Tuesday, November 3, 2009

The Vibrio pangenome

Shortly after I started grad school, the first bacterial genome sequences were published. In those days, genome sequencing resources were devoted to getting a broad sample of different bacteria and archaea. It was some time before different strains of the same bacterial species would be completely sequenced. When that finally happened, we were surprised to find that bacterial strains could have very different genomes, sometimes with thousands of different genes. In genomes that have only 2000-5000 genes to begin with, strains could differ by 20%. Along with other studies, this genome sequencing revealed just how much gene transfer goes on among bacteria and archaea.

From these came the concept of the "pangenome," the full complement of genes found in any genomes from a closely-related set of bacteria or archaea. The pangenome represents the full genetic potential of those organisms. An individual strain might have only a small fraction of this pangenome, but since gene transfer can happen relatively easily, members of a particular a strain could acquire genes from other strains.

Related to the concept of the pangenome is the core genome: the genes found in all the genomes of a closely-related set of organisms. Not surprisingly, the more bacterial species you compare, the bigger the pangenome, and the smaller the core genome.

A new paper in BMC Evolutionary Biology reports on the pangenome of Vibrio species. Vibrio are common marine bacteria. One species, V. cholerae, causes cholera in humans (clever name, eh?). Thompson et al. looked at 32 different Vibrio genomes and found that the overall pangenome contained 26,504 genes. That's approaching the genetic complexity of mammals (humans have on the order of 25,000 genes). Despite this massive pangenome, the core Vibrio genome is only 488 genes, which is about the size of the smallest bacterial genomes that we know of. For the strains of V. cholerae, the pangenome is 6,923 genes and the core genome is 1,520 genes.

Long gone are the simple mendelian days of one gene:one trait, passed from parent to child. Vibrio species mobilize DNA and share a large array of genes to an amazing degree. We've learned a lot of things since we started sequencing genomes, but the thing that sticks out to me is how little we know about how organisms actually work.

Thompson et al. 2009. Genomic taxonomy of vibrios. BMC Evolutionary Biology 9:258. doi:10.1186/1471-2148-9-258