Genome structure and content of the rice root‐knot nematode (Meloidogyne graminicola)

• Published in: Ecology and evolution 2020-10, Vol.10 (20), p.11006-11021
• Main Authors: Phan, Ngan Thi, Orjuela, Julie, Danchin, Etienne G. J., Klopp, Christophe, Perfus‐Barbeoch, Laetitia, Kozlowski, Djampa K., Koutsovoulos, Georgios D., Lopez‐Roques, Céline, Bouchez, Olivier, Zahm, Margot, Besnard, Guillaume, Bellafiore, Stéphane
• Format: Article
• Language: English
• Subjects: Agricultural production; Assembly; Bacteria; cereals; Crop production; Deoxyribonucleic acid; DNA; Environmental Sciences; Evolution; Evolutionary genetics; Fungi; Genes; Genetic engineering; Genomes; Genomics; horizontal gene transfer; Life Sciences; Meloidogyne; Meloidogyne graminicola; Mitochondrial DNA; Nematodes; Original Research; Parasitism; Pathogens; pest; Phenols; Phylogenetics; Porosity; Protocol; reference genome; Ribosomal DNA; Rice; root‐knot nematode; transposable element
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.6680

Discovered in the 1960s, Meloidogyne graminicola is 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. The genome of the rice root‐knot nematode (Meloidogyne graminicola) was assembled by combining short and long sequencing reads. Genes and transposable elements were annotated and then analyzed, revealing that lateral gene transfers from bacteria may have greatly contributed to the evolution of parasitism. This genome draft will foster comparative genomic studies to trace back the evolutionary history of M. graminicola and its closest relatives.