In the TV series Star Trek, the Borg are cybernetic aliens that assimilate humans and other creatures as a means of achieving perfection. So when Jill Banfield, a geomicrobiologist at the University of California, Berkeley, sifted through DNA in the mud of her backyard and discovered a strange linear chromosome that included genes from a variety of microbes, her Trekkie son proposed naming it after the sci-fi aliens.
The new type of genetic material was a mystery. Maybe it was part of a viral genome. Maybe it was a strange bacterium. Or maybe it was just an independent piece of DNA existing outside of cells. Whatever it is, it's "pretty exciting," says W. Ford Doolittle, an evolutionary biologist at Dalhousie University who was not involved with the work.
Researchers have found many examples of DNA floating independently outside the chromosome or chromosomes that make up an organism's standard genome. Small loops called plasmids, for example, exist inside microbes and ferry genes for thwarting antibiotics among different kinds of bacteria.
But Banfield wasn't looking for DNA that could move between organisms. Instead, she and graduate student Basem Al-Shayeb were searching for viruses that infect archaea, a type of microbe often found in places devoid of oxygen.
Researchers have found many examples of DNA floating independently outside the chromosome or chromosomes that make up an organism's standard genome. Small loops called plasmids, for example, exist inside microbes and ferry genes for thwarting antibiotics among different kinds of bacteria.
But Banfield wasn't looking for DNA that could move between organisms. Instead, she and graduate student Basem Al-Shayeb were searching for viruses that infect archaea, a type of microbe often found in places devoid of oxygen.
They would dig 1 meter or more below the surface and collect mud samples that might harbor archaea and their viruses. Next, they would sequence every stretch of DNA in the samples and use sophisticated computer programs to scan for sequences that signified a virus, rather than any other organism.
"We started off with a piece of mud and 10 trillion pieces of DNA," Banfield says. One sample, taken from the mud on her property, contained a gene-filled stretch of DNA almost 1 million bases long—and more than half the genes were novel.
"We started off with a piece of mud and 10 trillion pieces of DNA," Banfield says. One sample, taken from the mud on her property, contained a gene-filled stretch of DNA almost 1 million bases long—and more than half the genes were novel.
This linear stretch of DNA also had a particular pattern of bases at its beginning and end, distinct stretches of repetitive DNA between its genes, and two places along the sequence where DNA duplication could begin—which indicated the Borg could make copies of itself. Together, this suggested it was not just a random concoction of genes.
After they identified the first Borg sequence, the researchers began to scan microbial DNA in public databases to see whether they could find anything similar. They found a few variations in groundwater from Colorado—there, the first purported Borg showed up about 1 meter deep and got more abundant deeper down.
After they identified the first Borg sequence, the researchers began to scan microbial DNA in public databases to see whether they could find anything similar. They found a few variations in groundwater from Colorado—there, the first purported Borg showed up about 1 meter deep and got more abundant deeper down.
Other versions showed up in DNA from the discharge of an abandoned mercury mine in Napa, California, and from a shallow riverbed of the East River in Colorado.
Altogether, the researchers isolated 23 sequences they think may be Borgs—and 19 they have identified as having all the characteristics of the first Borg they discovered, they write this week on the preprint server bioRxiv.
Altogether, the researchers isolated 23 sequences they think may be Borgs—and 19 they have identified as having all the characteristics of the first Borg they discovered, they write this week on the preprint server bioRxiv.
Some are almost 1 million bases long. "I don't think anything else that's been discovered is as big as these guys are," among previously known extrachromosomal DNA elements, Doolittle says. READ MORE...
