Diagenode

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


Phan, Ngan Thi and Orjuela, Julie and Danchin, Etienne G J and Klopp,Christophe and Perfus-Barbeoch, Laetitia and Kozlowski, Djampa K andKoutsovoulos, Georgios D and Lopez-Roques, Céline and Bouchez, Olivier andZahm, Margot and Besnard, Guillaume and B

Discovered in the 1960s, 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 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 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 species. In particular, this will foster comparative genomic studies to trace back the evolutionary history of .  and its closest relatives.

Tags
Megaruptor

Share this article

Published
October, 2020

Source

Products used in this publication

  • Megaruptor 3
    B06010003
    Megaruptor® 3

活动

  • AACR 2024
    San Diego, California, USA
    Apr 5-Apr 10, 2024
 查看所有活动

新闻

 查看所有新闻


The European Regional Development Fund and Wallonia are investing in your future.

Extension of industrial buildings and new laboratories.


       Site map   |   Contact us   |   Conditions of sales   |   Conditions of purchase   |   Privacy policy   |   Diagenode Diagnostics