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Open AccessArticle

On the Close Relatedness of Two Rice-Parasitic Root-Knot Nematode Species and the Recent Expansion of Meloidogyne graminicola in Southeast Asia

1
CNRS-UPS-IRD, UMR5174, EDB, 118 route de Narbonne, Université Paul Sabatier, 31062 Toulouse, France
2
IRD, Cirad, University of Montpellier II, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
3
IRD, LMI RICE, University of Science and Technology of Hanoi, Agricultural Genetics Institute, Hanoi, Vietnam
4
IOIT/USTH, VAST and UMMISCO, IRD, 18 Hoang Quoc Viet, Hanoi, Vietnam
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2019, 10(2), 175; https://doi.org/10.3390/genes10020175
Received: 26 December 2018 / Revised: 13 February 2019 / Accepted: 20 February 2019 / Published: 25 February 2019
(This article belongs to the Special Issue Mitochondrial Genomes: Genetic and Transcriptomic Studies)
Meloidogyne graminicola is a facultative meiotic parthenogenetic root-knot nematode (RKN) that seriously threatens agriculture worldwide. We have little understanding of its origin, genomic structure, and intraspecific diversity. Such information would offer better knowledge of how this nematode successfully damages rice in many different environments. Previous studies on nuclear ribosomal DNA (nrDNA) suggested a close phylogenetic relationship between M. graminicola and Meloidogyne oryzae, despite their different modes of reproduction and geographical distribution. In order to clarify the evolutionary history of these two species and explore their molecular intraspecific diversity, we sequenced the genome of 12 M. graminicola isolates, representing populations of worldwide origins, and two South American isolates of M. oryzae. k-mer analysis of their nuclear genome and the detection of divergent homologous genomic sequences indicate that both species show a high proportion of heterozygous sites (ca. 1–2%), which had never been previously reported in facultative meiotic parthenogenetic RKNs. These analyses also point to a distinct ploidy level in each species, compatible with a diploid M. graminicola and a triploid M. oryzae. Phylogenetic analyses of mitochondrial genomes and three nuclear genomic sequences confirm close relationships between these two species, with M. graminicola being a putative parent of M. oryzae. In addition, comparative mitogenomics of those 12 M. graminicola isolates with a Chinese published isolate reveal only 15 polymorphisms that are phylogenetically non-informative. Eight mitotypes are distinguished, the most common one being shared by distant populations from Asia and America. This low intraspecific diversity, coupled with a lack of phylogeographic signal, suggests a recent worldwide expansion of M. graminicola. View Full-Text
Keywords: biological invasion; heterozygous genome; Meloidogyne; mitogenome; ribosomal DNA; root-knot nematode biological invasion; heterozygous genome; Meloidogyne; mitogenome; ribosomal DNA; root-knot nematode
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MDPI and ACS Style

Besnard, G.; Thi-Phan, N.; Ho-Bich, H.; Dereeper, A.; Trang Nguyen, H.; Quénéhervé, P.; Aribi, J.; Bellafiore, S. On the Close Relatedness of Two Rice-Parasitic Root-Knot Nematode Species and the Recent Expansion of Meloidogyne graminicola in Southeast Asia. Genes 2019, 10, 175. https://doi.org/10.3390/genes10020175

AMA Style

Besnard G, Thi-Phan N, Ho-Bich H, Dereeper A, Trang Nguyen H, Quénéhervé P, Aribi J, Bellafiore S. On the Close Relatedness of Two Rice-Parasitic Root-Knot Nematode Species and the Recent Expansion of Meloidogyne graminicola in Southeast Asia. Genes. 2019; 10(2):175. https://doi.org/10.3390/genes10020175

Chicago/Turabian Style

Besnard, Guillaume; Thi-Phan, Ngan; Ho-Bich, Hai; Dereeper, Alexis; Trang Nguyen, Hieu; Quénéhervé, Patrick; Aribi, Jamel; Bellafiore, Stéphane. 2019. "On the Close Relatedness of Two Rice-Parasitic Root-Knot Nematode Species and the Recent Expansion of Meloidogyne graminicola in Southeast Asia" Genes 10, no. 2: 175. https://doi.org/10.3390/genes10020175

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