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A quick guide to...Sequenced Genomes.

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Takifugu rubripes (Eukaryota)
The Japanese pufferfish is both a specialty in sushi restaurants and also a tool for discovering genes in the human genome. The pufferfish genome has many of the same genes as the human genome, but it is eight times smaller and therefore easier for gene hunters to navigate.

» Sequenced by: International Fugu Genome Consortium F. rubripes Abstract
» Related GNN articles:
Pufferfish genome reveals nearly a thousand potentially new human genes
A lean model genome: The Japanese pufferfish is sequenced
The pufferfish: Clues to the human genome puzzle
» Image: Courtesy B.Venkatesh, IMCB
Circular genome map of T. tengcongensis. Copyright Genome Research.
Tetraodon nigroviridis (Eukaryota)
Found in the rivers of Southeast Asia, the spotted green pufferfish is a popular aquarium pet. It is the second pufferfish to be sequenced, after Takifugu rubripes, which is on the menu at some sushi restaurants. The fish are used in research because their genomes are smaller than the human genome yet they contain many of the same genes.

» T. nigroviridis sequenced in 2004 by Genoscope and Broad Institute Abstract
» Image: Courtesy Genoscope
Thalassiosira pseudonana (Eukaryota)
Diatoms are microscopic ocean algae encased in ornate silica shells. The tiny organisms play an important role in Earth’s carbon cycle and may absorb as much carbon dioxide as all of the rainforests combined. Some diatom fossils date back 100 million years.

» T. pseudonana sequenced in 2004 by DOE Abstract
» Image: Courtesy Leila Hornick
Circular genome map of T. tengcongensis. Copyright Genome Research.
Thermoanaerobacter tengcongensis (Bacteria)
Discovered in a hot spring in Tengchong, China, in 1998, this bacterium lives at temperatures around 80°C (176°F). It breaks down sugars for energy and has many genes that are similar to those of Bacillus halodurans.

» Sequenced by: Beijing Genomics Institute T. tengcongensis MB4T Abstract
» Related GNN article: From a hot spring in China, T. tengcongensis is sequenced
» Image: © eChinaRomance.
A thin-section micrograph of Thermoplasma acidophilum. Courtesy Andreas Ruepp.
Thermoplasma acidophilum (Archaea)
This microbe thrives in acidic environments where temperatures reach 59°C (138°F). It has been found in coal refuse piles and solfatara fields. Unlike other microbes that live in harsh environments, this “extremophile” lacks a rigid cell wall but instead has a plasma membrane.

» Sequenced by: Max Planck Institute for Biochemistry T. acidophilum DSM 1728 Abstract
» Related GNN article: Thermoplasma acidophilum: Living the hot, acidic life
» Image: Courtesy Andreas Ruepp.
Circular genome map of Thermoplasma volcanium.
Thermoplasma volcanium (Archaea)
Compared to other species of Archaea, this microbe lives at a relatively low temperature—60°C (140°F). Like its cousin Thermoplasma acidophilum, it has been isolated from solfatara fields (left) and can live in environments that either have oxygen or lack oxygen.

» Sequenced by: AIST T. volcanium GSS1 Abstract
» Image: Courtesy Susan Bonvallet.
T. elongatus. Courtesy Satoshi Tabata, Kazusa DNA Research Institute.
Thermosynechococcus elongatus (Bacteria)
This bacterium lives in hot springs and carries out photosynthesis. Scientists have used the organism to study photosynthesis and circadian rhythms. The sequenced strain was isolated from a hot spring in Beppu, Japan.

» Sequenced by: Kazusa DNA Research InstituteT. elongatus BP-1 Abstract
» Image: T. elongatus. Courtesy Satoshi Tabata, Kazusa DNA Research Institute.
Thermotoga maritima. Copyright K. O. Stetter & R. Rachel, University of Regensburg, Germany.
Thermotoga maritima (Bacteria)
Originally isolated from geothermally heated sediment in Vulcano, Italy, this bacterium breaks down many simple and complex carbohydrates, including cellulose and xylan. If converted to fuels such as ethanol, cellulose and xylan are potential sources of renewable energy.

» Sequenced by: TIGR T. maritima MSB8 Abstract
» Image: © K. O. Stetter & R. Rachel, University of Regensburg, Germany.
Thermus thermophilus (Bacteria)
This bacterium, discovered in a hot springs in Japan in the 1980s, has a variety of commercial uses. Its proteins are used in DNA tests and to make beauty products, such as cosmetic lotion and hair goop. The “extremophile” is also a potential source of vitamin B.

» Sequenced by: University of Göttingen T. thermophilus HB27 Abstract
» Related GNN Article: Hip Hair from a Hot Microbe
» Image: Courtesy University of Göttingen
Treponema denticola (Bacteria)
This bacterium causes gum disease. Found in dental plaque, the spiral-shaped microbe can inflame gums and, in severe cases, can damage the roots of teeth. Most adults are infected by the bacterium at some point in their lives.

» Sequenced by: TIGR T. denticola 35405 Abstract
Treponema pallidum. Courtesy CDC.
Treponema pallidum (Bacteria)
Spread from person to person through sexual contact, this bacterium causes syphilis. The disease was first reported in Europe in the late 1400s, about the time that Columbus returned from the New World. Despite the effectiveness of penicillin in treating the disease, syphilis remains a global health problem.

» Sequenced by: TIGR & University of Texas T. pallidum Nichols Abstract
» Image: Courtesy CDC.
Treponema pallidum. Courtesy CDC.
Tropheryma whipplei (Bacteria)
This wily and elusive bacterium can lie dormant in the body for decades before causing Whipple's disease, a rare but potentially fatal illness. The first case of Whipple's disease was reported in 1907. In 2000, scientists grew the organism in the laboratory for the first time, making possible new research on the disease.

» Sequenced by: Genoscope & CNRS T. whipplei Twist Abstract
Sanger Institute, Stanford University & University of Birmingham T. whipplei TW08/27 Abstract
» Related GNN articles: Hiding from the World: Scientists Sequence the Elusive Whipple Genome
The Whipple Bacillus
» Image: Fredricks D.N. & D.A. Relman. J Infect Dis 183, 1229-1237 (2001). Reproduced with permission of David A. Relman and University of Chicago Press. Copyright: Infectious Diseases Society of America, 2001.
Ureaplasma urealyticum. Courtesy Stéphane Plouvier & Philippe Lambert.
Ureaplasma urealyticum (Bacteria)
This bacterium infects the human urogenital tract and is transmitted sexually. It can cause complications during pregnancy and may contribute to health problems in newborns. The organism belongs to the group of bacteria with very small genomes called mycoplasmas.

» Sequenced by: University of Alabama U. urealyticum serovar 3 Abstract
» Image: Courtesy Stéphane Plouvier & Philippe Lambert.
Vibrio cholerae. Courtesy John Heidelberg, TIGR.
Vibrio cholerae (Bacteria)
Unlike many human pathogens, the bacterium that causes cholera has not one but two chromosomes. This may give it a competitive advantage over other microbes trying to occupy the same environments. The bacterium was given the Latin name Vibrio because it possesses a flagellum and appears to vibrate.

» Sequenced by: TIGR V. cholerae El Tor N16961 Abstract
» Related GNN articles:
Cholera bacteria are more infectious after trip through human body
Potential cholera vaccine for travelers passes safety test
Comparative study reveals genes related to cholera pandemic
Cholera genome sequenced: Sequence of cholera genome paves way to new therapy
» Image: Courtesy John Heidelberg, TIGR.
Vibrio parahaemolyticus (Bacteria)
This bacterium lives in salt water and can cause a gastrointestinal illness when ingested along with raw or undercooked seafood. Most people recover from the illness, which lasts about three days. The bacterium is a problem in Asia, and infections may be on the rise in North America.

» Sequenced by: Osaka University V. parahaemolyticus RIMD 2210633 Abstract
» Image: Courtesy Genome Information Research Center, GIRC.
Vibrio vulnificus (Bacteria)
This relative of the cholera bacterium lives in warm coastal waters and can cause a severe and potentially fatal illness. Most people become infected by eating improperly cooked shellfish, particularly oysters, or by swimming with open wounds in seawater that contains the microbe.

» Sequenced by: Yang-Ming University V. vulnificus YJ016 Unpublished
Tsetse fly. Courtesy Serap Aksoy.
Wigglesworthia glossinidia (Bacteria)
This bacterium lives inside the tsetse fly, which transmits the parasite that causes African sleeping sickness. Scientists sequenced the bacterium in part to discover new ways to control the fly and prevent sleeping sickness. A British entomologist, Sir Vincent Brian Wigglesworth, first described the organism that bears his name.

» Sequenced by: Yale University School of Medicine W. glossinidia brevipalpis Abstract
» Related GNN articles: Wigglesworthia wiggles into the world of sequenced genomes
Using E. coli gene arrays to explore genome of the tsetse fly microbe Wigglesworthia glossinidia
» Image: Tsetse fly. Courtesy Serap Aksoy.
Wolbachia pipientis (Bacteria)
This bacterium lives in the reproductive cells of worms, spiders, and insects. Unable to live outside another organism, the microbe ensures its survival by manipulating the reproduction of its hosts, even to the point of determining their sex. The sequenced strain came from a fruit fly.

» Sequenced by TIGR W. pipientis wMel Abstract
» Image: Scott O’Neill
Tsetse fly. Courtesy Serap Aksoy.
Wolinella succinogenes (Bacteria)
This bacterium lives in the rumens of cows and is related to two microbes that cause stomach disorders in people, Helicobacter pylori and Campylobacter jejuni. Scientists had thought the bacterium was harmless to people, but the genome project revealed genes that may be used to cause disease.

» Sequenced by Max Planck Institute for Developmental Biology W. succinogenes DSMZ 1740 Abstract
» Image: Stephan Schuster.
Citrus canker fruit lesion. Fundecitrus - Brazil.
Xanthomonas axonopodis (Bacteria)
A major problem for citrus growers in Brazil and elsewhere, this bacterium causes an infectious disease in lemons, oranges, and other crops. Known as citrus canker, the highly contagious disease can ruin fruit.

» Sequenced by: FAPESP X. axonopodis pv. citri 306 Abstract
» Related GNN article: Two Xanthomonas bacteria that damage crops are sequenced
» Image: Fundecitrus - Brazil.
Black rot cabbage foliar lesion. IAPAR - Brazil.
Xanthomonas campestris (Bacteria)
This bacterium causes a disease in cabbage, broccoli, and other crops in the crucifer family. Known as black rot or blight, the disease can kill a plant or reduce yields. The bacterium also infects weeds, including the mustard weed Arabidopsis thaliana.

» Sequenced by: FAPESP X. campestris pv. campestris ATCC33913 Abstract
» Related GNN article: Two Xanthomonas bacteria that damage crops are sequenced
» Image: IAPAR - Brazil.
Xyella fastidiosa. Berkeley Electron Microscope Laboratory.
Xylella fastidiosa (Bacteria)
In places like California, Brazil, and Taiwan, this bacterium has damaged trees and crops, including elms, grapes, coffee, and alfalfa. It lives in the guts of winged insects known as sharpshooters, which carry the microbe from plant to plant.

» Sequenced by: ONSA Consortium X. fastidiosa 9a5c Abstract
DOE Joint Genome Institute X. fastidiosa Dixon, X. fastidiosa Ann-1 Abstract
AEG Brazilian Consortium X. fastidiosa Temecula1 Abstract
» Related GNN article: New strains of fruit and nut pathogen yield their genomes
Genome of bacteria Xylella fastidiosa, a threat to fruit and nut crops, is sequenced

» Image: Courtesy Berkeley Electron Microscope Laboratory.
Yarrowia lipolytica (Eukaryota)
A “non-conventional” species of yeast, this organism is often used in genetics research because it differs from other well-studied species. It could potentially be used to produce molecules that have applications in biotechnology. The organism was sequenced as part of a study that compared five species of yeast.

» Sequenced in 2004 by Institut Pasteur and others Y. lipolytica Abstract
» Image: Courtesy Malaysian Institute for Nuclear Technology Research.
Yersinia pseudotuberculosis (Bacteria)
This bacterium lives in soil and water but can infect people and cause digestive problems. It was sequenced to learn about one of its descendents, the bacterium that causes plague, Yersinia pestis. The two species are genetically similar, but ten percent of the genes in Yersinia pseudotuberculosis are no longer active in the deadly plague bacterium.

» Y. pseudotuberculosis sequenced in 2004 by Lawrence Livermore Laboratory
» Image: Courtesy May Tang and Ralph Isberg, Tufts University
Yersinia pestis. Courtesy Eric Paulos, Berkeley.
Yersinia pestis (Bacteria)
The bacterium that causes plague lives in rodents and causes two types of disease. Bubonic plague is transmitted to people by rat fleas. Pneumonic plague, which is more severe and often fatal, occurs when the bacterium is transmitted via air particles from the mouth of an infected individual or animal.

» Sequenced by: Sanger Institute Y. pestis CO92 Abstract
University of Wisconsin Y. pestis KIM Abstract
» Related GNN article: From stomach bug to blood-borne pathogen:The genome sequence of the plague bacterium
» Image: Courtesy Eric Paulos, Berkeley.

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