Scientists compare 12 fruit fly genomes

To the average person, one fruit fly hovering around an overripe banana looks pretty much like any other. Researchers found that, at first glance, the genomes of the various types of fruit flies appear quite similar. However, a more detailed examination reveals that only 77 percent of the approximately 13,700 protein-coding genes in D. melanogaster are shared with all of the other 11 species.

Scientists observed that different regions of the fruit fly genomes, including protein-coding genes and gene families, are evolving at different rates. For example, genes involved in taste and smell, detoxification and metabolism, sex and reproduction, and immunity and defense appear to be the most rapidly evolving in the fruit fly genomes.

The findings suggest that these particular protein-coding genes likely evolve in the fruit fly genome as a result of adaptation to changing environments and sexual selection. For instance, the fruit fly species D. sechellia, whose population lives on the Seychelles islands in the Indian Ocean, is losing gustatory (taste) receptors approximately five times faster than other fruit fly species that generally encounter a more diverse set of foods than those available on an island.

In a surprising finding, researchers found that the genes that produce selenoproteins appear to be absent in the D. willistoni genome. Selenoproteins are responsible for reducing excess amounts of the mineral selenium, an antioxidant found in a variety of food sources. Selenoproteins are present in all animals, including humans. D. willistoni appears to be the first animal known to lack these proteins. However, researchers suggest that D. willistoni may possibly encode selenoproteins in a different way, opening a new avenue for further research.

A project leader and co-author for the studies, William M. Gelbart, Ph.D., of Harvard University in Cambridge, Mass., said “The availability of the 12 fruit fly genomes resulted in a dramatic increase in resolution allowing us to examine how evolution has fine-tuned biological processes. Our work shows that discovery power increases with the number of genomes available for comparison.”

More than 40 companion manuscripts with further detailed analyses are in current and forthcoming issues of Bioinformatics, BioMed Central (BMC) Bioinformatics, BMC Evolution Biology, BMC Genomics, Genetics, Genome Biology, Genome Research, Journal of Insect Science, Molecular Biology and Evolution, Nature Genetics, Public Library of Science (PLoS) Genetics, PLoS One, Proceedings of the National Academy of Sciences, and Trends in Genetics.

In addition to their analyses aimed at gaining a better understanding of genomic evolution, consortium scientists used the 12 fruit fly genomes to identify thousands of new genes and other functional elements. This work will bolster efforts to find all functional elements in the reference genome sequence of D. melanogaster.

“Comparing the 12 fruit fly genomes allowed us to recognize evolutionary signatures characteristic of each function. These signatures enabled us to distinguish and identify thousands of new functional elements.” said Manolis Kellis, Ph.D., of the Massachusetts Institute of Technology in Cambridge, Mass., and a co-author of the Nature papers.