The ZS11 genome was displayed in JBrowse[1], providing 13 tracks for user-selective display, including nucleotide sequence, genes, transposable elements (TEs), expression profile data of different tissues and variation (SNPs, InDels and SVs) (Table 1). Users can filter the tracks of in batches in option box on the right. Transcription data of multiple tissues were obtained from BnTIR [2]. For each tissue in BnTIR and BnVIR, RNA-seq reads of all samples were merged and then about 25 Gb of reads were randomly extracted for quickly load in JBrowse. Generation of the gene expression and variation data are description in Methods.
Table 1. Description of data used in JBrowser
References | File | Description |
---|---|---|
ZS11 | zs11.v0.genome.fa | DNA sequence of ZS11 genome [3] |
zs11.v0.gff3 | Gene annotation of ZS11 genome [3] | |
zs11.v2.TE.gff | TE annotation of ZS11 genome [3] | |
1_root.bw | mRNA read coverage of root by mapping to ZS11 | |
2_stem.bw | mRNA read coverage of stem by mapping to ZS11 | |
3_leaf.bw | mRNA read coverage of leaf by mapping to ZS11 | |
4_bud.bw | mRNA read coverage of bud by mapping to ZS11 | |
5_flower.bw | mRNA read coverage of flower by mapping to ZS11 | |
6_silique.bw | mRNA read coverage of silique by mapping to ZS11 | |
7_silique_wall.bw | mRNA read coverage of silique wall by mapping to ZS11 | |
8_seed.bw | mRNA read coverage of seed by mapping to ZS11 | |
bna_2311_SVs.vcf | Information of SV identified in population of 2,311 B. napus accessions based on ZS11 genome | |
bna_2311_SNPs_InDels.vcf | Information of SNPs and InDels identified in population of 2,311 B. napus accessions ZS11 genome | |
Darmor-bzh | Darmor-bzh.v4.genome.fa | DNA sequence of Darmor-bzh genome [4] |
Brassica_napus.Darmor.v4.1.gene.gff3 | Gene annotation of Darmor-bzh genome [4] | |
1_root.bw | mRNA read coverage of root by mapping to Darmor-bzh | |
2_stem.bw | mRNA read coverage of stem by mapping to Darmor-bzh | |
3_leaf.bw | mRNA read coverage of leaf by mapping to Darmor-bzh | |
4_bud.bw | mRNA read coverage of bud by mapping to Darmor-bzh | |
5_flower.bw | mRNA read coverage of flower by mapping to Darmor-bzh | |
6_silique.bw | mRNA read coverage of silique by mapping to Darmor-bzh | |
7_silique_wall.bw | mRNA read coverage of silique wall by mapping to Darmor-bzh | |
8_seed.bw | mRNA read coverage of seed by mapping to Darmor-bzh | |
bna_2311_SNPs_InDels.vcf | Information of SNPs and InDels identified in population of 2,311 B. napus accessions Darmor-bzh genome |
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