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Category Archives: genomics

Carnivorous plant has deleted most of its junk DNA

The business end of a bladderwort, ready to suck in prey.
Enrique Ibarra-Laclette, Claudia Anahí Pérez-Torres and Paulina Lozano-Sotomayor.

Over the weekend Nature released a paper that describes the genome of a fascinating creature with a rather unglamorous name: the bladderwort. These plants live in swampy or liquid environments and find it hard to get sufficient nutrients there, so in order to survive the plants have turned carnivorous. The bladders that give the group of related species its name are actually feeding organs. When an organism brushes up against their triggers, the bladders swell by sucking in the surrounding water, along with any organisms it carries. They then seal off, allowing the plant to digest its prey.

The oddities continue at the molecular level. The genome of this bladderwort, Utricularia gibba, contains more genes than are found in the human genome (something common in plants). But it carries them all in a compact genome that's only a bit over 2 percent of the size of the human version. It does this largely by getting rid of just about everything that could possibly be considered superfluous—which may tell us important things about whether most of the DNA we carry really is superfluous.

First, the details, then some perspective.

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Carnivorous plant has deleted most of its junk DNA

The business end of a bladderwort, ready to suck in prey.
Enrique Ibarra-Laclette, Claudia Anahí Pérez-Torres and Paulina Lozano-Sotomayor.

Over the weekend Nature released a paper that describes the genome of a fascinating creature with a rather unglamorous name: the bladderwort. These plants live in swampy or liquid environments and find it hard to get sufficient nutrients there, so in order to survive the plants have turned carnivorous. The bladders that give the group of related species its name are actually feeding organs. When an organism brushes up against their triggers, the bladders swell by sucking in the surrounding water, along with any organisms it carries. They then seal off, allowing the plant to digest its prey.

The oddities continue at the molecular level. The genome of this bladderwort, Utricularia gibba, contains more genes than are found in the human genome (something common in plants). But it carries them all in a compact genome that's only a bit over 2 percent of the size of the human version. It does this largely by getting rid of just about everything that could possibly be considered superfluous—which may tell us important things about whether most of the DNA we carry really is superfluous.

First, the details, then some perspective.

Read 9 remaining paragraphs | Comments

Carnivorous plant has deleted most of its junk DNA

The business end of a bladderwort, ready to suck in prey.
Enrique Ibarra-Laclette, Claudia Anahí Pérez-Torres and Paulina Lozano-Sotomayor.

Over the weekend Nature released a paper that describes the genome of a fascinating creature with a rather unglamorous name: the bladderwort. These plants live in swampy or liquid environments and find it hard to get sufficient nutrients there, so in order to survive the plants have turned carnivorous. The bladders that give the group of related species its name are actually feeding organs. When an organism brushes up against their triggers, the bladders swell by sucking in the surrounding water, along with any organisms it carries. They then seal off, allowing the plant to digest its prey.

The oddities continue at the molecular level. The genome of this bladderwort, Utricularia gibba, contains more genes than are found in the human genome (something common in plants). But it carries them all in a compact genome that's only a bit over 2 percent of the size of the human version. It does this largely by getting rid of just about everything that could possibly be considered superfluous—which may tell us important things about whether most of the DNA we carry really is superfluous.

First, the details, then some perspective.

Read 9 remaining paragraphs | Comments

Carnivorous plant has deleted most of its junk DNA

The business end of a bladderwort, ready to suck in prey.
Enrique Ibarra-Laclette, Claudia Anahí Pérez-Torres and Paulina Lozano-Sotomayor.

Over the weekend Nature released a paper that describes the genome of a fascinating creature with a rather unglamorous name: the bladderwort. These plants live in swampy or liquid environments and find it hard to get sufficient nutrients there, so in order to survive the plants have turned carnivorous. The bladders that give the group of related species its name are actually feeding organs. When an organism brushes up against their triggers, the bladders swell by sucking in the surrounding water, along with any organisms it carries. They then seal off, allowing the plant to digest its prey.

The oddities continue at the molecular level. The genome of this bladderwort, Utricularia gibba, contains more genes than are found in the human genome (something common in plants). But it carries them all in a compact genome that's only a bit over 2 percent of the size of the human version. It does this largely by getting rid of just about everything that could possibly be considered superfluous—which may tell us important things about whether most of the DNA we carry really is superfluous.

First, the details, then some perspective.

Read 9 remaining paragraphs | Comments

Carnivorous plant has deleted most of its junk DNA

The business end of a bladderwort, ready to suck in prey.
Enrique Ibarra-Laclette, Claudia Anahí Pérez-Torres and Paulina Lozano-Sotomayor.

Over the weekend Nature released a paper that describes the genome of a fascinating creature with a rather unglamorous name: the bladderwort. These plants live in swampy or liquid environments and find it hard to get sufficient nutrients there, so in order to survive the plants have turned carnivorous. The bladders that give the group of related species its name are actually feeding organs. When an organism brushes up against their triggers, the bladders swell by sucking in the surrounding water, along with any organisms it carries. They then seal off, allowing the plant to digest its prey.

The oddities continue at the molecular level. The genome of this bladderwort, Utricularia gibba, contains more genes than are found in the human genome (something common in plants). But it carries them all in a compact genome that's only a bit over 2 percent of the size of the human version. It does this largely by getting rid of just about everything that could possibly be considered superfluous—which may tell us important things about whether most of the DNA we carry really is superfluous.

First, the details, then some perspective.

Read 9 remaining paragraphs | Comments

Scientists get the coelacanth genome and a hint of the origin of limbs

A coelacanth head at the Smithsonian Museum of Natural History.
dctim1

The coelacanth was discovered in 1938, but scientists already knew what the organism looked like. It's the lone representative of a lineage that we knew from fossils, the last of which were preserved while the dinosaurs still roamed the earth. Thus, the coelacanth earned the nickname of "living fossil," but that's a bit misleading. Although it looks similar, we have no real idea of how much or how little the organism has changed during those millions of years. After all, on the DNA level, the tuatara (the last representative of a lineage that originated in the Triassic) is the fastest evolving creature we know of.

Still, the coelacanth is interesting to scientists. It, along with the lungfish, is representative of a group called lobe-finned fishes, which have four limb-like fins. A series of fossils have revealed that these fins gradually transformed into the four limbs of modern tetrapods such as reptiles, birds, amphibians, and mammals. So, the coelacanth could tell us something about the base state that our limbs started out in. To find out, researchers have now sequenced its genome, and they found that genes essential to constructing our limbs were already active in the fins of the coelacanth.

The genome itself is just another example of all we can do with the massive DNA sequencing capacity that we've built up. Things only get interesting when you compare the coelacanth's genome to the genomes of other species. These tests do show that the coelacanth lives up to its dinosaur-era reputation, as its proteins are changing at the lowest rate of any vertebrate we've looked at. The new genome also makes it clear that the lungfish is more closely related to tetrapods than the coelacanth.

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No, the Neanderthal genome has not been completed

The new genome (in red) is shown in relationship to other human genomes.
http://www.eva.mpg.de/neandertal/index.html

Today, the people behind the Neanderthal genome project (Svante Pääbo's group at the Max Planck Institute) loosed yet another Neanderthal genome on the world, a genome that many press outlets are calling "complete." This one comes from a single toe bone found in the same cave as the finger bone that helped us identify the Denisovans, an extinct group of humans who inhabited Asia tens of thousands of years ago. Apparently, something about the cave environment has preserved ancient DNA extremely well.

That good preservation, combined with improved techniques, has provided a very high quality new sequence. Genome sequences are obtained randomly, typically in stretches about a hundred bases long. Over something the size of a human genome (about 3 billion bases), this randomness means that some areas will be sequenced many, many times, and others will be missed entirely or contain errors that repeated sequencing would allow us to catch. The typical measure of quality for a genome is called "coverage," and that's simply the number of times the average base would be sequenced if every base was covered equally.

In this case, the genome has 50-fold coverage. That's well above draft quality (which tends to be around 30-fold), but there will definitely still be gaps, errors, and places in the genome that aren't sequenced at all. Still, that's about as good as we're likely to get with ancient genomes; the sequence includes almost all of the non-repetitive DNA found in the human genome, and it will provide a valuable resource for comparative studies.

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Bigfoot genome paper “conclusively proves” that Sasquatch is real

Bigfoot cares for its young.
Katy Kristin

It's not often you come across a scientific paper which notes that the information it covers is like something "seen on the television series Monster Quest." And you rarely read a paper which concludes, "The data conclusively proves that the Sasquatch exist as an extant hominin and are a direct maternal descendant of modern humans." But today, we have such a paper—and there's nothing usual about it, including the journal where it appears.

Back in December, our own Nate Anderson drove me to the bottle with a flurry of questions about cryptozoology. One of the big motivators of Nate's interest in sasquatch was a report that a Texas group had sequenced the creature's genome. Not surprisingly, the team behind this startling research had some trouble publishing a paper describing their results.

By all appearances, they've solved that problem... by establishing a brand new journal, called De Novo (I'm not kidding; they apparently bought an existing journal and renamed it). The journal's site appears to be a mix of clip art and some basic HTML. Though it claims to be "open access," the site actually charges $30 to see the bigfoot paper (although their press person was kind enough to provide Ars with a free copy). Payment requires a Google Wallet account.

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Polynesians reached South America, picked up sweet potatoes, went home

An artist's depiction of the canoes used by the Polynesians of the Hawaiian islands.
Hawaii.edu

The sweet potato was one of a number of crops domesticated in the Andes and, like many of the rest, it became a global crop in the colonial era. But there were some hints that the sweet potato may have already started its global sweep before the Europeans ever took a bite out of one. Some of the early European explorers, including Captain Cook, reported finding it in places like Hawaii. All of which implies that the Polynesians, who managed to spread widely across the Pacific, had made it all the way to South America.

But it was difficult to be sure, given that European travelers later enhanced its spread within the Pacific and elsewhere. This has also created a complex genetic legacy that obscures its origins. Now, researchers have gone back and obtained DNA from museum samples, including some collected by Cook's crew, and find that the DNA indicates that Polynesians made it as far as South America.

Archeological remains appear to place sweet potato cultivation in the core of Polynesia by the year 1200, and it spread with further migrations to places like New Zealand and Hawaii. It's possible that the plant had naturally spread as seeds across the ocean and the Polynesians learned to cultivate it independently. One of the arguments against this is the fact that the Polynesian terms for the crop appear to be closely related to its name in Quechua, the language of the Peruvian Andes. ("Kuumala" and derivatives vs. "kumara" and relatives.)

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Native Australians have had (carnal) knowledge of India

Vllanova

As genetic studies continue to expand in scope, one of the things they're revealing is the complexity of humanity's shared legacy. Rather than a clean expansion out of Africa, we've found that the ancestors of Europeans and Asians mated with Neanderthals, while the group that populated Australia and New Guinea later went on to mate with Denisovans—a group we didn't even know existed a decade ago.

The native population of Australia and New Guinea is also exceptional as it appears to be one of the earliest branches off the group that migrated out of Africa; initial studies suggested that it had been isolated for nearly 40,000 years, since the groups first crossed from Indonesia to an area called the Sahul, which includes Australia, New Guinea, and the areas between them that would be above sea level during the peak of ice ages. But a new study has done a more detailed analysis and found an indication that the supposedly isolated population received a genetic (and possibly cultural) infusion about 4,000 years ago. And that it came not from the nearby islands of Indonesia, but from the Indian subcontinent.

The authors were using a genome-wide scan for places where human populations are known to have single-base differences in their DNA (termed SNPs, for single-nucleotide polymorphisms). They used a panel of samples that covered area of interest, along with some from other islands lying between there and the Asian mainland. In addition, they included African, European, and mainland Asian samples.

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