BTriDB: a comprehensive database of triplicated blocks for Brassica lineage

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Introduction
Brassica_evolution

Based on genome-wide, sequence-level comparative analysis of conserved sequence blocks, A. thaliana has undergone two recent genome duplication events (named α and β) within the crucifer lineage and one genome triplication event (named γ) shared with most dicots (asterids and rosids). A.thaliana and Brassica lineage were estimated to have diverged from a common ancestor approximately 20 million years ago. And about 14 million years ago,  Brassica ancestor underwent genome self-triplication event. And then, B. rapa and B. oleracea has diverged from Brassica ancestor about 4 million years ago. So, every block detected in A.thaliana was triplicated blocks in Brassica lineage.

Compared to 24 conserved blocks (A~X) on A.thaliana genome, triplicated blocks in B.rapa and B.oleracea were classified and according to their relative gene densities of homologous regions, syntenic sub-blocks with the highest gene densities were grouped as sub-genome LF, or sub-genome III. The sub-blocks with moderate gene densities were grouped as sub-genome MF1, or sub-genome I. And the sub-blocks with the least genes were grouped as sub-genome MF2, sub-genome II.

BSyndb (The Brassica Syntenic regions database) was constructed to provide users a useful and unique triplicated genes database in the field of studying  Brassica lineage. In this database, it supplied genomic data, transcriptome data, comparative genome information based on triplicated blocks, this data includes psuedochromosome sequence, scaffold sequence, genome structure, and gene location, gene structure, protein feature, gene functional annotation, and so on. All of the data can be downloaded on line very conveniently. This database also provided browse, search, download, manual,  sitemap, and instruction of web server. All of data information will update constantly. It is a usefulb database for scientific research in the genetics and molecular breeding fields.

News
  • (2012-03-26) The informations of Brassica comparative genomics were intergrated into Bolbase.
  • (2011-06-25) Brassica oleracea genome database  was on line.
  • (2011-04-13) Brassica oleracea genome gene function annotation was complete.
  • (2010-11-25) Brassica oleracea genome gene prediction was complete.
  • (2010-10-25) Brassica oleracea genomic map was complete.
  • (2010-08-01) Brassica oleracea detail genome assembly completely.
  • (2010-06-29) Brassica oleracea draft genome assembly completely.
  • (2009-02-17) Brassica oleracea genome project was launched.

Resources Links

NCBI

EMBL-EBI

DDBJ

KEGG

JGI

Phytozome

InterproScan

TAIR

BRAD

CPAN

MySQL

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Journals Links

NATURE

NATURE GENETICS

SCIENCE

Nucleic Acids Research

Bioinformatics

BMC Plant Biology

BMC Genomics

BMC bioinformatics

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