Long-reads assembly of the Brassica napus reference genome, Darmor-bzh
Long-reads assembly of the Brassica napus reference genome, Darmor-bzh
Abstract BackgroundThe combination of long-reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allow to access the gene catalogue of a given species but also reveals the architecture and organisation of chromosomes, including complex regions like 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, has been produced using short-reads and its contiguity was extremely low if compared to current assemblies of the Brassica genus. FindingsHere, we report the new long-reads assembly of Darmor-bzh genome (Brassica napus) generated by combining long-reads sequencing data, optical and genetic maps. Using the PromethION device and six flowcells, we generated about 16M long-reads representing 93X coverage and more importantly 6X with reads longer than 100Kb. This ultralong-reads dataset allows us to generate one of the most contiguous and complete assembly of a Brassica genome to date (contigs N50 > 10Mb). 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. ConclusionUsing 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 for the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.
Cruaud Corinne、Falentin Cyril、Boideau Franz、Boutte Julien、Deniot Gwena?lle、Engelen Stefan、Morice J¨|r?me、Belser Caroline、Rousseau-Gueutin Mathieu、Wincker Patrick、Silva Corinne Da、Maillet Loeiz、Denoeud France、Richard Gautier、de Carvalho Julie Ferreira、Delourme Regine、Lemainque Arnaud、Istace Benjamin、Aury Jean-Marc、Ch¨¨vre Anne-Marie
Genoscope, Institut Fran?ois Jacob, Commissariat ¨¤ l?ˉEnergie Atomique (CEA), Universit¨| Paris-SaclayIGEPP, INRAE, Institut Agro, Univ RennesIGEPP, INRAE, Institut Agro, Univ RennesIGEPP, INRAE, Institut Agro, Univ RennesIGEPP, INRAE, Institut Agro, Univ RennesG¨|nomique M¨|tabolique, Genoscope, Institut Fran?ois Jacob, CEA, CNRS, Univ Evry, Universit¨| Paris-SaclayIGEPP, INRAE, Institut Agro, Univ RennesG¨|nomique M¨|tabolique, Genoscope, Institut Fran?ois Jacob, CEA, CNRS, Univ Evry, Universit¨| Paris-SaclayIGEPP, INRAE, Institut Agro, Univ RennesG¨|nomique M¨|tabolique, Genoscope, Institut Fran?ois Jacob, CEA, CNRS, Univ Evry, Universit¨| Paris-SaclayG¨|nomique M¨|tabolique, Genoscope, Institut Fran?ois Jacob, CEA, CNRS, Univ Evry, Universit¨| Paris-SaclayIGEPP, INRAE, Institut Agro, Univ RennesG¨|nomique M¨|tabolique, Genoscope, Institut Fran?ois Jacob, CEA, CNRS, Univ Evry, Universit¨| Paris-SaclayIGEPP, INRAE, Institut Agro, Univ RennesIGEPP, INRAE, Institut Agro, Univ RennesIGEPP, INRAE, Institut Agro, Univ RennesGenoscope, Institut Fran?ois Jacob, Commissariat ¨¤ l?ˉEnergie Atomique (CEA), Universit¨| Paris-SaclayG¨|nomique M¨|tabolique, Genoscope, Institut Fran?ois Jacob, CEA, CNRS, Univ Evry, Universit¨| Paris-SaclayG¨|nomique M¨|tabolique, Genoscope, Institut Fran?ois Jacob, CEA, CNRS, Univ Evry, Universit¨| Paris-SaclayIGEPP, INRAE, Institut Agro, Univ Rennes
农业科学技术发展植物学遗传学
oilseed rapeBrassicaDarmor-bzhnanopore sequencingoptical mappingassemblychromosome-scaledirect RNA
Cruaud Corinne,Falentin Cyril,Boideau Franz,Boutte Julien,Deniot Gwena?lle,Engelen Stefan,Morice J¨|r?me,Belser Caroline,Rousseau-Gueutin Mathieu,Wincker Patrick,Silva Corinne Da,Maillet Loeiz,Denoeud France,Richard Gautier,de Carvalho Julie Ferreira,Delourme Regine,Lemainque Arnaud,Istace Benjamin,Aury Jean-Marc,Ch¨¨vre Anne-Marie.Long-reads assembly of the Brassica napus reference genome, Darmor-bzh[EB/OL].(2025-03-28)[2025-05-06].https://www.biorxiv.org/content/10.1101/2020.07.22.215749.点此复制
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