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

Abstract

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.

Nematicidal Evaluation and Active Compounds Isolation of Aspergillus japonicus ZW1 against Root-Knot Nematodes Meloidogyne incognita

“…Root-knot nematodes (Meloidogyne spp.) are economically important worldwide pathogens causing considerable damage to many crops, including cucumbers, tomatoes, rice [1][2][3][4], and even cotton [5,6]. Meloidogyne incognita is an important species of root-knot nematodes worldwide due to its direct impact on crop yields [7][8][9].…”

Adaptive response to olive cultivation in a generalist parasitic nematode (Meloidogyne javanica)

“…A non-coding region containing 63-bp tandem repeats, named 63R in M. javanica (Okimoto et al, 1991;Besnard et al, 2014), was thus sequenced. The use of an mtDNA locus also had the Okimoto et al, 1991;Besnard et al, 2019). Beforehand, such intra-individual variation needs to be carefully considered because it may limit the usefulness of mtDNA polymorphisms for population genetics (Lunt et al, 1998).…”

“…Our results sustain suggest an adaptive response of this the root parasite for dealing with environmental changes between natural olive stands and orchards.ON THE M. JAVANICA ASEXUAL EVOLUTION AND POPULATION DIFFERENTIATIONWhile low intraspecific genetic variation has been previously reported in Meloidogyne species(Castagnone-Sereno, 2002; Castagone-Sereno et al, 2019;Besnard et al, 2019), a full nuclear genome analysis recently brought strong insights for clonal evolution in the parthenogenetic…”

Genome structure and content of the rice root‐knot nematode (Meloidogyne graminicola)

“…graminicola , most of the genetic studies were based on mitochondrial DNA and nrDNA. These sequences revealed very low polymorphism and lack of phylogeographic signal among the isolates sampled at a global scale, suggesting a recent spread of this pathogen (Besnard et al., 2019). Divergent low‐copy nuclear homologous sequences were also found indicating either a potential hybrid origin or high heterozygosity in this species.…”

“…Secondly, the genome is heterozygous (heterozygosity = ca. 2%), and its assembly is made difficult by the presence of divergent haplotypes, especially when using short reads (Besnard et al., 2019). For instance, some divergent homologous regions may be separately assembled, while others could be merged in a unique consensus sequence (Besnard et al., 2019).…”