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Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode
Root-knot nematodes (genus Meloidogyne) are plant parasites causing huge economic loss in the agricultural industry and affecting severely numerous developing countries. Control methods against these plant pests are sparse, the preferred one being the deployment of plant cultivars bearing resistance...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7536185/ https://www.ncbi.nlm.nih.gov/pubmed/33020495 http://dx.doi.org/10.1038/s41597-020-00666-0 |
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author | Koutsovoulos, Georgios D. Poullet, Marine Elashry, Abdelnaser Kozlowski, Djampa K. L. Sallet, Erika Da Rocha, Martine Perfus-Barbeoch, Laetitia Martin-Jimenez, Cristina Frey, Juerg Ernst Ahrens, Christian H. Kiewnick, Sebastian Danchin, Etienne G. J. |
author_facet | Koutsovoulos, Georgios D. Poullet, Marine Elashry, Abdelnaser Kozlowski, Djampa K. L. Sallet, Erika Da Rocha, Martine Perfus-Barbeoch, Laetitia Martin-Jimenez, Cristina Frey, Juerg Ernst Ahrens, Christian H. Kiewnick, Sebastian Danchin, Etienne G. J. |
author_sort | Koutsovoulos, Georgios D. |
collection | PubMed |
description | Root-knot nematodes (genus Meloidogyne) are plant parasites causing huge economic loss in the agricultural industry and affecting severely numerous developing countries. Control methods against these plant pests are sparse, the preferred one being the deployment of plant cultivars bearing resistance genes against Meloidogyne species. However, M. enterolobii is not controlled by the resistance genes deployed in the crop plants cultivated in Europe. The recent identification of this species in Europe is thus a major concern. Here, we sequenced the genome of M. enterolobii using short and long-read technologies. The genome assembly spans 240 Mbp with contig N50 size of 143 kbp, enabling high-quality annotations of 59,773 coding genes, 4,068 non-coding genes, and 10,944 transposable elements (spanning 8.7% of the genome). We validated the genome size by flow cytometry and the structure, quality and completeness by bioinformatics metrics. This ensemble of resources will fuel future projects aiming at pinpointing the genome singularities, the origin, diversity, and adaptive potential of this emerging plant pest. |
format | Online Article Text |
id | pubmed-7536185 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-75361852020-10-19 Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode Koutsovoulos, Georgios D. Poullet, Marine Elashry, Abdelnaser Kozlowski, Djampa K. L. Sallet, Erika Da Rocha, Martine Perfus-Barbeoch, Laetitia Martin-Jimenez, Cristina Frey, Juerg Ernst Ahrens, Christian H. Kiewnick, Sebastian Danchin, Etienne G. J. Sci Data Data Descriptor Root-knot nematodes (genus Meloidogyne) are plant parasites causing huge economic loss in the agricultural industry and affecting severely numerous developing countries. Control methods against these plant pests are sparse, the preferred one being the deployment of plant cultivars bearing resistance genes against Meloidogyne species. However, M. enterolobii is not controlled by the resistance genes deployed in the crop plants cultivated in Europe. The recent identification of this species in Europe is thus a major concern. Here, we sequenced the genome of M. enterolobii using short and long-read technologies. The genome assembly spans 240 Mbp with contig N50 size of 143 kbp, enabling high-quality annotations of 59,773 coding genes, 4,068 non-coding genes, and 10,944 transposable elements (spanning 8.7% of the genome). We validated the genome size by flow cytometry and the structure, quality and completeness by bioinformatics metrics. This ensemble of resources will fuel future projects aiming at pinpointing the genome singularities, the origin, diversity, and adaptive potential of this emerging plant pest. Nature Publishing Group UK 2020-10-05 /pmc/articles/PMC7536185/ /pubmed/33020495 http://dx.doi.org/10.1038/s41597-020-00666-0 Text en © The Author(s) 2020, corrected publication 2020 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) applies to the metadata files associated with this article. |
spellingShingle | Data Descriptor Koutsovoulos, Georgios D. Poullet, Marine Elashry, Abdelnaser Kozlowski, Djampa K. L. Sallet, Erika Da Rocha, Martine Perfus-Barbeoch, Laetitia Martin-Jimenez, Cristina Frey, Juerg Ernst Ahrens, Christian H. Kiewnick, Sebastian Danchin, Etienne G. J. Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode |
title | Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode |
title_full | Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode |
title_fullStr | Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode |
title_full_unstemmed | Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode |
title_short | Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode |
title_sort | genome assembly and annotation of meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode |
topic | Data Descriptor |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7536185/ https://www.ncbi.nlm.nih.gov/pubmed/33020495 http://dx.doi.org/10.1038/s41597-020-00666-0 |
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