First author Mahul Chakraborty looks through several specimens of fruit flies to identify new phenotypes. Photo: UCI

DNA has come a long way since the first genomes were sequenced at the cusp of the 21st century.

But a new study of a fruit fly’s complete DNA contends there is a whole other dimension to the complex coding in even that relatively-simple genetic structure. The nuances that have so far escaped scientific scrutiny could hold the secrets of evolutionary mutations, as well as disease, according to the paper published last week in the journal Nature Genetics.

“We uncovered a vast amount of hidden genetic variation during our analyses, much of which affects important traits within the common fruit fly, D. melanogaster,” said Mahul Chakraborty, postdoctoral scholar at the University of California – Irvine, and first author of the study.

The key is in the more complex patterns that occur over vast stretches of the DNA sequences, according to the paper. Such structural variants (SVs) are vital to the creation and alteration of complex traits, according to the paper.

The genetic information was extracted from two female fruit flies, and then sequenced at the University of California High-Throughput Genomics Facility. The resulting data was 18.7 gigabytes for the insects. The data was then merged to compare and contrast the DNA, especially in reference to differences between the two in resistance to cold temperatures and to pesticides like nicotinoids.

The result: one of the SVs hidden at the simpler genetic view actually increased the activity of one of the genes about 50 times, which appeared to account for greater resistance to nicotine, they conclude.

“The study is the first of its kind in complex organisms like the fruit fly,” added J.J. Emerson, UC-Irvine professor and leader of the scientific team. “With this unique resource in hand, we have already characterized several candidate structural variation which show evidence.”

The paper concludes that the whole new dimension in looking for DNA patterns could drive the next phase of discovery and innovation in biology.

“The ubiquity of hidden variation in genome structure is merely an indication of the extent of the underlying genetic variation governing phenotypes,” they write. “The extensive hidden variation we observe segregates in D. melanogaster, a species that likely harbors fewer complex structural features than humans or livestock, as well as crop species like wheat and maize.

“Consequently, we suggest that the true medical and agricultural impact of structural variation is likely to be much greater than the already considerable estimates made without recourse to multiple reference-grade assemblies,” they add.

Forensic Magazine has profiled how next-generation sequencing, or massively parallel sequencing, has begun to show variation at the levels of alleles that has been previously unnoticed in traditional DNA sequencing methods.