A Micro-scope for Brassica napus Genomics

Welcome to BnaScope!

BnaScope is a comprehensive gene-centric research resources for Brassica napus. It integrates genomic resources from 22 accessions, including the gap-free reference genomes of ZS11 and Westar. We provide a unified platform for exploring standardized functional annotations, homoeolog relationships, and multi-omics data across the pan-genome, establishing a foundation for functional genomics and molecular breeding.

Please refer to the Help for tutorials and use the DataNotes for detailed data information.

News

Version: TBD

Join the BnaCurate Project
2026-02-04

Project have initiated a comprehensive manual curation of the ZS11 gene models. Check our BnaCurate page to track our 2-year roadmap and submit your own annotation corrections.We also welcome any further suggestions you may have for the BnaScope website.
Welcome to BnaScope
2026-01-05

This is the gap-free rapeseed reference genome database. The first version will be released in January 2026, and many features are currently still under modification and testing.

Fig.1. Assembly and annotation of the ZS11 and Westar genomes

A. Overview of the ZS11 v1 genome. B. Overview of the Westar (WE) v1 genome. Tracks from outermost to innermost represent centromere-specific repeats (A), telomere-specific repeats (B), GC content (C), gene density (D), transposon density (E), tandem repeats (F), and covariate blocks between subgenomes (G). Darker colors in the heatmap indicate higher densities. C. Comparison of RNA-seq mapping rates across different genome versions. D. GO enrichment analysis of the novel genes specific to the ZS11 v1 genome (which were missed in v0). The size of the circles represents the gene count, and the color gradient indicates the significance of enrichment. E. Comparison of the number of identified NLR genes between the v0 (grey) and v1 (red) genomes. F. Distribution of homologous copies of TT4 across ZS11 v0, Arabidopsis, Darmor-bzh v10, and ZS11 v1 genomes. The box-and-line graph indicates the gene expression levels of the 16 TT4 copies in ZS11 v1, ordered according to their arrangement in the genome. G. Manhattan plots of GWAS for SGC based on ZS11 v1 genome. The BLUP values of SGC from 2017-2019 were used. H. Manhattan plots around GTR2. Dots represent the log-transformed P values of SGC BLUP values for GWAS variants. Dot color represents the LD (r2) between the variant and the Lead SNP. The gene structure in the locus is shown below, with GTR2 located between the two grey dashed lines. I. Comparison of annotation metrics between the public versions and the newly re-annotated versions. From top to bottom are BUSCO (Protein mode), OMArk conserved, and OMArk consistent.

Fig.R1. Comparative Analysis of ZS11 and Westar Genome Versions

A.ZS11 v1 genomes. B. Westar v1 genomes. Green highlights the chromosomes that have achieved Telomere-to-Telomere (T2T) continuity. C. Chromosomal anchoring rates across different assembly versions. Grey indicates the proportion of unanchored sequences, while orange and blue represent the proportions of sequences anchored to chromosomes in the v1 and v0 genomes, respectively. D. Synteny analysis between the different assembly versions of ZS11 and Westar. Grey shaded areas indicate the centromeric regions in the v1 genomes. E. Summary statistics of ONT sequencing data. F. Summary statistics of the ZS11 and Westar genomes. G. The RNAseq mapping rates in the ZS11 and Westar genomes.

Fig.2. Pan- and Core Genome Analyses of Brassica napus Accessions.

A. Influence of the number of B. napus genomes on the number of pan gene families and core gene families. B. Compositions of gene families in the pan-genome and individual genomes. The histogram illustrates the distribution of gene families across 22 genomes based on their frequencies, while the pie chart shows the proportional representation of gene families categorized by composition. C. Presence and absence patterns of pan-gene families across the 22 genomes. D. Gene counts of each composition within individual genomes. E. Distribution of Ka/Ks ratios and exon counts in core, softcore, dispensable and private genes. Box edges represent interquartile range, whiskers extend 1.5 times the interquartile range, and centerlines indicate the median. Multiple comparisons were conducted using the Student-Newman-Keuls test with α = 0.001. F. Gene ontology (GO) enrichment analyses of core, dispensable and private gene families.

Fig.3. Genetic Variations from 22 B. napus Genomes and 505 Resequenced Accessions

A. Counts of different SV types across chromosomes in the pan-genome. B. Variants from each sample were merged using a nonredundant strategy, beginning with ZS11 and iteratively incorporating unique variants from additional accessions. C. Variant counts for each discovery class are displayed by accession. D. Distribution of PAV numbers against the distance to gene. E. The fixation index (Fst) between spring and semi-winter sub-population.

Gene Search

Gene Query Advanced Filter Homologs/Copies Gene Family Domain & Motif Sequence Retrieval

Omics Atlas

Expression Atlas Transposable Elements

Tools & Downloads

ID Converter Genome Browser BLAST GO Enrichment KEGG Enrichment Downloads

Data Statistics

Total Assemblies: 22 Genes: 2147467 Transcripts: 3443718

Darmor

Genes: 99802

Genome: 923.8 Mb

Transcripts: 161125

InterPro: 150672

Chromosomes: 19 (+218 scaffolds)

Westar (WE)

Genes: 99423

Genome: 1022.8 Mb

Transcripts: 143994

InterPro: 134518

Chromosomes: 19 (+2 scaffolds)

ZS11

Genes: 101387

Genome: 1030.6 Mb

Transcripts: 185264

InterPro: 173305

Chromosomes: 19 (+4 scaffolds)

95878 Genes

154241 Transcripts

887.9 Mb Genome

Chromosomes: 19 (+2819 scaffolds)

93594 Genes

148514 Transcripts

876.2 Mb Genome

Chromosomes: 19 (+1820 scaffolds)

97861 Genes

157834 Transcripts

918.1 Mb Genome

Chromosomes: 19 (+1940 scaffolds)

DaAe

97277 Genes

155776 Transcripts

1001.5 Mb Genome

Chromosomes: 19 (+3145 scaffolds)

Express617

98657 Genes

157315 Transcripts

925.1 Mb Genome

Chromosomes: 19 (+1412 scaffolds)

GH06

94172 Genes

150949 Transcripts

845.4 Mb Genome

Chromosomes: 19 (+1873 scaffolds)

GanganF73

101508 Genes

160035 Transcripts

1034.3 Mb Genome

Chromosomes: 19 (+4911 scaffolds)

95276 Genes

155279 Transcripts

934.2 Mb Genome

Chromosomes: 19 (+2016 scaffolds)

89101 Genes

141545 Transcripts

824.8 Mb Genome

Chromosomes: 19 (+1173 scaffolds)

98474 Genes

158310 Transcripts

964.3 Mb Genome

Chromosomes: 19 (+24 scaffolds)

ZS2

99367 Genes

161433 Transcripts

949.6 Mb Genome

Chromosomes: 19 (+1926 scaffolds)

Zy821

95461 Genes

153787 Transcripts

863.1 Mb Genome

Chromosomes: 19 (+1995 scaffolds)

no2127

96817 Genes

146343 Transcripts

1012.4 Mb Genome

Chromosomes: 19 (+3714 scaffolds)

p130

96552 Genes

157956 Transcripts

824.8 Mb Genome

Chromosomes: 19

p202

94174 Genes

152363 Transcripts

815.5 Mb Genome

Chromosomes: 19

quintaA

102295 Genes

163205 Transcripts

1004.3 Mb Genome

Chromosomes: 19 (+3703 scaffolds)

shengli3

99582 Genes

157991 Transcripts

1002.6 Mb Genome

Chromosomes: 19 (+3783 scaffolds)

xiaoyun

100662 Genes

160967 Transcripts

957.8 Mb Genome

Chromosomes: 19 (+967 scaffolds)

zheyou7

100147 Genes

159492 Transcripts

1016.2 Mb Genome

Chromosomes: 19 (+4971 scaffolds)