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Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining.

Danchin EG, Arguel MJ, Campan-Fournier A, Perfus-Barbeoch L, Magliano M, Rosso MN, Da Rocha M, Da Silva C, Nottet N, Labadie K, Guy J, Artiguenave F, Abad P - PLoS Pathog. (2013)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR 1355 ISA, Institut Sophia Agrobiotech, Sophia-Antipolis, France ; CNRS, UMR 7254 ISA, Institut Sophia Agrobiotech, Sophia-Antipolis, France ; Université de Nice Sophia-Antipolis, UMR ISA, Institut Sophia Agrobiotech, Sophia-Antipolis, France.

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.

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Gene Ontology terms relative abundance in candidate targets compared to whole proteomes.Kiviat diagram representing, the relative abundance of Gene Ontology (GO) terms, in percent for the whole M. incognita and M. hapla proteomes (in blue and red, respectively) as well as for the proteins that passed the OrthoMCL and BLAST filters (protein set 1 in green). (A) Relative abundance of GO terms assigned to whole RKN proteomes and protein set 1in the Biological Process category. (B) Relative abundance of GO terms assigned to whole RKN proteomes and protein set 1 in the Molecular Function category. (C) Relative abundance of GO terms assigned to whole RKN proteomes and protein set 1 in the Cellular Component category. In the three categories, the ten GO terms that presented the most different relative abundance (in percent) in protein set 1 compared to the whole RKN proteomes are presented.
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ppat-1003745-g003: Gene Ontology terms relative abundance in candidate targets compared to whole proteomes.Kiviat diagram representing, the relative abundance of Gene Ontology (GO) terms, in percent for the whole M. incognita and M. hapla proteomes (in blue and red, respectively) as well as for the proteins that passed the OrthoMCL and BLAST filters (protein set 1 in green). (A) Relative abundance of GO terms assigned to whole RKN proteomes and protein set 1in the Biological Process category. (B) Relative abundance of GO terms assigned to whole RKN proteomes and protein set 1 in the Molecular Function category. (C) Relative abundance of GO terms assigned to whole RKN proteomes and protein set 1 in the Cellular Component category. In the three categories, the ten GO terms that presented the most different relative abundance (in percent) in protein set 1 compared to the whole RKN proteomes are presented.

Mentions: Using a without a priori approach, we searched functional categories present in protein set 1. We compared the relative abundance of the different GO terms between protein set 1 and the two RKN whole proteomes. We remarked that despite substantially different numbers of predicted proteins in M. incognita and M. hapla, the relative abundance of GO terms was very similar in the two whole proteomes (Table S1, Figure 3). The higher number of protein models in M. incognita is due to its bigger genome with a peculiar structure, mainly constituted of regions in two copies with substantial divergence [7].


Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining.

Danchin EG, Arguel MJ, Campan-Fournier A, Perfus-Barbeoch L, Magliano M, Rosso MN, Da Rocha M, Da Silva C, Nottet N, Labadie K, Guy J, Artiguenave F, Abad P - PLoS Pathog. (2013)

Gene Ontology terms relative abundance in candidate targets compared to whole proteomes.Kiviat diagram representing, the relative abundance of Gene Ontology (GO) terms, in percent for the whole M. incognita and M. hapla proteomes (in blue and red, respectively) as well as for the proteins that passed the OrthoMCL and BLAST filters (protein set 1 in green). (A) Relative abundance of GO terms assigned to whole RKN proteomes and protein set 1in the Biological Process category. (B) Relative abundance of GO terms assigned to whole RKN proteomes and protein set 1 in the Molecular Function category. (C) Relative abundance of GO terms assigned to whole RKN proteomes and protein set 1 in the Cellular Component category. In the three categories, the ten GO terms that presented the most different relative abundance (in percent) in protein set 1 compared to the whole RKN proteomes are presented.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3814813&req=5

ppat-1003745-g003: Gene Ontology terms relative abundance in candidate targets compared to whole proteomes.Kiviat diagram representing, the relative abundance of Gene Ontology (GO) terms, in percent for the whole M. incognita and M. hapla proteomes (in blue and red, respectively) as well as for the proteins that passed the OrthoMCL and BLAST filters (protein set 1 in green). (A) Relative abundance of GO terms assigned to whole RKN proteomes and protein set 1in the Biological Process category. (B) Relative abundance of GO terms assigned to whole RKN proteomes and protein set 1 in the Molecular Function category. (C) Relative abundance of GO terms assigned to whole RKN proteomes and protein set 1 in the Cellular Component category. In the three categories, the ten GO terms that presented the most different relative abundance (in percent) in protein set 1 compared to the whole RKN proteomes are presented.
Mentions: Using a without a priori approach, we searched functional categories present in protein set 1. We compared the relative abundance of the different GO terms between protein set 1 and the two RKN whole proteomes. We remarked that despite substantially different numbers of predicted proteins in M. incognita and M. hapla, the relative abundance of GO terms was very similar in the two whole proteomes (Table S1, Figure 3). The higher number of protein models in M. incognita is due to its bigger genome with a peculiar structure, mainly constituted of regions in two copies with substantial divergence [7].

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR 1355 ISA, Institut Sophia Agrobiotech, Sophia-Antipolis, France ; CNRS, UMR 7254 ISA, Institut Sophia Agrobiotech, Sophia-Antipolis, France ; Université de Nice Sophia-Antipolis, UMR ISA, Institut Sophia Agrobiotech, Sophia-Antipolis, France.

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.

Show MeSH
Related in: MedlinePlus