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Genome Digest

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

Sep 18, 2012
Beth Marie Mole

Globe trotting parasiteSpecies: Plasmodium vivaxGenome size: ~27 million base pairs

Interesting fact: The malaria parasite, Plasmodium vivax, can share alleles across the globe, according to researchers at Case Western Reserve University and the Cleveland Clinic Lerner Research Institute. The researchers sequenced isolates of the parasite from Madagascar, Cambodia, El Salvador, and a monkey-adapted strain from South America, and found evidence for a high amount of gene sharing, raising concern that the parasites could rapidly spread drug resistance genes around the world. The parasites are such good travelers because they can lie dormant in a patient’s liver for months and reemerge in a new locale.

E. Chan et al.,Whole genome sequencing of field isolates provides robust characterization of genetic diversity in Plasmodium vivax,” PLOS Neglected Tropical Diseases, 6: e1811, 2012.

Brown-eyed girlSpecies: Denisova homininsGenome size: ~3 billion base pairs

A Denisova cave in Siberia where remnants of the girl were found
Credit: Wikimedia Commons, ?????????????

Interesting fact: New technology allowed researchers to sequence the genome of an ancient cave girl—from a finger-bone the size of a lady bug—more than 30 times over. The new method, developed by an international team of researchers, amplified DNA from single strands rather than double strands. The more precise look at the ancient girl’s genome revealed that she had brown eyes, brown hair, and dark skin. The girl, estimated to have lived around 80,000 years ago in a Siberian cave, is a Denisovian, a cousin of Neanderthals.

M. Meyer et al., “A high-coverage genome sequence from an archaic Denisovan individual,” Science, doi: 10.1126/science.1224344, 2012.

Shape shifterSpecies: Candida albicansGenome size: 27 million base pairs

Candida albicans
Credit: Wikimedia Commons, Y tambe

Interesting fact: Candida albicans, the common fungus that causes yeast infections and other opportunistic infections in people, can switch from a single-celled budding yeast to a filamentous form, which is necessary to cause an infection. Comparing the genome of C. albicans with the harmless, bread- and beer-making yeast, Saccharomyces cerevisiae—which uses filamentous growth to forage for nutrients—researchers at the University of Toronto in Canada identified genes responsible for the string-like growth strategy, as well as master regulators for the growth switch, Flo8 and Mss11, which could serve as novel drug targets to treat C. albicans infections.

O. Ryan et al., “Global gene deletion analysis exploring yeast filamentous growth,” Science, 337: 1353-56, 2012.

Rabid virusSpecies: Ikoma lyssavirus Genome size: 12 thousand base pairs

African civet
Credit: Wikimedia Commons, ellyuzh

Interesting fact: Lyssaviruses, single-strand negative-sense RNA viruses, cause rabies in animals and humans around the world. Vaccines are highly effective at protecting against the common deadly virus, but little is known about viral variation that might undermine vaccine protection. Researchers from the Wildlife Zoonosis & Vector-Borne Diseases Research Group in Surrey, United Kingdom, sequenced the most genetically distinct rabies virus yet, found in a rabid African civet in Tanzania. The new genomic information could help researchers stay one step ahead of the virus.

D. Marston et al., “Complete genome sequence of Ikoma lyssavirus,” Journal of Virology, doi:10.1128/JVI.01628-1, 2012.

An extreme weedSpecies: Thellungiella salsugineaGenome size: ~233.7 million base pairs

Arabidopsis thaliana
Credit: Wikimedia Commons, Roepers

Interesting fact: The weed Thellungiella salsuginea can grow in salty, dry, cold, low-oxygenated soil, in contrast to its cousin, the relatively wimpy weed and widely used model organism Arabidopsis thaliana, which grow in more moderate

conditions. Researchers at the National Center for Plant Gene Research in Beijing, China, sequenced the genome of T. salsuginea and compared it to that of A. thaliana to find the genes responsible for the hardier plant’s resilience. They found that the two relatives diverged between 7 and 12 million years ago and that T. salsuginea contained more genes for leaf wax production, hormone signaling, and control of osmotic equilibrium.

H. Wu et al., “Insights into salt tolerance from the genome of Thellungiella salsuginea,” Proceedings of the National Academy of Science, 109: 12219-24, 2012.

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