Comparative Genomics

The genomes of related species exhibit conservation of gene order (collinearity) and conservation of gene sequence because the genomes of present day species have evolved from common ancestral genomes. Comparative genomics enables the application of information gained from intensely studied model systems to related organisms that are important for human health and agriculture.

Model organisms offer many advantages, often including small genomes (with less repetitive DNA), short generation times and well established genetic and genomics resources. The model organism of interest to research at the AAFC Saskatoon Research Centre is Arabidopsis thaliana because it is a member of the family Brassicaceae (cruciferae) and therefore closely related to Brassica including canola (Brassica rapa and B. napus), oilseed mustards (B. nigra, B. juncea and Sinapis alba) and a wide variety of vegetable crops such as brussel sprouts and broccoli (B. oleracea). Arabidopsis has been the focus of genetic and biochemical research for over 50 years, more recently a large number of genomic resources have been amassed for this species including the genome sequence that was completed and released at the end of 2000 (Arabidopsis Genome Initiative, 2000). It is expected that comparative genome analysis between Arabidopsis and related crop species will expedite research in the more complex Brassica genomes.

The AAFC Saskatoon Research Centre has established a database of partially sequenced expressed genes (or ESTs) from B. napus. (EST Inquries). These sequences provide an excellent resource for a number of research activities, including comparative mapping to target regions in Arabidopsis, identifing expressed candidate genes, anchoring Brassica BAC contigs, SNP discovery, and develoing micro-arrays to monitor changes in gene expression. We are exploiting the strong conservation of DNA nucleotide sequence observed between Brassica species and Arabidopsis (average 87% identity in the coding regions) to identify the closest Arabidopsis gene homologue of each B. napus EST. As of August 10, 2001, the Arabidopsis genome contains annotations for approximately 27,000 genes, of which 40-50% have been assigned a function. Homology between the annotated genes of the Arabidopsis genome and the related B. napus EST sequences allows us to identify not only the comparative map position of each EST within the Arabidopsis genome but the likely function of many ESTs.

There are standard bioinformatics tools available, such as BLAST (Basic Local Alignment Search Tool) that will find regions of similarity between given sequences. Although these are the standard tools for comparing genomic sequence, the plain text report they produce is not always the most informative way to visualize the relationship. This is especially true when trying to visualize alignments over a large region such as a BAC, average size 100,000bp; a chromosome, average size 20-30 Mbp; or the whole genome. We have developed a software application to assist in visualizing such relationships.

• Access the Brassica / Arabidopsis Comparative Genome Viewer here.