BnIR Brassica napus multi-omics information resource ————A multi-omics database with various tools for Brassica napus research and breeding

About genomics

For the genome, based on the previously published BnPIR database, we added the data of Ningyou7 and Express617 genome assemblies [1-3]. Totally, we collected the published genomic datasets from 11 representative core germplasms and annotated the gene function, domains, GO terms, and metabolic pathways of genes. The genome alignment were performed, and the genomic modules of collinearity, gene indexes, and phylogenetic relationships of homologous genes were updated. Based on the phylogenetic tree of homologous genes constructed with Arabidopsis as the outgroup, users can browse and compare the gene structures and functional domains of homologous genes in the gene search module to understand whether the homologous genes have undergone functional differentiation at the sequence level. Gene cluster, Gene index, Gene family, Pathway and Transcription factor respectively provide the information query of gene cluster, gene index, gene family, pathway and transcription factor of 11 rapeseed genomes. Genome synteny provides Gbrowser_syn[4] and Dotplot[5] browser for users to browse the alignment results between genomes. Pan-browser provides the previously constructed rapeseed pan-genome browser[6].

Tutorials for each sub-module

  • Gene Search
  • Gene cluster
  • Gene family
  • Gene index
  • Genome synteny
  • Pan-browser
  • Pathway
  • Transcription factor(TF)
  • References

    1. Lee H, Chawla HS, Obermeier C, Dreyer F, Abbadi A, Snowdon R. Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus. Front Plant Sci. 2020; 11:496.
    2. Zou J, Mao L, Qiu J, Wang M, Jia L, Wu D, et al. Genome-wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed. Plant Biotechnol J. 2019; 17:1998-2010.
    3. Song JM, Liu DX, Xie WZ, Yang Z, Guo L, Liu K, et al. BnPIR: Brassica napus pan-genome information resource for 1689 accessions. Plant Biotechnol J. 2021; 19:412-414.
    4. McKay SJ, Vergara IA, Stajich JE. Using the generic synteny browser (GBrowse_syn). Curr Protoc Bioinformatics. 2010; Chapter 9:Unit-9.12.
    5. Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, et al. JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 2016; 17:66.
    6. Song JM, Guan Z, Hu J, Guo C, Yang Z, Wang S, et al. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nat Plants. 2020; 6:34-45.