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

Autor: Phan NT; IRD-CIRAD-University of Montpellier UMR Interactions Plantes Microorganismes Environnement (IPME) Montpellier France., Orjuela J; IRD-CIRAD-University of Montpellier UMR Interactions Plantes Microorganismes Environnement (IPME) Montpellier France., Danchin EGJ; Institut Sophia Agrobiotech INRAE CNRS Université Côte d'Azur Sophia Antipolis France., Klopp C; Plateforme BioInfo Genotoul UR875 INRAE Castanet-Tolosan cedex France., Perfus-Barbeoch L; Institut Sophia Agrobiotech INRAE CNRS Université Côte d'Azur Sophia Antipolis France., Kozlowski DK; Institut Sophia Agrobiotech INRAE CNRS Université Côte d'Azur Sophia Antipolis France., Koutsovoulos GD; Institut Sophia Agrobiotech INRAE CNRS Université Côte d'Azur Sophia Antipolis France., Lopez-Roques C; US 1426 GeT-PlaGe Genotoul INRAE Castanet-Tolosan France., Bouchez O; US 1426 GeT-PlaGe Genotoul INRAE Castanet-Tolosan France., Zahm M; Plateforme BioInfo Genotoul UR875 INRAE Castanet-Tolosan cedex France., Besnard G; CNRS-UPS-IRD UMR5174 EDB Université Paul Sabatier Toulouse France., Bellafiore S; IRD-CIRAD-University of Montpellier UMR Interactions Plantes Microorganismes Environnement (IPME) Montpellier France.
Jazyk: angličtina
Zdroj: Ecology and evolution [Ecol Evol] 2020 Sep 13; Vol. 10 (20), pp. 11006-11021. Date of Electronic Publication: 2020 Sep 13 (Print Publication: 2020).
DOI: 10.1002/ece3.6680
Abstrakt: 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.
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
(© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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