Cargando…
Genome structure and content of the rice root‐knot nematode (Meloidogyne graminicola)
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 comp...
Autores principales: | , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7593179/ https://www.ncbi.nlm.nih.gov/pubmed/33144944 http://dx.doi.org/10.1002/ece3.6680 |
_version_ | 1783601326561689600 |
---|---|
author | 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 |
author_facet | 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 |
author_sort | Phan, Ngan Thi |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7593179 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-75931792020-11-02 Genome structure and content of the rice root‐knot nematode (Meloidogyne graminicola) 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 Ecol Evol Original Research 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. John Wiley and Sons Inc. 2020-09-13 /pmc/articles/PMC7593179/ /pubmed/33144944 http://dx.doi.org/10.1002/ece3.6680 Text en © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Research 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 Genome structure and content of the rice root‐knot nematode (Meloidogyne graminicola) |
title | Genome structure and content of the rice root‐knot nematode (Meloidogyne graminicola) |
title_full | Genome structure and content of the rice root‐knot nematode (Meloidogyne graminicola) |
title_fullStr | Genome structure and content of the rice root‐knot nematode (Meloidogyne graminicola) |
title_full_unstemmed | Genome structure and content of the rice root‐knot nematode (Meloidogyne graminicola) |
title_short | Genome structure and content of the rice root‐knot nematode (Meloidogyne graminicola) |
title_sort | genome structure and content of the rice root‐knot nematode (meloidogyne graminicola) |
topic | Original Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7593179/ https://www.ncbi.nlm.nih.gov/pubmed/33144944 http://dx.doi.org/10.1002/ece3.6680 |
work_keys_str_mv | AT phannganthi genomestructureandcontentofthericerootknotnematodemeloidogynegraminicola AT orjuelajulie genomestructureandcontentofthericerootknotnematodemeloidogynegraminicola AT danchinetiennegj genomestructureandcontentofthericerootknotnematodemeloidogynegraminicola AT kloppchristophe genomestructureandcontentofthericerootknotnematodemeloidogynegraminicola AT perfusbarbeochlaetitia genomestructureandcontentofthericerootknotnematodemeloidogynegraminicola AT kozlowskidjampak genomestructureandcontentofthericerootknotnematodemeloidogynegraminicola AT koutsovoulosgeorgiosd genomestructureandcontentofthericerootknotnematodemeloidogynegraminicola AT lopezroquesceline genomestructureandcontentofthericerootknotnematodemeloidogynegraminicola AT bouchezolivier genomestructureandcontentofthericerootknotnematodemeloidogynegraminicola AT zahmmargot genomestructureandcontentofthericerootknotnematodemeloidogynegraminicola AT besnardguillaume genomestructureandcontentofthericerootknotnematodemeloidogynegraminicola AT bellafiorestephane genomestructureandcontentofthericerootknotnematodemeloidogynegraminicola |