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Long-read assembly of the Brassica napus reference genome Darmor-bzh

BACKGROUND: The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organization of chromosomes, including complex r...

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Autores principales: Rousseau-Gueutin, Mathieu, Belser, Caroline, Da Silva, Corinne, Richard, Gautier, Istace, Benjamin, Cruaud, Corinne, Falentin, Cyril, Boideau, Franz, Boutte, Julien, Delourme, Regine, Deniot, Gwenaëlle, Engelen, Stefan, de Carvalho, Julie Ferreira, Lemainque, Arnaud, Maillet, Loeiz, Morice, Jérôme, Wincker, Patrick, Denoeud, France, Chèvre, Anne-Marie, Aury, Jean-Marc
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7736779/
https://www.ncbi.nlm.nih.gov/pubmed/33319912
http://dx.doi.org/10.1093/gigascience/giaa137
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author Rousseau-Gueutin, Mathieu
Belser, Caroline
Da Silva, Corinne
Richard, Gautier
Istace, Benjamin
Cruaud, Corinne
Falentin, Cyril
Boideau, Franz
Boutte, Julien
Delourme, Regine
Deniot, Gwenaëlle
Engelen, Stefan
de Carvalho, Julie Ferreira
Lemainque, Arnaud
Maillet, Loeiz
Morice, Jérôme
Wincker, Patrick
Denoeud, France
Chèvre, Anne-Marie
Aury, Jean-Marc
author_facet Rousseau-Gueutin, Mathieu
Belser, Caroline
Da Silva, Corinne
Richard, Gautier
Istace, Benjamin
Cruaud, Corinne
Falentin, Cyril
Boideau, Franz
Boutte, Julien
Delourme, Regine
Deniot, Gwenaëlle
Engelen, Stefan
de Carvalho, Julie Ferreira
Lemainque, Arnaud
Maillet, Loeiz
Morice, Jérôme
Wincker, Patrick
Denoeud, France
Chèvre, Anne-Marie
Aury, Jean-Marc
author_sort Rousseau-Gueutin, Mathieu
collection PubMed
description BACKGROUND: The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organization of chromosomes, including complex regions such as telomeres and centromeres. The Brassica genus is not exempt, and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, was produced using short reads and its contiguity was extremely low compared with current assemblies of the Brassica genus. FINDINGS: Herein, we report the new long-read assembly of Darmor-bzh genome (Brassica napus) generated by combining long-read sequencing data and optical and genetic maps. Using the PromethION device and 6 flowcells, we generated ∼16 million long reads representing 93× coverage and, more importantly, 6× with reads longer than 100 kb. This ultralong-read dataset allows us to generate one of the most contiguous and complete assemblies of a Brassica genome to date (contig N50 > 10 Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes. CONCLUSION: Using these cutting-edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable to the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.
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spelling pubmed-77367792020-12-17 Long-read assembly of the Brassica napus reference genome Darmor-bzh Rousseau-Gueutin, Mathieu Belser, Caroline Da Silva, Corinne Richard, Gautier Istace, Benjamin Cruaud, Corinne Falentin, Cyril Boideau, Franz Boutte, Julien Delourme, Regine Deniot, Gwenaëlle Engelen, Stefan de Carvalho, Julie Ferreira Lemainque, Arnaud Maillet, Loeiz Morice, Jérôme Wincker, Patrick Denoeud, France Chèvre, Anne-Marie Aury, Jean-Marc Gigascience Data Note BACKGROUND: The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organization of chromosomes, including complex regions such as telomeres and centromeres. The Brassica genus is not exempt, and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, was produced using short reads and its contiguity was extremely low compared with current assemblies of the Brassica genus. FINDINGS: Herein, we report the new long-read assembly of Darmor-bzh genome (Brassica napus) generated by combining long-read sequencing data and optical and genetic maps. Using the PromethION device and 6 flowcells, we generated ∼16 million long reads representing 93× coverage and, more importantly, 6× with reads longer than 100 kb. This ultralong-read dataset allows us to generate one of the most contiguous and complete assemblies of a Brassica genome to date (contig N50 > 10 Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes. CONCLUSION: Using these cutting-edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable to the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits. Oxford University Press 2020-12-15 /pmc/articles/PMC7736779/ /pubmed/33319912 http://dx.doi.org/10.1093/gigascience/giaa137 Text en © The Author(s) 2020. Published by Oxford University Press GigaScience. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Data Note
Rousseau-Gueutin, Mathieu
Belser, Caroline
Da Silva, Corinne
Richard, Gautier
Istace, Benjamin
Cruaud, Corinne
Falentin, Cyril
Boideau, Franz
Boutte, Julien
Delourme, Regine
Deniot, Gwenaëlle
Engelen, Stefan
de Carvalho, Julie Ferreira
Lemainque, Arnaud
Maillet, Loeiz
Morice, Jérôme
Wincker, Patrick
Denoeud, France
Chèvre, Anne-Marie
Aury, Jean-Marc
Long-read assembly of the Brassica napus reference genome Darmor-bzh
title Long-read assembly of the Brassica napus reference genome Darmor-bzh
title_full Long-read assembly of the Brassica napus reference genome Darmor-bzh
title_fullStr Long-read assembly of the Brassica napus reference genome Darmor-bzh
title_full_unstemmed Long-read assembly of the Brassica napus reference genome Darmor-bzh
title_short Long-read assembly of the Brassica napus reference genome Darmor-bzh
title_sort long-read assembly of the brassica napus reference genome darmor-bzh
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7736779/
https://www.ncbi.nlm.nih.gov/pubmed/33319912
http://dx.doi.org/10.1093/gigascience/giaa137
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