Abstract
AbstractBackgroundThe 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.
Publisher
Cold Spring Harbor Laboratory
Reference56 articles.
1. Jain M , Koren S , Miga KH , Quick J , Rand AC , Sasani TA , et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol [Internet]. Nat Biotechnol; 2018 [cited 2020 Jul 16];36. Available from: https://pubmed.ncbi.nlm.nih.gov/29431738/
2. Belser C , Istace B , Denis E , Dubarry M , Baurens FC , Falentin C , et al. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nature plants [Internet]. Nat Plants; 2018 [cited 2020 Jul 16];4. Available from: https://pubmed.ncbi.nlm.nih.gov/30390080/
3. De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing;Plant Cell. American Society of Plant Biologists,2017
4. Istace B , Friedrich A , d’Agata L , Faye S , Payen E , Beluche O , et al. de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer. Gigascience [Internet]. Oxford Academic; 2017 [cited 2020 Jul 16];6. Available from: https://academic.oup.com/gigascience/article-pdf/6/2/giw018/25513794/giw018.pdf
5. bol-D134-Reference - Genome - Assembly - NCBI [Internet]. [cited 2020 Jul 16]. Available from: https://www.ncbi.nlm.nih.gov/assembly/GCA_902726615.1
Cited by
3 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献