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Long-reads assembly and annotation of the Brassica napus reference genome, Darmor-bzh

ABSTRACT: Long-reads assembly and annotation of the Brassica napus reference genome, Darmor-bzh

PROVIDER: PRJEB40412 | ENA |

REPOSITORIES: ENA

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

Project description:Abstract 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.

| S-EPMC7736779 | biostudies-literature

RNA-seq data on leaf 8 blade tissue of 62 individual Brassica napus (Darmor) plants grown in the field.

Project description:62 individual Brassica napus plants of the same accession grown in the same field were expression-profiled in autumn 2016 and phenotyped extensively until harvest in spring 2017. Machine learning models were used to link gene expression to the phenotypes of individual plants, with the purpose of assessing how much phenotype information in encoded in ‘noisy’ gene expression variation among individual plants of the same background grown under the same uncontrolled field conditions. Rosette leaf 8 blades of 62 individual Brassica napus plants of the same winter-type accession (BnASSYST-120, Darmor) grown in the same field (50°58'24.9\\"N 3°46'49.1\\"E, Merelbeke, Belgium) were RNA-seq profiled. No treatments or stresses were applied, all plants were profiled individually under uncontrolled field conditions. Sown at 2016-09-08, rosette leaf 8 sampled for RNA-seq at 2016-11-28, plants harvested at 2017-06-13.

2022-10-10 | E-MTAB-11904 | biostudies-arrayexpress

Brassica napus cultivar:Darmor

Project description:Brassica napus Darmor Gene Expression Profiling - Darmor_WTP4_R3 transcriptome

| PRJNA618441 | ENA

Brassica napus cultivar:Darmor

Project description:Brassica napus Darmor Gene Expression Profiling - Darmor_WTP5_R4 transcriptome

| PRJNA618357 | ENA

Brassica napus cultivar:Darmor

Project description:Brassica napus Darmor Gene Expression Profiling - Darmor_WTP2_R3 transcriptome

| PRJNA619247 | ENA

Brassica napus cultivar:Darmor

Project description:Brassica napus Darmor Gene Expression Profiling - Darmor_WTP2_R4 transcriptome

| PRJNA619248 | ENA

Brassica napus cultivar:Darmor

Project description:Brassica napus Darmor Gene Expression Profiling - Darmor_CTP3_R3 transcriptome

| PRJNA618820 | ENA

Brassica napus cultivar:Darmor

Project description:Brassica napus Darmor Gene Expression Profiling - Darmor_WTP3_R2 transcriptome

| PRJNA618511 | ENA

Brassica napus cultivar:Darmor

Project description:Brassica napus Darmor Gene Expression Profiling - Darmor_CTP4_R3 transcriptome

| PRJNA618661 | ENA

Brassica napus cultivar:Darmor

Project description:Brassica napus Darmor Gene Expression Profiling - Darmor_WTP5_R2 transcriptome

| PRJNA618486 | ENA

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