Cargando…
De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing
Leptosphaeria maculans and Leptosphaeria biglobosa are ascomycete phytopathogens of Brassica napus (oilseed rape, canola). Here we report the complete sequence of three Leptosphaeria genomes (L. maculans JN3, L. maculans Nz-T4 and L. biglobosa G12-14). Nz-T4 and G12-14 genome assemblies were generat...
Autores principales: | , , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219404/ https://www.ncbi.nlm.nih.gov/pubmed/30398473 http://dx.doi.org/10.1038/sdata.2018.235 |
_version_ | 1783368652790169600 |
---|---|
author | Dutreux, Fabien Da Silva, Corinne d’Agata, Léo Couloux, Arnaud Gay, Elise J. Istace, Benjamin Lapalu, Nicolas Lemainque, Arnaud Linglin, Juliette Noel, Benjamin Wincker, Patrick Cruaud, Corinne Rouxel, Thierry Balesdent, Marie-Hélène Aury, Jean-Marc |
author_facet | Dutreux, Fabien Da Silva, Corinne d’Agata, Léo Couloux, Arnaud Gay, Elise J. Istace, Benjamin Lapalu, Nicolas Lemainque, Arnaud Linglin, Juliette Noel, Benjamin Wincker, Patrick Cruaud, Corinne Rouxel, Thierry Balesdent, Marie-Hélène Aury, Jean-Marc |
author_sort | Dutreux, Fabien |
collection | PubMed |
description | Leptosphaeria maculans and Leptosphaeria biglobosa are ascomycete phytopathogens of Brassica napus (oilseed rape, canola). Here we report the complete sequence of three Leptosphaeria genomes (L. maculans JN3, L. maculans Nz-T4 and L. biglobosa G12-14). Nz-T4 and G12-14 genome assemblies were generated de novo and the reference JN3 genome assembly was improved using Oxford Nanopore MinION reads. The new assembly of L. biglobosa showed the existence of AT rich regions and pointed to a genome compartmentalization previously unsuspected following Illumina sequencing. Moreover nanopore sequencing allowed us to generate a chromosome-level assembly for the L. maculans reference isolate, JN3. The genome annotation was supported by integrating conserved proteins and RNA sequencing from Leptosphaeria-infected samples. The newly produced high-quality assemblies and annotations of those three Leptosphaeria genomes will allow further studies, notably focused on the tripartite interaction between L. maculans, L. biglobosa and oilseed rape. The discovery of as yet unknown effectors will notably allow progress in B. napus breeding towards L. maculans resistance. |
format | Online Article Text |
id | pubmed-6219404 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-62194042018-11-07 De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing Dutreux, Fabien Da Silva, Corinne d’Agata, Léo Couloux, Arnaud Gay, Elise J. Istace, Benjamin Lapalu, Nicolas Lemainque, Arnaud Linglin, Juliette Noel, Benjamin Wincker, Patrick Cruaud, Corinne Rouxel, Thierry Balesdent, Marie-Hélène Aury, Jean-Marc Sci Data Data Descriptor Leptosphaeria maculans and Leptosphaeria biglobosa are ascomycete phytopathogens of Brassica napus (oilseed rape, canola). Here we report the complete sequence of three Leptosphaeria genomes (L. maculans JN3, L. maculans Nz-T4 and L. biglobosa G12-14). Nz-T4 and G12-14 genome assemblies were generated de novo and the reference JN3 genome assembly was improved using Oxford Nanopore MinION reads. The new assembly of L. biglobosa showed the existence of AT rich regions and pointed to a genome compartmentalization previously unsuspected following Illumina sequencing. Moreover nanopore sequencing allowed us to generate a chromosome-level assembly for the L. maculans reference isolate, JN3. The genome annotation was supported by integrating conserved proteins and RNA sequencing from Leptosphaeria-infected samples. The newly produced high-quality assemblies and annotations of those three Leptosphaeria genomes will allow further studies, notably focused on the tripartite interaction between L. maculans, L. biglobosa and oilseed rape. The discovery of as yet unknown effectors will notably allow progress in B. napus breeding towards L. maculans resistance. Nature Publishing Group 2018-11-06 /pmc/articles/PMC6219404/ /pubmed/30398473 http://dx.doi.org/10.1038/sdata.2018.235 Text en Copyright © 2018, The Author(s) http://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/ The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files made available in this article. |
spellingShingle | Data Descriptor Dutreux, Fabien Da Silva, Corinne d’Agata, Léo Couloux, Arnaud Gay, Elise J. Istace, Benjamin Lapalu, Nicolas Lemainque, Arnaud Linglin, Juliette Noel, Benjamin Wincker, Patrick Cruaud, Corinne Rouxel, Thierry Balesdent, Marie-Hélène Aury, Jean-Marc De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing |
title | De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing |
title_full | De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing |
title_fullStr | De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing |
title_full_unstemmed | De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing |
title_short | De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing |
title_sort | de novo assembly and annotation of three leptosphaeria genomes using oxford nanopore minion sequencing |
topic | Data Descriptor |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219404/ https://www.ncbi.nlm.nih.gov/pubmed/30398473 http://dx.doi.org/10.1038/sdata.2018.235 |
work_keys_str_mv | AT dutreuxfabien denovoassemblyandannotationofthreeleptosphaeriagenomesusingoxfordnanoporeminionsequencing AT dasilvacorinne denovoassemblyandannotationofthreeleptosphaeriagenomesusingoxfordnanoporeminionsequencing AT dagataleo denovoassemblyandannotationofthreeleptosphaeriagenomesusingoxfordnanoporeminionsequencing AT coulouxarnaud denovoassemblyandannotationofthreeleptosphaeriagenomesusingoxfordnanoporeminionsequencing AT gayelisej denovoassemblyandannotationofthreeleptosphaeriagenomesusingoxfordnanoporeminionsequencing AT istacebenjamin denovoassemblyandannotationofthreeleptosphaeriagenomesusingoxfordnanoporeminionsequencing AT lapalunicolas denovoassemblyandannotationofthreeleptosphaeriagenomesusingoxfordnanoporeminionsequencing AT lemainquearnaud denovoassemblyandannotationofthreeleptosphaeriagenomesusingoxfordnanoporeminionsequencing AT linglinjuliette denovoassemblyandannotationofthreeleptosphaeriagenomesusingoxfordnanoporeminionsequencing AT noelbenjamin denovoassemblyandannotationofthreeleptosphaeriagenomesusingoxfordnanoporeminionsequencing AT winckerpatrick denovoassemblyandannotationofthreeleptosphaeriagenomesusingoxfordnanoporeminionsequencing AT cruaudcorinne denovoassemblyandannotationofthreeleptosphaeriagenomesusingoxfordnanoporeminionsequencing AT rouxelthierry denovoassemblyandannotationofthreeleptosphaeriagenomesusingoxfordnanoporeminionsequencing AT balesdentmariehelene denovoassemblyandannotationofthreeleptosphaeriagenomesusingoxfordnanoporeminionsequencing AT auryjeanmarc denovoassemblyandannotationofthreeleptosphaeriagenomesusingoxfordnanoporeminionsequencing |