Gene nomenclature by default, or BLASTing to Babel

The current proliferation of mammalian genomes is creating a nomenclature issue caused by naming genes based on their best BLAST hit to a gene in another annotated genome. The rat genome is relying heavily on the mouse genome for nomenclature, but not all rat genes have direct orthologues in the mouse; often, there are paralogous groups of genes -- due to expansions of that gene subfamily in one or the other genome. Many of these genes have already been assigned names in the rat, so that renaming them based on BLAST scores leads to duplicate sets of names. The supposed orthology created by name sharing across genomes is not always found. These inaccurate names are appearing in frequently used sites, such as the University of California Santa Cruz Genome Browser. The example of rat cytochrome P450 (Cyp) genes is presented here, but other gene families are also likely to be affected.