JBrowse2 Genome Browser

• 22 genomes of B. napus with reference sequences (FASTA) and gene annotation.
• Transposable elements (TEs): we integrated 1,058,755 TEs annotated by the EDTA pipeline across 22 genomes.
• ZS11 variation: SNP/InDel variation information derived from 505 resequencing accessions.
• ZS11v1 multi-omics: the platform re-analyzed and aggregated RNA-seq, ATAC-seq, and ChIP-seq tracks for integrative exploration.
• Comparative synteny (collinearity): minimap2 PAF-based tracks across key assemblies (ZS11 and Westar as anchors).Synteny is filtered: alignments shorter than 50 kb are removed to focus on robust collinear blocks.

1) Choose an Assembly

• Click ADD （Linear genome view）to change accession

2) Turn on Tracks

• Open the Track Selector and enable the Gene track (and other tracks of interest, e.g. Synteny, Expression).

3) Search & Navigate

• Search by gene ID or jump to a region like chr:start-end.
• Click a gene to open details; expand subfeatures to inspect isoforms and sequences.

4) Compare Using Synteny

• Use the Linear synteny view or Dotplot view to follow collinear blocks and jump between corresponding loci.