to-telomere assembly for the Dorylaimida, an early-branching nematode order. Phylogenetic analyses suggest that horizontal gene transfers (HGTs) have played a pivotal role in the emergence of plant parasitism in this phylum. Remarkably, we identify the first documented case of a plant-derived HGT in a nematode genome. This gene encodes a predicted secreted effector of parasitism, underscoring the diversity of evolutionary events that contributed to the parasitic arsenal. Indeed, beyond bacteria and fungi, plants seem to have themselves provided crucial genes for parasitism that may now be used by the nematodes to manipulate them. Our comparative genomic analyses across more than 70 nematode species uncovered an epigenetic toolkit unprecedented in any other invertebrate genome. Indeed, X. index harbors a complete set of canonical DNA methyltransferases, a full-length ATRX chromatin remodeler, and a homolog of the 3D-chromatin architectural CTCF protein. Consistent with this repertoire, we detected genome-wide CpG methylation, which inversely correlates with gene expression and chromatin accessibility. Conclusions: Overall, these findings reveal a vertebrate-like epigenetic machinery in an early-branching nematode and call for a fundamental reassessment of the prevailing epigenetic paradigm in nematodes and, more broadly, in animals.

Grapevine is severely affected by two major nepoviruses that cause grapevine degeneration: the grapevine fanleaf virus (GFLV) and the arabis mosaic virus (ArMV), specifically transmitted by the dagger nematodes Xiphinema index and X. diversicaudatum, respectively. While natural resistance to X. index has been shown to be a promising alternative for controlling X. index and GFLV transmission, the resistance interaction between X. diversicaudatum and grapevine has not yet been documented. In the present study, we evaluated the host suitability to X. diversicaudatum in materials previously characterised for their resistance to X. index. Two X. index-resistant accessions VRH8771 (F1 hybrid) and Nemadex Alain Bouquet (BC1 hybrid) derived from muscadine, together with the X. index-susceptible reference accession V. vinifera cv. Cabernet-Sauvignon and the X. index-resistant reference accession V. riparia ‘10128’, were challenged with a X. diversicaudatum population obtained from woody host plants and a reference isolate of X. index. The reproduction factors of X. diversicaudatum and its numbers per gram of roots paralleled those of X. index, showing a resistance interaction to the population of the former species and suggesting that resistance determinants to both nematode vectors might be the same or linked. Nevertheless, these two criteria illustrated a poorer host suitability of grapevine materials to this X. diversicaudatum population than to X. index.

Root-knot nematode (RKN) species are predominant pests of crops, attacking stone fruit crops Prunus spp. under Mediterranean climate conditions worldwide. Natural resistance for rootstock breeding is a control method that is gaining interest as an alternative to the highly toxic nematicides. This review first reports an outline of the root-knot nematodes parasitizing stone fruit crops and the Prunus species and rootstocks. It then describes the main sources of resistance detected among the Prunus germplasm and focuses on the major resistance genes identified and their characteristics (spectrum, durability, histological mechanism, effect of temperature, interaction with other pests and diseases, etc.). In peach, besides the RMia reference gene, the new genes PkMi and Mf, also located on chromosome 2, need to be characterized regarding their spectrum and relationship. The two other Prunus reference genes, Ma from plum (complete spectrum) and RMja from almond (more restricted spectrum), are orthologs that belong to a TIR-NB-LRR (TNL) cluster on chromosome 7. The review finally summarizes the positional cloning of the Ma gene and the characterization of its unique TNL structure, encompassing a five-times repeated post-LRR domain. Deciphering how this structure is functionally involved in Ma’s remarkable biological properties is a real challenge for the future.

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.

Plants trigger appropriate defense responses, notably, through intracellular nucleotide-binding (NB) and leucine-rich repeat (LRR)-containing receptors (NLRs) that detect secreted pathogen effector proteins. In NLR resistance genes, the toll/interleukin-1 receptor (TIR)-NB-LRR proteins (TNLs) are an important subfamily, out of which approximately half the members carry a post-LRR (PL) domain of unknown role. We first investigated the requirement of the PL domain for TNL-mediated immune response by mutating the most conserved amino acids across PL domains of Arabidopsis thaliana TNLs. We identified several amino acids in the PL domain of RPS4, required for its ability to trigger a hypersensitive response to AvrRps4 in a Nicotiana tabacum transient assay. Mutating the corresponding amino acids within the PL domain of the tobacco TNL gene N also affected its function. Consequently, our results indicate that the integrity of the PL domain at conserved positions is crucial for at least two unrelated TNLs. We then tested the PL domain specificity for function by swapping PL domains between the paralogs RPS4 and RPS4B. Our results suggest that the PL domain is involved in their TNL pair specificity, ‘off state’ stability, and NLR complex activation. Considering genetically paired Arabidopsis TNLs, we finally compared the PL and TIR domains of their sensor and executor sequences, respectively. While TIR and PL domains from executors present complete motifs, sensors showed a lack of conservation with degenerated motifs. We here provide a contribution to the functional analysis of the PL domain in order to decipher its role for TNL function. [ ] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

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.

The soil-borne nematodeXiphinema indexis closely linked to its main host, the grapevine, and presents a major threat to vineyards worldwide due to its ability to transmitGrapevine fanleaf virus(GFLV). The phylogeography ofX. indexhas 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 markerCytBand illustrated the low intraspecific divergence of this mainly meiotic parthenogenetic species. To generate a higher polymorphism level, we then concatenated the sequences ofCytBand three mitochondrial markers,ATP6,CO1andND4, 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 19^th-century phylloxera crisis. Finally, our study enabled us to draw a first scaffold ofX. indexdiversity at the global scale.

Root-knot nematodes (RKN) (Meloidogyne spp.) are worldwide pests that affect a considerable number of plants, among which stone fruit (Prunus spp.) are severely attacked. Prevalent RKN species are Meloidogyne arenaria, M. incognita, and M. javanica in stone fruit but the emergent M. ethiopica and M. enterolobii are also reported to challenge perennial crops. In Prunus spp., the complete-spectrum resistance (R) gene Ma from plum and the more restricted-spectrum R genes RMia from peach and RMja from almond completely inhibit nematode multiplication and gall formation of the RKN species that they control. This study aimed to update the resistance spectra of these three major genes by evaluating their activity toward one isolate of the yet-untested RKN species mentioned above. To state whether a given gene controls a particular species, the principle of our experiment was to genotype with appropriate markers a number of individuals segregating for this gene and then to phenotype these individuals. A perfect matching of the genotype and the phenotype of individuals indicates that the gene of interest is active against and, thus, controls the corresponding isolate of this RKN species. Segregating materials used were an Ma F1 plum progeny, an RMia F2 peach progeny, and an RMja F2 almond progeny. In addition to previous data, our results establish a clear spectrum for each of the three genes toward isolates from both the three prevalent species and the two emerging species. Ultimately, our results reveal that (i) Ma controls all of them, (ii) RMja controls all species except M. incognita and M. floridensis, and (iii) RMia controls M. arenaria, M. incognita, and M. ethiopica but not M. javanica or M. enterolobii. Our data should have wide implications for RKN resistance management and breeding and for deciphering the molecular mechanisms of the spectrum of RKN R genes.