Top Genomes of 2012

Wikimedia, Eliza42015 Tomato, tomäto Species: Tomato, Solanum lycopersicum Genome size: 900 million base pairs After a 9-year effort by researchers in 14 countries, the first genome sequence of a tomato—of the original Heinz ketchup variety—was released this May. Anticipation of the fleshy fruit’s genome stems from what the sequences could tell researchers about the tomato’s economically important relatives, including potato, eggplant, tobacco, and pepper. The potato, for instance, which has also recently had its genome sequenced, is 92 percent genetically similar to the tomato. Now, scientists can start figuring out how the differing 8 percent of their genes make tomato plants producing luscious, above ground fruit, while potato plants result in knobby, subterranean tubers. The tomato genome sequence also revealed that the species has triplicated its genome—twice. A triplication event happened around 130 million years ago, then again about 60 million years ago, right around the time that many dinosaur species went extinct. The copy error could have helped tomato plants survive the transitional era. The Tomato Genome Consortium, “The tomato genome sequence provides insights into fleshy fruit evolution,” Nature, doi:10.1038/nature11119, 2012. (Cited 17 times) Flickr, abbybatchelder Incubating offspring Species: Human fetus, homo sapiens Genome size: 3 billion base pairs Following up on a 1997 Lancet study that found fetal DNA circulating in maternal blood, this year saw a steady stream of studies and clinical trials on sequencing fetal DNA, including a whole fetal genome, published in June. The new technology relies on the fact that DNA from the baby makes up 3 to 10 percent of the cell-free DNA floating through a pregnant woman’s blood stream. As expected, the new technology has exploded onto the market as non-invasive screens for genetic disorders in fetuses as early as 9 weeks into pregnancy. Currently, the three tests on the marker focus on finding aneuploidies—abnormalities in the number of chromosomes or chromosomal regions, including trisomy 21, the cause of Down syndrome. But, the continued advancement of sequencing technologies promises more extensive tests in the near future. For more on prenatal genetic tests, the state of the industry, and the associated ethical issues, check out The Scientist’s article, “Year of the Fetus.” J.O. Kitzman et. al., “Noninvasive whole-genome sequencing of a human fetus,” Science Translational Medicine, 137: 137ra76, 2012. (Cited 10 times) Flickr, wbeem Gorilla, exposed Species: Western lowland gorilla, Gorilla gorilla gorilla Genome size: 3.04 billion base pairs In March, a 30-year-old, 300-pound captive gorilla named Kamilah revealed new similarities between us and our second-closest relatives. By analyzing Kamilah’s fully sequenced genome—all 21,000 genes of it—researchers at the Sanger Institute in Cambridge, United Kingdom, found that gorillas split from humans and chimps around 10 million years ago—3 million years before humans diverged from chimps. Thus it’s not surprising that most human and chimp genes are more genetically similar to each other than to gorilla genes, but researchers found that 30 percent of gorilla genes are also closely related to human and chimp genes—sometimes more similar than those genes are between human and chimps. Such shared genetics suggests that the three species continued to interbreed after their evolutionary divorce. “As the climate changed, populations fragmented, evolved separately, and the small splinter groups either died out or found creative ways to carry on, such as breeding with other groups,” lead author Aylwyn Scally of the Sanger Institute told New Scientist. Kamilah’s genome also showed that 500 of the genes shared between apes and humans—mostly involved in hearing and brain development—evolved in gorillas after the two species split. A. Scally et. al., “Insights into hominid evolution from the gorilla genome sequence,” Nature, 483: 169-75, 2012. (Cited 13 times) Wikimedia, Pkuczynski All-purpose pork Species: Domestic pig, Sus scrofa domesticus Genome size: ~3 billion base pairs After decades of genetic work, and 10,000 years of a human-pig relationship, researchers last month (November) sequenced the full genome of a domesticated pig—a female from Illinois named T.J. Tabasco. The most immediate applications of this new genetic information will most likely be seen on the farm, where breeders will try to elbow out genes that are linked to disease susceptibility, such as the porcine reproductive and respiratory syndrome that costs the pig industry $600 million each year. But, in addition to the promise of healthier, meatier animals for food production, the new genomic data could be used for medical advances: researchers have been working for years to use pigs as models for human disease and have even envisioned using them to grow human organs for transplantation. Exploiting similarities in anatomy, pigs are already models for human eye diseases, cystic fibrosis, and diabetes. Now, researchers are working to develop pig models of Alzheimer’s disease, cancer, and muscular dystrophy. M.A.M. Groenen et al., “Analysis of pig genomes provide insight into porcine demography and evolution,”Nature, 491: 393-98, 2012 (Cited 3 times) Wikimedia, Carport Spirited grains Species: Barley, Hordeum vulgare L. Genome size: ~5.3 billion base pairs Barley is the world’s fourth most important cereal crop, and one of the first domesticated grains, but more importantly, it’s critical for the production of beer and whiskey. So, the study released this past October revealing the whole genome sequence—twice the size of the human genome—met cheers from agricultural producers, distillers, and brew masters alike. The genome draft—produced by the International Barley Genome Sequencing Consortium, a team of researchers at 22 organizations around the world—is a high-resolution map of the grain’s haploid genome, including most of its 32,000 genes. Agricultural researchers hail the new data as a way to make the staple grain more resistant to disease and resilient during climate change, thereby fortifying food security. But, beer and whiskey drinkers are looking to use the new data to brew better spirits. K. Mayer et al., “A physical, genetic and functional sequence assembly of the barley genome,” Nature, 491: 711-16, 2012. (Not yet cited)

Top Genomes of 2012

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