Raw sequence reads of Incognita-group Meloidogyne nematodes and close Meloidogyne outgroup species

The Root Knot Nematodes (RKN) are amongst the world’s most important crop pests, infecting all the major agricultural crops, and causing very significant reduction in yields . The tropical RKN of the Meloidogyne incognita group (MIG) are particularly serious pests, with global distributions covering areas on all continents with mild winter temperatures. The MIG have been highlighted as one of the most serious threats to temperate agricultural regions as climate change progresses. Here we have sequenced 19 new Meloidogyne genomes giving us a comparative genomics dataset of 21 genomes, representing 6 species, with from 1-9 unique intraspecific isolates of each. We use it to examine the phylogenomic relationships between all the species, the origins of the apomictic species, test hypotheses of hybridisation, examine ploidy, and describe levels of intra and interspecific variation. Together these comparative genomic approaches give a detailed view of these crop pests’ history, and provide an important platform for agricultural genomics in the future.