Global comparative genomics of the burrowing nematode, Radopholus similis

Authors: Wram, Catherine; Hesse, Cedar; HUMPHREYS-PEREIRA, DANNY - Universidad De Costa Rica; Reis Vieira, Paulo; EVES-VAN DEN AKKER, SEBASTIAN - University Of Cambridge; Myers, Roxana; COYNE, DANIEL - International Institute For Tropical Agriculture; DIGENNARO, PETER - University Of Wisconsin; LOPEZ-NICORA, HORACIO - The Ohio State University; CEDEÑO RAMÍREZ, ALEJANDRO - Corteva Agriscience; EMMANUEL, OLAJIDE - International Institute Of Tropical Agriculture (IITA); SAIKAI, KANAN - International Institute Of Tropical Agriculture (IITA); DUNCAN, LARRY - University Of Florida; GUZMÁN-PIEDRAHITA, OSCAR - Universidad De Caldas; ADEWUYI, DAMILARE - International Institute For Tropical Agriculture; COBON, JENNIFER - Department Of Agriculture And Fisheries; CHINNARSRI, BUNCHA - Kasetsart University; INSERRA, RENATO - Florida Department Of Agriculture And Consumer Services; Zasada, Inga

Submitted to: PhytoFrontiers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/22/2025
Publication Date: 4/14/2026
Citation: Wram, C.L., Hesse, C.N., Humphreys-Pereira, D., Reis Vieira, P.C., Eves-Van Den Akker, S., Myers, R.Y., Coyne, D., Digennaro, P., Lopez-Nicora, H., Cedeño Ramírez, A., Emmanuel, O., Saikai, K., Duncan, L., Guzmán-Piedrahita, O., Adewuyi, D., Cobon, J., Chinnarsri, B., Inserra, R., Zasada, I.A. 2026. Global comparative genomics of the burrowing nematode, Radopholus similis. PhytoFrontiers. 6(2):251-265. https://doi.org/10.1094/PHYTOFR-08-25-0072-R.
DOI: https://doi.org/10.1094/PHYTOFR-08-25-0072-R

Interpretive Summary: Burrowing Nematode is a major threat to banana and citrus production globally, reducing banana production by up to 80%. Stopping this pest is mainly done by prevention of introductions to new cropping areas and utilizing nematode-free planting material. DNA sequencing of 18 worldwide isolates was used to gain a better understanding of how this nematode has moved throughout the world, why it can infect different hosts, and what genes may be involved in hosting a bacterium that can be used for biological control. Genes that potentially are responsible for the ability to infect citrus, host bacteria, and track this nematode around the globe were found. Information gained indicates that this species may be difficult to manage due to its genetic variation. This information will be useful to plant pathologists, plant disease diagnosticians, regulatory officials and others involved in the management of plant diseases.

Technical Abstract: Radopholus similis is a devastating pest to tropical agriculture, including economically important crops such as banana and citrus. To gain a better understanding of the biology of R. similis, the genomes of 18 populations from five continents were sequenced in order to utilize comparative genomics to 1) provide a snapshot of global genetic distinctiveness of R. similis and understand the drivers of this genetic variation 2) determine if populations of R. similis originating from different hosts had made any host specific adaptations, 3) provide insight into the endosymbiotic relationship R. similis has with Wolbachia, and 4) confirm the mode of reproduction of R. similis. A whole genome single nucleotide polymorphism (SNP) analysis was used to reveal through PCA and a phylogenomic maximum likelihood tree that the largest drivers of genetic variation in the populations studied were continent and Wolbachia host status. Multi-gene mitochondrial trees confirmed SNP results. Both methods support greater genetic variation of R. similis in Africa and Asia. Genetically isolated populations in Colombia and Australia were also identified and are potential introduction from Africa. Additionally, 186 unique SNPs, including in 12 potential effectors, were associated with R. similis populations originating from non-banana hosts and warrant further investigation particularly focused on host differentiation. Four genes potentially associated with the ability of R. similis to host Wolbachia also warrent further research. Overall, this work provides genomic resources to the nematology community and foundational information on an important understudied nematode.