I think usually the gene name isn't changed. For example, I've noticed that bacterial genomes tend to start with the dnaA gene (many different sequences). I li

I think usually the gene name isn't changed. For example, I've noticed that bacterial genomes tend to start with the dnaA gene (many different sequences). I like to think of genes as their amino acid or dna sequence only, and internally whenever I need to manage a ton of sequences their names are just hashes of those sequences.