BnVIR Brassica napus variation information resource
eg: AT5G10140
 or FLC
————Bridging the genotype–phenotype gap to accelerate mining candidate variation of traits in Brassica napus

// Brief introduction of JBrowser module

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
// Reference

[1] Buels, R., Yao, E., Diesh, C.M., Hayes, R.D., Munoz-Torres, M., Helt, G., Goodstein, D.M., Elsik, C.G., Lewis, S.E., Stein, L., et al. (2016). JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 17: 66.
[2] Liu, D., Yu, L., Wei, L., Yu, P., Wang, J., Zhao, H., Zhang, Y., Zhang, S., Yang, Z., Chen, G., et al. (2021). BnTIR: an online transcriptome platform for exploring RNA-seq libraries for oil crop Brassica napus. Plant Biotechnol. J. 19: 1895-1897.
[3] Song, J.M., Guan, Z., Hu, J., Guo, C., Yang, Z., Wang, S., Liu, D., Wang, B., Lu, S., Zhou, R., et al. (2020). Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nat. Plants 6: 34-45.
[4] Chalhoub, B., Denoeud, F., Liu, S., Parkin, I.A., Tang, H., Wang, X., Chiquet, J., Belcram, H., Tong, C., Samans, B., et al. (2014). Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.Science 345: 950-953.

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