If bacteria can’t grow in a Petri dish, sequencing them is difficult.
What’s the News: Want the genome of a bacterium you found in your belly button? Or, for that matter, of a bacterium producing a promising new antibiotic? Well, unless you can get it to thrive in a Petri dish and create a billion sister cells for analysis, you’re out of luck.
But sequencing the genomes of notoriously finicky bacteria, like those on skin, could be on the horizon with a new procedure that bypasses the Petri dish step. Pairing a new algorithm with an earlier technique, scientists from the Venter Institute and their collaborators can now get all that information from a single cell.
Scientists have now sequenced the genome of the Atlantic cod, revealing something unusual: the cod is missing an important component of the adaptive immune system found in almost all jawed vertebrates. In particular, when the researchers compared the cod’s genome to that of the stickleback (a closely related fish that has already been sequenced), they saw that the Atlantic cod does not have genes that code for the proteins MHC II, CD4, and invariant chain, all of which work together to help the body recognize and fight off invading bacteria and parasites.
What’s the News: Due to a vicious disease, the population of the endangered Tasmanian devil has decreased by at least 70 percent since 1996. The cancer, devil facial tumor disease, spreads when an infected devil bites another, typically during feeding or mating. Because Tasmanian devils are so genetically similar, their bodies don’t recognize the intruding cancer cells as foreign.
But now, researchers have sequenced the genome of two devils and created a genetic test that could help breeders select genetically diverse mates. The test will help conservationists breed future generations of Tasmanian devils that are prepared for the cancer, as well as other types of diseases.
Considering the huge numbers of species that have had their DNA sequenced in the wake of the genomics revolution, it might be surprising that scientists are so excited about a tiny freshwater crustacean. But this one is special: The genome of the water flea contains a staggering 30,907 genes—the most ever seen in an animal, and about 8,000 more than humans have.
Daphnia has a large number of never-before seen genes…. “More than one-third of Daphnia‘s genes are undocumented in any other organism — in other words, they are completely new to science,” said Don Gilbert, coauthor and Department of Biology scientist at IU Bloomington. [Discovery News]
According John Colbourne, coauthor of the study in Science, those never-before-seen genes are not dead weight, but rather some of the most important in the crustacean’s genome for responding to changes in its environment.
Not all of the crustacean’s genes are active at any given time. Rather, a large portion of them are switched on or off with changes in the flea’s environment. They are “more or less environment-specific,” Colbourne says. Although they are “coding for the same proteins, they’re being expressed differently depending on what environmental stresses you expose the animal to.” [Scientific American]
Welcome to the family of critters with sequenced genomes, orangutans. In Nature this week, scientists unveil the draft DNA sequencing of our great ape cousins—the only great apes that live exclusively in Asia.
The researchers assembled the draft genome of the female Sumatran orangutan (Pongo abelii) using a whole-genome “shotgun” strategy, an old-fashioned approach that cost about $20 million. In addition, the researchers gathered sequence data from five wild Sumatran orangutans and five Bornean orangutans (Pongo pygmaeus) using a faster and thousandfold cheaper next-generation platform. [LiveScience]
What did scientists find in there? For one thing, orangutans share about 97 percent of the their genome with humans, compared to the 99 percent we famously share with chimpanzees. The two orangutan species—inhabiting the Indonesian islands of Borneo and Sumatra—diverged about 400,000 years ago, lead author Devin Locke says. That’s much more recently than scientists had thought.
They also discovered that over the last 15 million years, orangutan DNA changed at a different rate than either ours or chimps’. Orangutans have undergone fewer mutations of the DNA, have a lower gene turnover rate, and have fewer duplicated DNA segments.
In a medical sense, you’d be wise to steer clear of filoviruses, a group that includes the deadly Ebola, and bornaviruses, which cause neurological diseases. But in a genetic sense, it may not be possible to avoid them. A new study in PLoS pathogens shows that bits and pieces of these viruses have been floating around in the human genome, as well as those of other mammals and vertebrates, for millions of years.
It’s not that having genetic material left behind by viruses is odd—previous research had shown that viruses account for 8 percent of the human genome. But scientists thought most of that material came from retroviruses, which use their host’s DNA to replicate and leave some of their genetic material behind. What’s weird about this is that filoviruses and bornaviruses are not retroviruses—they’re RNA viruses, which don’t use the host to reproduce in the same way.