Fruit fly genome contains whole genomes of a kind of bacteria, study finds

A fruit fly genome is not a just made up of fruit fly DNA – at least for one fruit fly species. New research from the University of Maryland School of Medicine's (UMSOM) Institute for Genome Sciences (IGS) shows that one fruit fly species contains whole genomes of a kind of bacteria, making this finding the largest bacteria-to-animal transfer of genetic material ever discovered. The new research also sheds light on how this happens.

The IGS researchers, led by Julie Dunning Hotopp, PhD, Professor of Microbiology and Immunology at UMSOM and IGS, used new genetic long-read sequencing technology to show how genes from the bacteria Wolbachia incorporated themselves into the fly genome up to 8,000 years ago.

The researchers say their findings show that unlike Darwin's finches or Mendel's peas, genetic variation isn't always small, incremental, and predictable.

Scientist Barbara McClintock first identified "jumping genes" in the 1940s like those that can move around within or transfer into other species genomes. However, researchers continue to discover their significance in evolution and health.

We did not have the technology previously to unequivocally demonstrate these genomes-inside-genomes showing such extensive lateral gene transfer from the bacteria to the fly. We used state-of-the-art long-read genetic sequencing to make this important discovery."

Julie Dunning Hotopp, Professor, Microbiology and Immunology, University of Maryland School of Medicine

The new research has been published in the June issue of Current Biology.

In the past, researchers had to break DNA into short pieces in order to sequence it. Then they needed to assemble them, like a jigsaw puzzle, to look at a gene or section of DNA. Long-read sequencing, however, allows for sequences more than 100,000 DNA letters, turning a million-piece jigsaw puzzle into one made for toddlers.

In addition to the long reads, the researchers validated junctions between integrated bacteria genes and the host fruit fly genome. To determine if the bacteria genes were functional and not just DNA fossils, the researchers sequenced the RNA from fruit flies specifically looking for copies of RNA that were created from templates of the inserted bacterial DNA. They showed the bacteria genes were encoded into RNA and were edited and rearranged into newly modified sequences indicating that the genetic material is functional.

An analysis of these unique sequences revealed that the bacteria DNA integrated into the fruit fly genome in the last 8,000 years-;exclusively within chromosome 4-;expanding the chromosome size by making up about 20 percent chromosome 4. Whole bacterial genome integration supports a DNA-based rather than an RNA-based mechanism of integration.

Dr. Dunning Hotopp and colleagues found a full bacterial genome of the common bacteria Wolbachia transferred into the genome of the fruit fly Drosophila ananassae. They also found nearly a complete second genome and much more with almost 10 copies of some bacterial genome regions.

"There always have been some skeptics about lateral gene transfer, but our research clearly demonstrates for the first time the mechanism of integration of Wolbachia DNA into this fruit fly's genome," Dr. Dunning Hotopp said.

"This new research shows basic science at its best," said Dean E. Albert Reece, MD, PhD, MBA, who is also Executive Vice President for Medical Affairs, UM Baltimore, the John Z. and Akiko K. Bowers Distinguished Professor, and Dean, University of Maryland School of Medicine. "It will make a contribution to our understanding of evolution and may even prove to help us understand how microbes contribute to human health."

Wolbachia is an intracellular bacteria that infects numerous types of insects. Wolbachia transmits its genes maternally through female egg cells. Some research has showed that these infections are more mutualistic than parasitic, giving insects advantages, such as resistance to certain viruses.

Sequenced just three years before the human genome, fruit flies have long been used in genomic research because of the abundance of common fly-human genetic similarities. In fact, 75 percent of genes causing human disease can also be found in the fruit fly.

Authors from the Institute of Genome Sciences, University of Maryland School of Medicine, at the time of writing, include Eric S. Tvedte; Mark Gasser; Xuechu Zhao, Lab Research Specialist; Luke J. Tallon, Executive Scientific Director, Maryland Genomics; Lisa Sadzewicz, Executive Director, Maryland Genomics Administration; Robin E. Bromley, Lab Research Supervisor; Matthew Chung; John Mattick, PostDoc, and Benjamin C. Sparklin.

Eric S. Tvedte is currently affiliated with NCBI at the National Institutes of Health, Bethesda, MD; Mark Gasser is currently affiliated with Applied Physics Laboratory, Johns Hopkins University, Laurel, MD; Matthew Chung is currently affiliated with the National Institute for Allergy and Infectious Disease at the National Institutes of Health, Bethesda, MD; and Benjamin C. Sparkin is currently affiliated with AstraZeneca, Rockville, MD.

This work was supported by National Institute of Allergy and Infectious Diseases grant U19AI110820 and National Institutes of Health grant R01CA206188.