Identification of Novel Target Genes for Safer and More Specific Control of Root-Knot Nematodes from a Pan-Genome Mining

Abstract

Root-knot nematodes are globally the most aggressive and damaging plant-parasitic nematodes. Chemical nematicides have so far constituted the most efficient control measures against these agricultural pests. Because of their toxicity for the environment and danger for human health, these nematicides have now been banned from use. Consequently, new and more specific control means, safe for the environment and human health, are urgently needed to avoid worldwide proliferation of these devastating plant-parasites. Mining the genomes of root-knot nematodes through an evolutionary and comparative genomics approach, we identified and analyzed 15,952 nematode genes conserved in genomes of plant-damaging species but absent from non target genomes of chordates, plants, annelids, insect pollinators and mollusks. Functional annotation of the corresponding proteins revealed a relative abundance of putative transcription factors in this parasite-specific set compared to whole proteomes of root-knot nematodes. This may point to important and specific regulators of genes involved in parasitism. Because these nematodes are known to secrete effector proteins in planta, essential for parasitism, we searched and identified 993 such effector-like proteins absent from non-target species. Aiming at identifying novel targets for the development of future control methods, we biologically tested the effect of inactivation of the corresponding genes through RNA interference. A total of 15 novel effector-like proteins and one putative transcription factor compatible with the design of siRNAs were present as non-redundant genes and had transcriptional support in the model root-knot nematode Meloidogyne incognita. Infestation assays with siRNA-treated M. incognita on tomato plants showed significant and reproducible reduction of the infestation for 12 of the 16 tested genes compared to control nematodes. These 12 novel genes, showing efficient reduction of parasitism when silenced, constitute promising targets for the development of more specific and safer control means.

Mining Novel Effector Proteins from the Esophageal Gland Cells ofMeloidogyne incognita

“…As in previous studies (Danchin et al, 2013; Huang et al, 2003), the majority of these proteins are unique to M. incognita , showing no homology to proteins in the non-redundant database and containing no detectable functional domains. Only a few of the effector proteins secreted from any parasite are widely conserved, and more often than not, they are exclusively produced by one pathogen or a group of closely related pathogens.…”

“…These observations indicate that proteins secreted in the gelatinous matrix could be involved in egg laying and perhaps the reproductive success of the parasite. Interestingly, another very recent study by Danchin et al (2013) also identified Minc00801 as an ‘effector-like’ candidate. These authors showed that silencing of its transcript using siRNA resulted in a significant reduction in the number of M. incognita induced galls.…”

“…An impressive number of M. incognita effectors have been identified (Bellafiore et al, 2008; Danchin et al, 2013; Huang et al, 2003) but a complete panel of effectors remains elusive even with the availability of the M. incognita genome (Abad et al, 2008). Identification of effectors frequently relies on the ascertainment of gland cell–specific expression of effector genes as well as the documentation of an N-terminal signal peptide for protein secretion and the absence of transmembrane domains, which otherwise would suggest a retention inside the nematode gland cells.…”

Cellular Signaling Pathways and Posttranslational Modifications Mediated by Nematode Effector Proteins

“…Consistent with this idea, protease-like effectors have been identified in M. incognita (Neveu et al, 2003;Danchin et al, 2013), G. pallida (Jones et al, 2009), H. glycines (Noon et al, 2015), and Meloidogyne chitwoodi (Roze et al, 2008). Phytonematodes not only secrete protease-like effectors but also target host proteases.…”

Advances in Understanding the Molecular Mechanisms of Root Lesion Nematode Host Interactions

“…Issues such as acceptance of genetically modified plants and the cost of their implementation are likely to delay commercial application of genetic engineering to deliver commercial crops with resistance to PPNs. Nevertheless, information on genes whose products are vital for any process of nematode parasitism can be used to inform the development of new nematicides (17). This approach is being applied to develop more environmentally friendly nematicides via a set of bioinformatic and proteomic filters that ensure selection of molecules specific enough to target and control PPNs, whilst avoiding potential effects on beneficial soil organisms (e.g., 17).…”