Multiple independent adaptations to different ranges of host plants indicate high adaptability despite clonal reproduction in the nematode pest Meloidogyne incognita

The most devastating nematodes to worldwide agriculture are the root-knot nematodes with Meloidogyne incognita being considered as the most ubiquitous. At the species level, M. incognita is polyphagous with thousands of host plants. However, this wide host range seems to be due to an assemblage of different isolates that each have distinct and more restricted host compatibilities. In this species, four host races have been defined as a function of distinct ranges of compatible and incompatible plants. To assess whether there is an evolutionary signal underlying these host races, we sequenced the genomes of 11 isolates across these four different races. By aligning the genomes of the isolates to the M. incognita reference genome, we identified SNPs and small-scale insertions/deletions. We showed that there are relatively low point variations between the different isolates, despite their various different ecological characteristics. Furthermore, these variations neither correlate with the four host races, the geographical origin of the samples nor the host plant on which they have been collected. These results suggest that multiple independent adaptations to different hosts and environmental conditions have occurred and illustrate the high adaptive potential of this agricultural pest despite its clonal mode of reproduction. Although the recognition of variation in M. incognita host range exists, we recommend the discontinuation of the terminology 9race9 considering there is no genetic signal underlying and supporting the concept of races in M. incognita.