A genomic investigation of Meloidogyne javanica: genome assembly, comparative analysis, and virulence

Winter, Michael

Abstract

The Meloidogyne incognita group (MIG) of nematodes, including Meloidogyne javanica, contains some of the most destructive crop pathogens worldwide. Genetic resistance, such as through the Mi-1 gene, is used to limit M. javanica infection, but resistant strains like VW5 have emerged, increasing the threat posed by this species. Understanding of the molecular mechanisms driving speciation and adaptation in the MIG is limited by outdated genomic resources. We generated a chromosome-scale, fully annotated genome assembly of M. javanica, revealing an allotetraploid genome composed of two diploid subgenomes (A and B). Subgenome B shows evidence of chromosomal fission, despite considerable synteny with subgenome A. This assembly provides a valuable resource for studying allopolyploid genome evolution and pathogenicity mechanisms in the Meloidogyne genus. Using the novel M. javanica assembly as a reference, we phased and annotated genomes of other MIG species, as well as Meloidogyne luci. We performed synteny and phylogenetic analyses across these species at a subgenome scale, finding conserved synteny and collinearity between subgenomes and species. No clear evidence of large-scale dominance was found, and instead we reveal a more nuanced picture whereby dominance seems to be balanced, occurring strongly at individual loci but with no clear subgenome scale trend. Phylogenetic analysis indicates that subgenomes are more closely related to orthologous subgenomes in other species than to homoeologous subgenomes within the same species, suggesting a shared ancestry. We also find that M. luci is allopolyploid, with subgenomes orthologous to those of the MIG. This suggests that many clade I Meloidogyne species are likely allopolyploids, with shared parent species. This highlights the utility of this group as models for studying the evolutionary dynamics of allopolyploid genomes. Finally, we investigate a genomic region involved in resistance evasion of the Mi-1 gene in the VW5 lineage of M. javanica. We discovered a ~650 Kbp deletion on one subgenomic copy, encompassing the single complete copy of the Cg-1 region. The loss of key transcripts from this deletion suggests a possible mechanism for resistance evasion and adaptation through gene loss, where the absence of a secreted effector may enable the nematode to evade host defences. Overall, this work provides new genomic resources and insights into the evolutionary dynamics of subgenomes, selection pressures, and resistance adaptations, helping to advance research and control methods for these globally significant plant pathogens.

Citation

Winter, M. (2024). A genomic investigation of Meloidogyne javanica: genome assembly, comparative analysis, and virulence. (Thesis). University of Hull. https://hull-repository.worktribe.com/output/5088328

• Thesis Type: Thesis
• Deposit Date: Mar 25, 2025
• Publicly Available Date: Apr 11, 2025
• Keywords: Biological science
• Public URL: https://hull-repository.worktribe.com/output/5088328
• Additional Information: Genomics and Bioinformatics; School of Natural Sciences; University of Hull
• Award Date: Dec 11, 2024