Genome Digest

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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