Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure

Winter, Michael R.; Taranto, Adam P.; Yimer, Henok Zemene; Coomer Blundell, Alison; Siddique, Shahid; Williamson, Valerie M.; Lunt, David H.

Abstract

We present the chromosome-scale genome assembly of the allopolyploid root-knot nematode Meloidogyne javanica. We show that the M. javanica genome is predominantly allotetraploid, comprising two subgenomes, A and B, that most likely originated from hybridisation of two ancestral parental species. The assembly was annotated using full-length non-chimeric transcripts, comparison to reference databases, and ab initio prediction techniques, and the subgenomes were phased using ancestral k-mer spectral analysis. Subgenome B appears to show fission of chromosomal contigs, and while there is substantial synteny between subgenomes, we also identified regions lacking synteny that may have diverged in the ancestral genomes prior to or following hybridisation. This annotated and phased genome assembly forms a significant resource for understanding the origins and genetics of these globally important plant pathogens.

Citation

Winter, M. R., Taranto, A. P., Yimer, H. Z., Coomer Blundell, A., Siddique, S., Williamson, V. M., & Lunt, D. H. (2024). Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure. PLoS ONE, 19(6), Article e0302506. https://doi.org/10.1371/journal.pone.0302506

• Journal Article Type: Article
• Acceptance Date: Apr 19, 2024
• Online Publication Date: Jun 6, 2024
• Publication Date: Jun 1, 2024
• Deposit Date: Jun 7, 2024
• Publicly Available Date: Jun 11, 2024
• Journal: PLOS ONE
• Print ISSN: 1932-6203
• Publisher: Public Library of Science
• Peer Reviewed: Peer Reviewed
• Volume: 19
• Issue: 6
• Article Number: e0302506
• DOI: https://doi.org/10.1371/journal.pone.0302506
• Public URL: https://hull-repository.worktribe.com/output/4705733