Comparative genomics of apomictic root-knot nematodes: Hybridization, ploidy, and dynamic genome change

The root-knot nematodes (genus Meloidogyne) are important plant parasites causing substantial agricultural losses. The Meloidogyne incognita group (MIG) of species,most ofwhich are obligatory apomicts (mitotic parthenogens), are extremely polyphagous and important problems for global agriculture.While understanding the genomic basis for their variable success on different crops could benefit future agriculture, analyses of their genomes are challenging due to complex evolutionary histories that may incorporate hybridization, ploidy changes, and chromosomal fragmentation. Here, we sequence 19 genomes, representing five speciesof key root-knotnematodes collectedfromdifferentgeographicorigins.We showthat ahybridoriginthat predatedspeciation within the MIG has resulted in each species possessing two divergent genomic copies. Additionally, the apomictic MIG species are hypotriploids, with a proportion of one genome present in a second copy. The hypotriploid proportion varies among species. The evolutionary history of theMIG genomes is revealed to be very dynamic, with noncrossover recombination both homogenizing the genomic copies, and acting as amechanismfor generating divergence between species. Interestingly, the automicticMIGspecies M. floridensis differs from the apomict species in that it has become homozygous throughout much of its genome.