Global Comparative Genomics of the Burrowing Nematode, <i>Radopholus similis</i>

Radopholus similis is a devastating pest to tropical agriculture, including economically important crops such as banana and citrus. To better understand the diverse biology of R. similis, the genomes of 18 populations from five continents were sequenced and compared to (i) provide a snapshot of the global genetic diversity of R. similis and identify influencers of genetic diversity; (ii) determine whether R. similis populations show evidence of host-specific adaption; (iii) provide insight into the endosymbiotic relationship of R. similis with Wolbachia; and (iv) provide support for the mode of reproduction of R. similis. A whole-genome single-nucleotide polymorphism (SNP) analysis through principal component analysis and a phylogenomic maximum likelihood tree revealed that the largest correlative factors with genetic diversity in these populations were continent and Wolbachia host status. Both methods demonstrated that the greatest genetic diversity of R. similis is in Africa and Asia. Genetically isolated populations from Colombia and Australia were identified using SNP-based phylogeny and Weir and Cockerham's F ST as potential recent introductions from Africa. Additionally, 186 unique SNPs, including in 12 potential effectors genes, were associated with R. similis populations originating from non-banana hosts and warrant further investigation, with particular in relation to how R. similis differentiates hosts. Four genes potentially associated with the ability of R. similis to host Wolbachia would also warrant further research. Overall, this work provides substantial genomic resources to the nematology community and foundational genomic and population information on an economically important and understudied plant-pathogenic nematode pest. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2026.