My lab studies the fruit fly (Drosophila melanogaster), which is one of the most well-studied animal systems. Historically, fruit flies have been studied because the genetics is very easy. Early on, the way to study genetics was to cause the flies to become mutated (altering their DNA randomly), and then see what happened. Well, some pretty funky things happened.
Sometimes, the resulting flies looked all bristly -- researchers named that mutation "hedgehog". Sometimes, they looked like a tube -- researchers called that mutation, well, "tube". And so, names like "armadillo", "wingless", "cactus", "pipe", and "dachshund" were born.
Later, scientists found that these mutations mapped to genes within the flies' DNA. Naturally, these genes were named after the mutation that the researchers originally found.
It turns out that one of the first mutations geneticists worked with was a spontaneous mutation that they named "white". Well, guess what this mutation did? It turned the turned the flies' eyes from red to white. So when the genes were later named for the mutation involved in their discovery, the gene responsible for turning the flies' eyes red was called "white". Brilliant!
So this is why many genes in the fly genome are named backwards.