Genome Digest

STOCK.XCNG, BLEARWICKE Wandering Aboriginals Species: Aboriginal Australian, Homo sapiens Genome size: 3 billion base pairs Interesting fact: The first sequence of the Australian Aboriginal genome was obtained from an 80-year-old lock of hair, which had been a gift from a young Aboriginal man to a British ethnologist traveling in Australia in the 1920s. The sequence revealed that the ancestors of modern-day Aboriginals, along with the ancestors of New Guineans and other Oceanians, migrated out of Africa around 60,000 years ago—preceding the ancestors of Europeans and mainland Asians by about 20,000 years. M. Rasmussen et al., “An Aboriginal Australian genome reveals separate human dispersals into Asia,” Science, doi: 10.1126/science.1211177, 2011. Immune-regulating bacteria Species: Segmented filamentous bacteria (SFB) Genome size: 1.57 million base pairs Interesting fact: In 2009, researchers discovered that segmented filamentous bacteria (SFB) dwelling in the small intestines of mice can recruit T helper 17 (Th17) cells and provoke autoimmune arthritis in genetically susceptible mice—thus becoming some of the first solid evidence that resident gut bacteria can regulate host immunity. With only 1,500 genes, SFB has a stripped-down genome compared to its nearest relatives, and likely depends on other gut bacteria for the production of amino acids and essential nutrients. A. Sczesnak et al., “The genome of Th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment,” Cell Host & Microbe, doi: 10.1016/j.chom.2011.08.005, 2011. Megavirus particle WIKIPEDIA, CHANTAL ABERGEL Gargantuan virus Species: Megavirus chilensis Genome size: 1.3 million base pairs Interesting fact: This distant relative of Mimivirus, the first giant virus discovered, was isolated off the Chilean coast and bears the distinction of being the largest viral genome to be sequenced. Due to its gargantuan size, as well as considerable gene overlap with Mimivirusand some extant eukaryotes, researchers hypothesize both giant viruses could have descended from a eukaryotic ancestor. D. Arslan et al., “Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae,” PNAS, doi: 10.1073/pnas.1110889108, 2011. Deadly prostate cancer Species: 23 advanced, drug-resistant prostate cancers, Homo sapiens Genome size: 3 billion base pairs Interesting fact: Exome sequencing of lethal and highly aggressive human prostate cancers identified recurrent mutations in a small number of genes including some previously linked to tumorigenesis, such as p53 (tumor suppression) and GPC6 (cell division). In addition, the researchers discovered three tumor types with 10 times the number of point mutations as other advanced prostate tumors. Although the cause of these “hypermutated genomes” remains unknown, the researchers speculate they may enhance the drug resistance ability of the tumors. A. Kumar et al., “Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers,” PNAS, doi:10.1073/pnas.1108745108, 2011. Leishmania parasite FLICKR, AJC1 Flesh-eating protozoans Species: Four species of Leishmania parasites: Leishmania mexicana, Leishmania major, Leishmania infantum, and Leishmania braziliensis Genome size: Around 32 million base pairs Interesting fact: An international team of researchers has sequenced the genome of the protozoan parasite, Leishmania mexicana (found in Central and South America) and made further corrections to the already-published draft genomes of three related species: L. major, L. infantum, and L. braziliensis. The parasites are well known for causing slow-healing sores on the skin and in nasal passages, and in more severe cases, in internal organs such as the liver and spleen. A comparison of their genomes revealed that although there is little difference in the gene content across the species, there can be substantial large-scale variation in chromosome and gene copy numbers. M.B. Rogers et al., “Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania,” Genome Res, doi:10.1101/gr.122945.111, 2011. Pig parasite Species: Intestinal roundworm, Ascaris suum Genome size: 273 million base pairs Interesting fact: Ascaris suum is a 15- to 30-centimeter-long roundworm that infects pigs and can cause Ascariasis, a disease characterized by fever, diarrhea, inflammation, and respiratory problems. A close relative of A. suum, Ascaris lumbricoides, is known to infect humans and cause thousands of deaths every year. Containing approximately 18,500 protein-coding genes, the A. suum genome has already revealed potential drug targets that could help curb the devastating effects of the parasitic worm, in particular, molecules that enable the parasite to evade host immune responses. A.R. Jex et al., “Ascaris suum draft genome,” Nature, doi:10.1038/nature10553, 2011.

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