Computational tools for Brassica-Arabidopsis comparative genomics

Area of Science:

• Genomics
• Bioinformatics
• Plant Science

Background:

• Comparative genomics between Brassica and Arabidopsis has relied on RFLP data, requiring significant interpretation.
• Recent advances provide extensive genome survey sequence (GSS) data and draft physical maps for Brassica species.
• The Multinational Brassica Genome Project is sequencing the Brassica rapa genome, enabling computational approaches.

Purpose of the Study:

• To develop databases and bioinformatics tools for Brassica comparative genomics.
• To create a draft physical map of Brassica rapa integrated with Arabidopsis genome sequence anchors.
• To explore novel methods for visualizing Brassica-Arabidopsis sequence homology data.

Main Methods:

• In silico mapping of all publicly available Brassica sequences to the Arabidopsis TIGR v5 genome sequence.
• Utilizing the ATIDB database with Generic Genome Browser (GBrowse) for data visualization.
• Employing a MySQL database with Perl BioColon API for data interrogation and mining of paralogous sequences.

Main Results:

• A draft physical map of Brassica rapa has been created and integrated with Arabidopsis genome sequence anchors.
• Publicly available Brassica sequences have been mapped in silico to the Arabidopsis genome and published in ATIDB.
• An in silico approach successfully identified paralogous sequences, with significance coded and partitioned using a multiple alignment tool.

Conclusions:

• Computational approaches, supported by new databases and tools, are revolutionizing Brassica comparative genomics.
• The developed tools facilitate a systematic dissection of Brassica genome structure and its relationship to Arabidopsis.
• Direct database interrogation via API enables extensive data mining for future genomic research.