Genomic characteristics of root-knot nematodes: a major group of crop pests

Nematodes constitute one of the most species-rich groups of animals, only paralleled by arthropods. They have a worldwide distribution being present in many biomes from deep sea sediments to deserts. Around 15% of them parasitize plants and they cause enormous damage to the global agricultural production despite the control methods deployed. Among those, the root-knot nematodes (genus Meloidogyne) are the most problematic. These species parasitize and stunt the roots and have a wide range of host plants. Root-knot nematodes display a variety of reproductive modes comprising obligatory and facultative sexual reproduction as well as full asexual reproduction with no functional meiosis. The most widespread and damaging species have this asexual mode of reproduction and are polyploid. Since 2008 we have been studying the genomes of these parasites with each generation of sequencing technology allowing improvement of the genome assemblies and new discoveries. The Meloidogyne incognita genome was the first to be sequenced and revealed a duplicated structure with high average nucleotide divergence between genome copies. This also allowed discovering Meloidogyne-specific genes and a whole repertoire of plant-cell wall degrading enzymes acquired by horizontal gene transfers. Second generation sequencing allowed producing more complete genomes but also suggesting that the polyploid species underwent recent hybridization events resulting in highly diverged subgenomes. Sequencing multiple populations confirmed the absence of meiotic recombination in M. incognita and recent activity of transposable elements. More recently, third-generation long-read sequencing technology allowed spectacular improvement in the contiguity of the assemblies and the identification of the A and B subgenomes as well as their evolutionary relations in the polyploid species. Helped by assemblies approaching chromosome-scale resolution, new discoveries were made on the intrinsic composition of the genome itself like unusual centromeres and telomeres, opening new perspectives in understanding the genome biology of these species.