Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies.Plant-parasitic nematodes are responsible for global agricultural losses amounting to an estimated $157 billion annually. Although chemical nematicides are the most reliable means of controlling root-knot nematodes, they are increasingly being withdrawn owing to their toxicity to humans and the environment. Novel and specific targets are thus needed to develop new strategies against these pests.The Southern root-knot nematode Meloidogyne incognita is able to infect the roots of almost all cultivated plants, making it perhaps the

SummaryBecause plant wilting has been described as a consequence of cadmium (Cd 2þ ) toxicity, we investigate Cd 2þ effects on plant water losses, gas exchanges and stomatal behaviour in Arabidopsis thaliana L. Effects of 1-week Cd 2þ application in hydroponic condition (CdCl 2 10-100 mM) were analyzed. A 10-lM Cd 2þ concentration had no significant effect on the plant-water relationship and carbon assimilation. At higher Cd 2þ concentrations, a Cd 2þ -dependent decrease in leaf conductance and CO 2 uptake was observed despite the photosynthetic apparatus appeared not to be affected as probed by fluorescence measurements. In epidermal strip bioassays, nanomolar Cd 2þ concentrations reduced stomatal opening under light in A. thaliana, Vicia faba and Commelina communis. Application of 5 mM ABA limited the root-to-shoot translocation of cadmium. However, the Cd 2þ -induced stomatal closure was likely ABA-independent, since a 5-day treatment with 50 lM Cd 2þ did not affect the plant relative water content. Additionally, a similar Cd 2þ -induced stomatal closure was observed in the ABA insensitive mutant abi1-1. Interestingly, this mutant displayed a higher transpiration rate than the wild type but did not accumulate more Cd 2þ , arguing that Cd 2þ uptake is not dependent only on the transpiration flow. Application of putative calcium channels inhibitors suppressed the inhibitory effect of Cd 2þ in epidermal strip experiments, suggesting that Cd 2þ could enter the guard cell through calcium channels. Patch-clamp studies with V. faba guard cell protoplasts showed that plasma membrane K þ channels were insensitive to external Cd 2þ application whereas Ca 2þ channels were found permeable to Cd 2þ . In conclusion, we propose that Cd 2þ affects guard cell regulation in an ABA-independent manner by entering the cytosol via Ca 2þ channels.Abbreviations: ABA, Abscissic acid; DMSO, dimethyl sulfoxide; DW, dry weight; FW, fresh weight; NPPB, 5-nitro-2,3-phenylpropylaminobenzoic acid; RWC, relative water content.

Root-knot nematodes (genus Meloidogyne) exhibit a diversity of reproductive modes ranging from obligatory sexual to fully asexual reproduction. Intriguingly, the most widespread and devastating species to global agriculture are those that reproduce asexually, without meiosis. To disentangle this surprising parasitic success despite the absence of sex and genetic exchanges, we have sequenced and assembled the genomes of three obligatory ameiotic and asexual Meloidogyne. We have compared them to those of relatives able to perform meiosis and sexual reproduction. We show that the genomes of ameiotic asexual Meloidogyne are large, polyploid and made of duplicated regions with a high within-species average nucleotide divergence of ~8%. Phylogenomic analysis of the genes present in these duplicated regions suggests that they originated from multiple hybridization events and are thus homoeologs. We found that up to 22% of homoeologous gene pairs were under positive selection and these genes covered a wide spectrum of predicted functional categories. To biologically assess functional divergence, we compared expression patterns of homoeologous gene pairs across developmental life stages using an RNAseq approach in the most economically important asexually-reproducing nematode. We showed that >60% of homoeologous gene pairs display diverged expression patterns. These results suggest a substantial functional impact of the genome structure. Contrasting with high within-species nuclear genome divergence, mitochondrial genome divergence between the three ameiotic asexuals was very low, signifying that these putative hybrids share a recent common maternal ancestor. Transposable elements (TE) cover a ~1.7 times higher proportion of the genomes of the ameiotic asexual Meloidogyne compared to the sexual relative and might also participate in their plasticity. The intriguing parasitic success of asexually-reproducing Meloidogyne species could be partly explained by their TE-rich composite genomes, resulting from allopolyploidization events, and promoting plasticity and functional divergence between gene copies in the absence of sex and meiosis.