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Article

Comparative Genomics Reveals Novel Target Genes towards Specific Control of Plant-Parasitic Nematodes

1
Embrapa Genetic Resources and Biotechnology, Brasília DF 70770-917, Brazil
2
National Institute of Science and Technology—INCT PlantStress Biotech—EMBRAPA, Brasília DF 70770-917, Brazil
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Institute of Biological Sciences, Campus Universitário Darcy Ribeiro, University of Brasília, Brasília DF 70910-900, Brazil
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Department of Agronomy-Entomology, Rural Federal University of Pernambuco, Recife PE 52171-900, Brazil
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INRAE, Plant Health and Environment, University Côte d’Azur, CNRS, ISA, F-06903 Sophia-Antipolis CEDEX, France
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Genomic Sciences and Biotechnology PPG, Catholic University of Brasília, Brasilia DF 71966-700, Brazil
*
Author to whom correspondence should be addressed.
Genes 2020, 11(11), 1347; https://doi.org/10.3390/genes11111347
Received: 20 October 2020 / Revised: 6 November 2020 / Accepted: 10 November 2020 / Published: 13 November 2020
(This article belongs to the Special Issue Genomics of Plant-Nematode Interactions)
Plant-parasitic nematodes cause extensive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. Chemical methods that have been deployed to control nematodes have largely been banned from use due to their poor specificity and high toxicity. Hence, there is an urgent need for the development of cleaner and more specific control methods. Recent advances in nematode genomics, including in phytoparasitic species, provide an unprecedented opportunity to identify genes and functions specific to these pests. Using phylogenomics, we compared 61 nematode genomes, including 16 for plant-parasitic species and identified more than 24,000 protein families specific to these parasites. In the genome of Meloidogyne incognita, one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein databases. Among these phytoparasite-specific proteins, ca. 1000 shared the same properties as known secreted effectors involved in essential parasitic functions. Of these, 68 were novel and showed strong expression during the endophytic phase of the nematode life cycle, based on both RNA-seq and RT-qPCR analyses. Besides effector candidates, transcription-related and neuro-perception functions were enriched in phytoparasite-specific proteins, revealing interesting targets for nematode control methods. This phylogenomics analysis constitutes a unique resource for the further understanding of the genetic basis of nematode adaptation to phytoparasitism and for the development of more efficient control methods. View Full-Text
Keywords: comparative genomics; plant-parasitic nematodes; phylogenomics; parasite-specific genes; pest control; de novo gene birth; horizontal gene transfers comparative genomics; plant-parasitic nematodes; phylogenomics; parasite-specific genes; pest control; de novo gene birth; horizontal gene transfers
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MDPI and ACS Style

Grynberg, P.; Coiti Togawa, R.; Dias de Freitas, L.; Antonino, J.D.; Rancurel, C.; Mota do Carmo Costa, M.; Grossi-de-Sa, M.F.; Miller, R.N.G.; Brasileiro, A.C.M.; Messenberg Guimaraes, P.; Danchin, E.G.J. Comparative Genomics Reveals Novel Target Genes towards Specific Control of Plant-Parasitic Nematodes. Genes 2020, 11, 1347. https://doi.org/10.3390/genes11111347

AMA Style

Grynberg P, Coiti Togawa R, Dias de Freitas L, Antonino JD, Rancurel C, Mota do Carmo Costa M, Grossi-de-Sa MF, Miller RNG, Brasileiro ACM, Messenberg Guimaraes P, Danchin EGJ. Comparative Genomics Reveals Novel Target Genes towards Specific Control of Plant-Parasitic Nematodes. Genes. 2020; 11(11):1347. https://doi.org/10.3390/genes11111347

Chicago/Turabian Style

Grynberg, Priscila, Roberto Coiti Togawa, Leticia Dias de Freitas, Jose D. Antonino, Corinne Rancurel, Marcos Mota do Carmo Costa, Maria F. Grossi-de-Sa, Robert N.G. Miller, Ana C.M. Brasileiro, Patricia Messenberg Guimaraes, and Etienne G.J. Danchin 2020. "Comparative Genomics Reveals Novel Target Genes towards Specific Control of Plant-Parasitic Nematodes" Genes 11, no. 11: 1347. https://doi.org/10.3390/genes11111347

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