Genome Components
The BolBase database have collected three important genome components about Brassica oleracea, including 45,758 putative genes (about 35400 were anchored on pseudomolecular chromosome of Brassica oleracea genome), 307,789,645 bp repeat regions (representing 57% of all genome sequences for Brassica oleracea) and 3,581 Non-coding RNA (312 miRNAs, 517 rRNAs, 1434 snRNAs, 1318 tRNA).

Putative Genes Section

Method: all B.oleracea putative genes were predicted by Denovo prediction (Augustus, Genscan etc.), homolog prediction and EST prediction method, respectively. At last, all predicting results of putative gene sets were integrated into final genes sets by glean method.

Gene Clusters

       1. Gene Family

       2. Orthologs Group (OrthoMCL Cluster)

Choose a Number of Range:     

       3. Tandem Duplicated Arrays

Choose a Number:    

Putative Genes List
       1.Chromosomes

C01   C02   C03   C04   C05   C06   C07   C08   C09   Cun

       2. Scaffolds

Repeat elements Section

Method: LTR_FINDER, Piler, RepeatModeler and RepeatScout were used to search B.oleracea genome sequences. Through the generated repeats datasets by above method, we filtered out contaminated repeat sequences and constructed denovo repeats database. And then we employed repeatmasker with denovo repeats database to get all B.oleracea repeats datasets. In order to obtain accurately repeats regions, we manully check all B.oleracea repeats datasets by the structure characteristics and sequence homology.

Repeats Type
       1. Simple Repeats

  • SSR

       2. Transposable Elements

Repeat Element List
      1. Chromosomes

C01   C02   C03   C04   C05   C06   C07   C08   C09   Cun

       2. Scaffolds

Non-coding_RNAs Section

Method: Based on the structure characteristics of tRNA, we employed tRNAscan-SE-1.23 software to detect tRNA sequences from B.oleracea genome; and we used the sequence homology of plant full-length rRNA sequences to confirm location of rRNA on B.oleracea pseudochromosomes; We extracted miRNA and snRNA information by INFERNAL software of Rfam with Rfam-9.1 gene family covariance model.

Non-coding RNAs Type

Non-coding RNA List
      1. Chromosomes

C01   C02   C03   C04   C05   C06   C07   C08   C09   Cun

       2. Scaffolds

@2012 Department of Genomics and Molecular Biology, Oil Crops Research Institute.


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