Ngan Thi Phan auteur aut IRD Orjuela J. auteur aut IRD Danchin E. G. J. auteur aut IRD Klopp C. auteur aut IRD Perfus-Barbeoch L. auteur aut IRD Kozlowski D. K. auteur aut IRD Koutsovoulos G. D. auteur aut IRD Lopez-Roques C. auteur aut IRD Bouchez O. auteur aut IRD Zahm M. auteur aut IRD Besnard G. auteur aut IRD Bellafiore Stéphane auteur aut IRD text journalArticle eng text/pdf reformatted digital access Discovered in the 1960s, Meloidogyne graminicolais a root-knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavailability of a sufficiently complete and well-assembled genome. In this study, using a combination of Oxford Nanopore Technologies and Illumina sequencing data, we generated a highly contiguous reference genome (283 scaffolds with an N50 length of 294 kb, totaling 41.5 Mb). The completeness scores of our assembly are among the highest currently published for Meloidogyne genomes. We predicted 10,284 protein-coding genes spanning 75.5% of the genome. Among them, 67 are identified as possibly originating from horizontal gene transfers (mostly from bacteria), which supposedly contribute to nematode infection, nutrient processing, and plant defense manipulation. Besides, we detected 575 canonical transposable elements (TEs) belonging to seven orders and spanning 2.61% of the genome. These TEs might promote genomic plasticity putatively related to the evolution of M. graminicola parasitism. This high-quality genome assembly constitutes a major improvement regarding previously available versions and represents a valuable molecular resource for future phylogenomic studies of Meloidogyne species. In particular, this will foster comparative genomic studies to trace back the evolutionary history of M. graminicola and its closest relatives. specialized cereals horizontal gene transfer pest reference genome root-knot nematode transposable element VIET NAM 076 074 10 20 11006-11021 2020 2045-7758 https://www.documentation.ird.fr/hor/fdi:010079696 10.1002/ece3.6680 2045-7758 [F B010079696] https://www.documentation.ird.fr/hor/fdi:010079696 https://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers20-09/010079696.pdf IRD - Base Horizon / Pleins textes 2020-10-09 2025-02-24 fdi:010079696 fre