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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.


Michael R. Winter

Adam P. Taranto

Henok Zemene Yimer

Alison Coomer Blundell

Shahid Siddique

Valerie M. Williamson


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.


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.

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
Public URL


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Copyright Statement
Copyright: © 2024 Winter et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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