Tuesday, 2 August 2022

Evolution News - An Entire Bacterial Genome Integrated Into the Genome of a Fruit Fly

2022 News - Researchers Discover One of the Largest Known Bacteria-to-Animal Gene Transfer Inside a Fruit Fly | University of Maryland School of Medicine

The fruit fly, Drosophila ananassae, is not just an ordinary fruit fly. In fact it's not just a fruit fly. It is actually a hybrid but not even a bog-standard hybrid between related species. It is actually a hybrid between two entirely different organisms. It is a hybrid between a fruit fly and a bacterium. This fusion of genomes is believed to have happened about 8,000 years ago.

So, if anything was designed to challenge the childish creationist notion of 'kinds' it is this biological peculiarity, because it is not a fruit fly and it's not a bacterium. It's Drosophila ananassae.

Biologically, there is no real mystery here because horizontal gene transfer has been known to science for several decades and the bacterium involved, Wolbachia is a common endoparasite or endosymbiont in many insects. Some insects have even come to depend on it for some functions, such as reproduction in the tsetse fly, resistance to some viruses and avoiding being parasitised by parasitoid wasps.

But what is unusual is for an entire genome, from what was presumably an endosymbiont, to be transferred to the host genome. The scientists from the University of Maryland who made this discovery have published their findings, open access, in the journal Cell Biology. The press release from the University of Maryland explains the research and its significance:
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.

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. Julia C. Dunning Hotopp, senior author
Professor of Microbiology and Immunology
School of Medicine and Institute for Genome Sciences
University of Maryland
Baltimore, MD, USA.
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.

This new research shows basic science at its best. It will make a contribution to our understanding of evolution and may even prove to help us understand how microbes contribute to human health.

Dean E. Albert Reece, MD, PhD, MBA, (not involved with the research)
Executive Vice President for Medical Affairs,
Akiko K. Bowers Distinguished Professor, and Dean University of Maryland School of Medicine
Baltimore, MD, USA.
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.

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.

The team give more technical details in their open access paper in Cell Biology:
  • Wolbachia DNA integrated into Drosophila ananassae chromosome 4 <8,000 years ago
  • The DNA integrated via nonhomologous recombination in at least two separate locations
  • Some regions, like the cytoplasmic incompatibility genes, have high copy numbers
  • There are transcripts generated from areas of the integrated DNA that are spliced

Eukaryotic genomes can acquire bacterial DNA via lateral gene transfer (LGT).1 A prominent source of LGT is Wolbachia,2 a widespread endosymbiont of arthropods and nematodes that is transmitted maternally through female germline cells.3,4 The DNA transfer from the Wolbachia endosymbiont wAna to Drosophila ananassae is extensive5, 6, 7 and has been localized to chromosome 4, contributing to chromosome expansion in this lineage.6 As has happened frequently with claims of bacteria-to-eukaryote LGT, the contribution of wAna transfers to the expanded size of D. ananassae chromosome 4 has been specifically contested8 owing to an assembly where Wolbachia sequences were classified as contaminants and removed.9 Here, long-read sequencing with DNA from a Wolbachia-cured line enabled assembly of 4.9 Mbp of nuclear Wolbachia transfers (nuwts) in D. ananassae and a 24-kbp nuclear mitochondrial transfer. The nuwts are <8,000 years old in at least two locations in chromosome 4 with at least one whole-genome integration followed by rapid extensive duplication of most of the genome with regions that have up to 10 copies. The genes in nuwts are accumulating small indels and mobile element insertions. Among the highly duplicated genes are cifA and cifB, two genes associated with Wolbachia-mediated cytoplasmic incompatibility. The wAna strain that was the source of nuwts was subsequently replaced by a different wAna endosymbiont. Direct RNA Nanopore sequencing of Wolbachia-cured lines identified nuwt transcripts, including spliced transcripts, but functionality, if any, remains elusive.

So, there is a lot for Creationists to think about in this finding:
  1. What 'kind' is Drosophila ananassae, with its combination of both a Drosophila genome and aWolbachia genome?
  2. What happened about 8,000 years ago when this combination occurred, if it wasn't evolution, in this case by horizontal gene transfer - one of the recognised mechanisms by which evolution occurs, according the Theory of Evolution.
  3. Why should the fact that the entire genome of an unrelated species can integrate fully into the genome of another, not be regarded as evidence of common ancestry, albeit in this case, very remote common ancestry?

Thank you for sharing!

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