Genome Digest

What researchers are learning as they sequence, map, and decode species’ genomes

By | December 7, 2012

Wikimedia, Hans HillewaertDecoding our daily bread

Species: Bread wheat, Triticum aestivum
Genome size: ~17 billion base pairs

Bread wheat is the third most-produced crop after maize and rice, and accounts for one fifth of all the calories consumed by humans each year. Naturally, then, researchers want to find ways to improve yields. But the bread wheat genome has long defied complete sequencing, largely because it’s so big—roughly 5 times the size of the human genome—and because it’s a complex hybrid comprising three separate genomes.

Now, researchers have used whole-genome shotgun techniques to generate a draft of its hexaploid genome, and compared it with the sequences of its diploid ancestral and progenitor genomes. They showed that many genes were lost in domestication, and identified several classes of genes involved in energy harvesting, metabolism, and growth that may be associated with crop productivity. The research should help scientists find genes related to desirable traits, such as drought and disease resistance, and breed those genes into new lines to boost yields and secure future supplies of this staple crop.

R. Brenchley et al., “Analysis of the bread wheat genome using whole-genome shotgun sequencing,” Nature, 491: 705-710, 2012.
 

Wikimedia, PkuczynskiThe whole hog

Species: Domestic pig, Sus scrofa domesticus
Genome size: ~3 billion base pairs

The domestic pig is an important livestock species, and a new annotated draft sequence of the genome of T.J. Tabasco—a female specimen from Illinois—should help breeders produce healthier, meatier pigs. But there is more to the pig genome than tastier bacon and ribs. Comparing the new genome sequence to those of wild pigs from Europe and East Asia, researchers revealed that domestic pigs have experienced rapid evolution of genes involved in olfaction and immune response. They also found many possible disease-causing variants, which should help to develop even better porcine models of human disease. And the research could improve prospects for using genetically engineered pigs to provide organs for transplantation into humans. The idea is that organs transplanted from transgenic pigs carrying genes that deceive the immune system of recipients would not be rejected. (For more on this topic, see The Scientist’s recent feature, “Replacement Parts.”)

M.A.M. Groenen et al., “Analysis of pig genomes provide insight into porcine demography and evolution,” Nature, 491: 393-398, 2012.
 

Wikimedia, KGHSketching a lethal invader

Species: Pancreatic ductal adenocarcinoma
Genome size: ~3.1 billion base pairs

Pancreatic cancer is among the deadliest of all cancers: only about 5 percent of patients survive more than 5 years, and there are few effective therapies. To better understand the disease, researchers performed exome sequencing on 99 tumors from patients with pancreatic ductal adenocarcinoma, the most common form of pancreatic cancer. They identified 2,016 mutations that result in changes to proteins, defining 16 known “significantly mutated” genes and several new ones, including a gene involved in DNA damage repair and several others best known for their roles in axon guidance during embryonic development. Together with analysis of animal models of the disease, the findings indicate that some axon guiding components feed into signaling pathways related to cancer development, and could point the way to potential new drug targets.

A. V. Biankin et al., “Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes,” Nature, 491: 399-405, 2012.
 

Wikimedia, Steve EvansCracking open the watermelon

Sepecies: Watermelon, Citrullus lanatus
Genome size: ~425 million base pairs

Favored for their sweet and juicy flesh, watermelons are eaten across the world. Now, an international team of researchers has squeezed out some fresh insights about the fruit’s genome. They sequenced the genome of an East Asian cultivar and compared it to sequences from 20 different watermelons from three sub-species, including wild varieties, to create a map of genetic variation and identify regions that have changed. It turns out that many genes related to disease resistance were lost during domestication. Armed with this information, commercial producers hope to recover some of these lost natural defenses. The researchers also analysed 23,440 protein-encoding genes, and identified genes valuable for fruit quality traits, such as sugar accumulation, which could help them to produce even sweeter watermelons.

S. Guo et al., “The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions,” Nature Genetics, doi:10.1038/ng.2470, 2012.
 

Wikimedia, Nick HobgoodRevealing a chemical relationship

Species: Tunicate bacterial symbiont, Candidatus Endolissoclinum faulkneri

Otherwise known as sea squirts, tunicates are filter-feeding marine animals that spend their lives attached to docks, rocks, and reefs. They contain all sorts of biologically active chemicals thought to be essential for survival, many of which are produced by symbiotic bacteria housed by the tunicate. One tropical reef-dwelling tunicate, called Lissoclinum patella, together with its symbiont Candidatus Endolissoclinum faulkneri, produces an abundant supply of highly toxic chemicals called patellazoles, thought to play a key role in defense. Using DNA collected from the tunicate, researchers have now sequenced the genome of this symbiont. They found that although many genes are being eliminated, the genetic pathway involved in the synthesis of patellazoles is preserved, suggesting that secondary metabolism—or the production of organic compounds not directly involved in growth, development, or reproduction—is an essential part of the symbiotic interaction.

J.C. Kwan et al., “Genome streamlining and chemical defense in a coral reef symbiosis,” Proceeding of the National Academy of Sciences, doi: 10.1073/pnas.1213820109, 2012.

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Comments

Avatar of: Dov Henis

Dov Henis

Posts: 14

December 8, 2012

Rethink, recomprehend life, genome, genetics...:

Earth Life

In plain English, not in academEnglish verbiage.

- Earth life is just another naturally selected mass format.

- The primal base organisms of Earth life are the genes, i.e. the RNA nucleotides.

- All Earth life formats are progenies of genes evolution.

- Genomes are organisms evolved, and continuously modified, by the genes as their functional templates.

- Genetics is a progeny of culture, which is reaction to circumstances.

- The drive and goal of evolution of ALL mass formats is to enhance their energy constraint, to postpone their reconversion to energy, which goes on at constant rate since the Big Bang.

Dov Henis (comments from 22nd century)

http://universe-life.com/

http://universe-life.com/2011/09/30/earthlife-genesis-from-aromaticityh-bonding/

Avatar of: Mounthell

Mounthell

Posts: 22

December 12, 2012

Thanks, Dov, however the basis of life is not things but the exchanging of resources --  the substances, both tangible and intangible, of interactions -- among them.

A little bird just happened to chirp the cosmic joke to me: the set of dynamics underlying life's myriad complexity is simplicity itself, but the explanation necessary to overcome our happy certitudes, e.g., focusing on one or another reified "thing," requires a forest worth of book volumes.

Before flitting off, the little neo-dinosaur remonstrated that "At the end of each day, you humans should confront yourselves in the mirror and caution, 'I am dumber than a boid,' commenters to, and referees of articles and prize winners especially."

Avatar of: Cheaptrx

Cheaptrx

Posts: 50

December 17, 2012

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 well as I wish you make good articles again soon.

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