Category Archives: Genome

In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of viruses, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA.[1]

The term was created in 1920 by Hans Winkler,[2] professor of botany at the University of Hamburg, Germany. The Oxford English Dictionary suggests the name to be a blend of the words gene and chromosome. A few related -ome words already existedsuch as biome, rhizome and, more recently, connectomeforming a vocabulary into which genome fits systematically.[3]

Some organisms have multiple copies of chromosomes: diploid, triploid, tetraploid and so on. In classical genetics, in a sexually reproducing organism (typically eukarya) the gamete has half the number of chromosomes of the somatic cell and the genome is a full set of chromosomes in a gamete. The halving of the genetic material in gametes is accomplished by the segregation of homologous chromosomes during meiosis.[4] In haploid organisms, including cells of bacteria, archaea, and in organelles including mitochondria and chloroplasts, or viruses, that similarly contain genes, the single or set of circular and/or linear chains of DNA (or RNA for some viruses), likewise constitute the genome. The term genome can be applied specifically to mean what is stored on a complete set of nuclearDNA (i.e.,the "nuclear genome") but can also be applied to what is stored within organelles that contain their own DNA, as with the "mitochondrial genome" or the "chloroplast genome". Additionally, the genome can comprise non-chromosomal genetic elements such as viruses, plasmids, and transposable elements.[5]

When people say that the genome of a sexually reproducing species has been "sequenced", typically they are referring to a determination of the sequences of one set of autosomes and one of each type of sex chromosome, which together represent both of the possible sexes. Even in species that exist in only one sex, what is described as a "genome sequence" may be a composite read from the chromosomes of various individuals. Colloquially, the phrase "genetic makeup" is sometimes used to signify the genome of a particular individual or organism. The study of the global properties of genomes of related organisms is usually referred to as genomics, which distinguishes it from genetics which generally studies the properties of single genes or groups of genes.

Both the number of base pairs and the number of genes vary widely from one species to another, and there is only a rough correlation between the two (an observation known as the C-value paradox). At present, the highest known number of genes is around 60,000, for the protozoan causing trichomoniasis (see List of sequenced eukaryotic genomes), almost three times as many as in the human genome.

An analogy to the human genome stored on DNA is that of instructions stored in a book:

In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish the complete nucleotide sequence of a viral RNA-genome (bacteriophage MS2). The next year, Phage -X174, with only 5386 base pairs, became the first DNA-genome project to be completed, by Fred Sanger. The first complete genome sequences for representatives from all 3 domains of life were released within a short period during the mid-1990s. The first bacterial genome to be sequenced was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research in 1995. A few months later, the first eukaryotic genome was completed, with the 16 chromosomes of budding yeast Saccharomyces cerevisiae being released as the result of a European-led effort begun in the mid-1980s. Shortly afterward, in 1996, the first genome sequence for an archaeon, Methanococcus jannaschii, was completed, again by The Institute for Genomic Research.

The development of new technologies has made it dramatically easier and cheaper to do sequencing, and the number of complete genome sequences is growing rapidly. The US National Institutes of Health maintains one of several comprehensive databases of genomic information.[6] Among the thousands of completed genome sequencing projects include those for mouse, rice, the plant Arabidopsis thaliana, the puffer fish, and bacteria like E. coli. In December 2013, scientists reported, for the first time, the entire genome of a Neanderthal, an extinct species of humans. The genome was extracted from the toe bone of a 130,000-year-old Neanderthal found in a Siberian cave.[7][8]

New sequencing technologies, such as massive parallel sequencing have also opened up the prospect of personal genome sequencing as a diagnostic tool, as pioneered by Manteia Predictive Medicine. A major step toward that goal was the completion in 2007 of the full genome of James D. Watson, one of the co-discoverers of the structure of DNA.[9]

Whereas a genome sequence lists the order of every DNA base in a genome, a genome map identifies the landmarks. A genome map is less detailed than a genome sequence and aids in navigating around the genome. The Human Genome Project was organized to map and to sequence the human genome. A fundamental step in the project was the release of a detailed genomic map by Jean Weissenbach and his team at the Genoscope in Paris.[10][11]

Excerpt from:
Genome - Wikipedia, the free encyclopedia

Video Now Available Genetics and Genomics of Thyroid Neoplasms On Dec. 6th, Electron Kebebew, M.D., chief of the Endocrine Oncology Branch, National Cancer Institute, NIH, presented Genetics and Genomics of Thyroid Neoplasms: Moving Closer Towards Personalized Patient Care, as part of the 2013-2014 Genomics in Medicine Lecture Series, sponsored by NHGRI in collaboration with Suburban Hospital and Johns Hopkins. Video of his talk is now available. See the video Presidential Bioethics Report on Incidental Findings The Presidential Commission for the Study of Bioethical Issues released a report on Dec. 12, 2013, entitled Anticipate and Communicate: Ethical Management of Incidental and Secondary Findings in the Clinical, Research, and Direct-to-Consumer Contexts. Although not specifically focused on genomics, the report and its guidelines have implications for genomics research and medicine. Read the report Read the press release The Genomics Landscape Jumping into the deep end of genomic medicine When NHGRI published its new strategic vision for genomics in 2011, we recognized that we had a lot to learn about the research needed to apply genomics to clinical care. At the same time, it seemed critical that we begin to establish a foundation of research programs that would facilitate the implementation of genomic medicine, so we decided to jump in and start swimming! Read more Video Now Available The African Diaspora: Integrating Culture, Genomics and History Videos of the symposium "The African Diaspora: Integrating Culture, Genomics and History" are now available. The event included talks on using genomics in ancestral research and differences in health. NHGRI organized the symposium with the Smithsonian National Museum of Natural History and the National Museum of African American History and Culture. Watch the videos

Excerpt from:
National Human Genome Research Institute (NHGRI) - Homepage

The Human Genome Project (HGP) is an international scientific research project with a primary goal of determining the sequence of chemical base pairs which make up human DNA, and of identifying and mapping the total genes of the human genome from both a physical and functional standpoint.[1] It remains the largest collaborative biological project.[2]

The first official funding for the Project originated with the US Department of Energys Office of Health and Environmental Research, headed by Charles DeLisi, and was in the Reagan Administrations 1987 budget submission to the Congress.[3] It subsequently passed both Houses. The Project was planned for 15 years.[4]

In 1990, the two major funding agencies, DOE and NIH, developed a memorandum of understanding in order to coordinate plans, and set the clock for initiation of the Project to 1990.[5] At that time David Galas was Director of the renamed Office of Biological and Environmental Research in the U.S. Department of Energys Office of Science, and James Watson headed the NIH Genome Program. In 1993 Aristides Patrinos succeeded Galas, and Francis Collins succeeded James Watson, and assumed the role of overall Project Head as Director of the U.S. National Institutes of Health (NIH) National Human Genome Research Institute. A working draft of the genome was announced in 2000 and a complete one in 2003, with further, more detailed analysis still being published.

A parallel project was conducted outside of government by the Celera Corporation, or Celera Genomics, which was formally launched in 1998. Most of the government-sponsored sequencing was performed in universities and research centres from the United States, the United Kingdom, Japan, France, Germany, Spain and China.[6] Researchers continue to identify protein-coding genes and their functions; the objective is to find disease-causing genes and possibly use the information to develop more specific treatments. It also may be possible to locate patterns in gene expression, which could help physicians glean insight into the body's emergent properties.

The Human Genome Project originally aimed to map the nucleotides contained in a human haploid reference genome (more than three billion). Several groups have announced efforts to extend this to diploid human genomes including the International HapMap Project, Applied Biosystems, Perlegen, Illumina, J. Craig Venter Institute, Personal Genome Project, and Roche-454.

The "genome" of any given individual is unique; mapping "the human genome" involves sequencing multiple variations of each gene.[7] The project did not study the entire DNA found in human cells; some heterochromatic areas (about 8% of the total genome) remain unsequenced.

The project began with the culmination of several years of work supported by the US Department of Energy, in particular workshops in 1984[8] of the US Department of Energy.[9] This 1987 report stated boldly, "The ultimate goal of this initiative is to understand the human genome" and "knowledge of the human is as necessary to the continuing progress of medicine and other health sciences as knowledge of human anatomy has been for the present state of medicine." The proposal was made by Dr. Alvin Trivelpiece and was approved by Deputy Secretary William Flynn Martin. This chart[10] was used in the Spring of 1986 by Trivelpiece, then Director of the Office of Energy Research in the Department of Energy, to brief Martin and Under Secretary Joseph Salgado regarding his intention to reprogram $4 million to initiate the project with the approval of Secretary Herrington. This reprogramming was followed by a line item budget of $16 million the following year. Candidate technologies were already being considered for the proposed undertaking at least as early as 1985.[11]

James D. Watson was head of the National Center for Human Genome Research at the National Institutes of Health in the United States starting from 1988. Largely due to his disagreement with his boss, Bernadine Healy, over the issue of patenting genes, Watson was forced to resign in 1992. He was replaced by Francis Collins in April 1993, and the name of the Centre was changed to the National Human Genome Research Institute (NHGRI) in 1997.

The $3-billion project was formally founded in 1990 by the US Department of Energy and the National Institutes of Health, and was expected to take 15 years.[12] In addition to the United States, the international consortium comprised geneticists in the United Kingdom, France, Australia, Japan and myriad other spontaneous relationships.[13]

Due to widespread international cooperation and advances in the field of genomics (especially in sequence analysis), as well as major advances in computing technology, a 'rough draft' of the genome was finished in 2000 (announced jointly by U.S. President Bill Clinton and the British Prime Minister Tony Blair on June 26, 2000).[14] This first available rough draft assembly of the genome was completed by the Genome Bioinformatics Group at the University of California, Santa Cruz, primarily led by then graduate student Jim Kent. Ongoing sequencing led to the announcement of the essentially complete genome in April 2003, 2 years earlier than planned.[15] In May 2006, another milestone was passed on the way to completion of the project, when the sequence of the last chromosome was published in the journal Nature.[16]

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Human Genome Project - Wikipedia, the free encyclopedia

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27 November 2013 - 100 Species Conservation Track now available on hg19

After 15.4 years of CPU run-time in 9,905,594 individual 'jobs' and 99 cluster runs for lastz pair-wise alignment...we are excited to announce the release of a 100 species alignment on the hg19/GRCh37 human Genome Browser.

This new Conservation track shows multiple alignments of 100 species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package. This adds 40 more species to the existing 60-way on the mm10 mouse browser. For more information about the 100 species Conservation track, see its description page.

We'd also like to acknowledge the hard work of the UCSC Genome Browser staff who pulled together the information for this track: Hiram Clawson and Pauline Fujita.

24 October 2013 - Job Opening: UCSC Genome Browser Trainer

The Center for Biomolecular Science and Engineering (CBSE) at University of California Santa Cruz seeks an articulate, self-motivated educator for the two-year position of UCSC Genome Browser trainer. The trainer develops curriculum and provides in-person training on the UCSC Genome Browser at universities, hospitals, institutes, and professional meetings in the United States and internationally. Typical audiences include graduate and post-graduate biologists and doctors, with Genome Browser experience ranging from novice users to bioinformatics specialists. Presentations include formal talks, problem-solving sessions, and two-day workshops.

This position requires a Master's degree in a biological science, depth in molecular biology, experience in a research environment, working knowledge of the UCSC Genome Browser, understanding of its role in research methodology, and experience teaching or training in a scientific environment. Preferred qualifications include a PhD in a relevant field, experience with video production, and experience with HTML or web content management systems.

For more information and to apply for this position, see Job #1304619 on the UCSC Staff Employment website.

23 October 2013 - dbSNP 138 Available for hg19: We are pleased to announce the release of four tracks derived from NCBI dbSNP Build 138 data, available on the human assembly (GRCh37/hg19). Read more.

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UCSC Genome Browser - Official Site

A genome sequenced from the toe bone of a Neanderthal woman has yielded several new insights into the evolution of early humans and their contemporaries.

The existence of a mysterious ancient human lineage and the genetic changes that separate modern humans from their closest extinct relatives are among the many secrets now revealed in the first high-quality genome sequence from a Neanderthal woman, researchers say.

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TheNeanderthal womanwhose toe bone was sequenced also reveals inbreeding may have been common among her recent ancestors, as her parents were closely related, possibly half-siblings or another near relation.

Although modern humans are the world's only surviving human lineage, others also once lived on Earth. These includedNeanderthals, the closest extinct relatives of modern humans, and the relatively newfoundDenisovans, whosegenetic footprintapparently extended from Siberia to the Pacific islands of Oceania. Both Neanderthals and Denisovans descended from a group that diverged from the ancestors of all modern humans. [See Photos of Neanderthal Bone & Denisovan Fossils]

The first signs of Denisovans came from a finger bone and a molar tooth discovered in Denisova Cave in southern Siberia in 2008. To learn more about Denisovans, scientists examined a woman's toe bone, which was unearthed in the cave in 2010 and showed physical features resembling those of both Neanderthals and modern humans. The fossil is thought to be about 50,000 years old, and slightly older than previously analyzed Denisovan fossils.

Human interbreeding

The scientists focused mostly on the fossil'snuclear DNA, the genetic material from the chromosomes in the nucleus of the cell that a person receives from both their mother and father. They also examined the genome of this fossil's mitochondria the powerhouses of the cell, which possess their own DNA and get passed down solely from the mother.

The investigators completely sequenced the fossil's nuclear DNA, with each position (or nucleotide) sequenced an average of 50 times. This makes the sequence's quality at least as high as that of genomes sequenced from present-day people.

Excerpt from:
Neanderthal genome suggests new, mysterious human lineage

Image Caption: The newly sequenced genome of the Amborella plant will be published in the journal Science on 20 December 2013. The genome sequence sheds new light on a major event in the history of life on Earth: the origin of flowering plants, including all major food crop species. Credit: Sangtae Kim

redOrbit Staff & Wire Reports Your Universe Online

The newly-sequenced genome of the Amborella plant is shedding new light on the origin of the more than 300,000 flowering plants on the Earth today, including all major food crop species.

Amborella trichopoda, a small understory tree found only on the main island of New Caledonia in the South Pacific, is unique as the sole survivor of an ancient evolutionary lineage that traces back to the last common ancestor of all flowering plants. This heritage gives the plant a special role in the study of flowering plants, the researchers said.

In the same way that the genome sequence of the platypus a survivor of an ancient lineage can help us study the evolution of all mammals, the genome sequence of Amborella can help us learn about the evolution of all flowers, said study researcher Victor Albert of the University at Buffalo.

The researchers who sequenced the Amborella genome say that it provides conclusive evidence that the ancestor of all flowering plants, including Amborella, evolved following a genome doubling event that occurred about 200 million years ago. Some duplicated genes were lost over time but others took on new functions, including contributions to the development of floral organs, the researchers said.

Genome doubling may, therefore, offer an explanation to Darwins abominable mystery the apparently abrupt proliferation of new species of flowering plants in fossil records dating to the Cretaceous period, said Claude dePamphilis of Penn State University, one of the studys researchers.

Generations of scientists have worked to solve this puzzle.

Comparative analyses of the Amborella genome are already providing scientists with a new perspective on the genetic origins of important traits in all flowering plants, including all major food crop species.

Because of Amborellas pivotal phylogenetic position, it is an evolutionary reference genome that allows us to better understand genome changes in those flowering plants that evolved later, including genome evolution of our many crop plants hence, it will be essential for crop improvement, said Doug Soltis of the University of Florida.

Original post:
Genome Sequence Gives Insight Into Evolution Of Flowering Plants

Affecting the Shelf Life of Chromosomes

12/19/2013

Just like the chicken or milk you buy at a store, chromosomes have a shelf life too. Of course, chromosomes dont spoil because of growing bacteria. Instead, they go bad because they lose a little of the telomeres at their ends each time they are copied. Once these telomeres get too short, the chromosome stops working and the cell dies. Turns out food and chromosomes have another thing in commonthe rates of spoilage of both can...read more >

12/17/2013

SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This Winter 2013 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know. ...read more >

12/12/2013

The most interesting board games cant be played right out of the box. You can admire the board and the game pieces, but before the fun can begin you need to spend some time reading the instructions and understanding the strategy. Gene Ontology (GO) annotations are a little bit like that. You can get interesting information very quickly by just reading the GO terms on the Locus Summary page of your favorite yeast protein in SGD....read more >

12/03/2013

Our friend Saccharomyces cerevisiae has it pretty easy when it comes to sex. There is no club scene or online dating. Pretty much if an a and an are close enough together, odds are that they will shmoo towards each other and fuse to create a diploid cell. No fuss, no muss. Of course there arent any visual cues that indicate whether a yeast is aor . Instead yeast relies on detecting gender-specific pheromones each cell...read more >

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Saccharomyces Genome Database - Official Site

Neanderthals

Nidhi Subbaraman NBC News

Dec. 18, 2013 at 1:01 PM ET

Bence Viola

Researchers extracted DNA from this toe bone of a Siberian Neanderthal female who lived about 50,000 years ago.

The first high-quality genome sequence of a Siberian Neanderthal female is throwing up racy details about our ancient relatives sex lives: Siberian Neanderthals mated within their families, the new research shows, while another group, the Denisovans, interbred with Neanderthals, humans and a third, as yet undiscovered mystery hominin living in Asia.

The first anthropologists relied on skull shapes and bone lengths of fossils to identify ancestors in the hominin family tree. Recently though, geneticists have bulked up their toolset, and have identified new species from material taken from mere milligrams of bone. This time, they didn't even need that.

"There is not even a bone splinter here," Svante Pbo, a geneticist at the Max Planck Institute for Evolutionary Anthropology, said of the unknown species. "Its an inference from those other genomes."

By comparing genetic evidence of the Neanderthal female who lived some 50,000 years ago, with the sequence of a Denisovan girl published in August last year, Pbo and team discovered a small but discrete signature of a much older species, which the paleoanthropologists suspect might be Homo erectus. The full analysis of the Siberian Neanderthal genome is published in the Thursday issue of Nature.

Bence Viola

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Sex and the Siberian Neanderthal: Incest and inter-species action

Dec. 19 (UPI) -- The most complete sequence of the Neanderthal genome shows inbreeding as well as interbreeding among at least four different types of early humans.

DNA extracted from the fossilized toe of a 50,000 year-old Siberian Neanderthal woman revealed that she was the child of two closely related parents, who were either half-siblings or double first cousins, the offspring of two siblings who married siblings.

Researchers found that Neanderthals and Denisovans, another type of early human, were closely related and that their common ancestor split off from the ancestor of modern humans around 400,000 years ago.

Further analysis suggests that the population sizes of Denisovans and Neanderthals were small, leading to interbreeding. Researchers also found evidence of interbreeding with a mysterious fourth type of early human.

The international team of anthropologists and geneticists published their findings in the journal Nature.

These two types of early humans eventually died out but left some of their genetic history because they occasionally interbred with modern humans. Researchers said that close to 1.5 to 2.1 percent of modern non-African genomes can be traced back to Neanderthals.

The paper really shows that the history of humans and hominins during this period was very complicated, said Montgomery Slatkin, a professor at UC Berkeley. There was lot of interbreeding that we know about and probably other interbreeding we havent yet discovered.

Graduate student Fernando Racimo found 87 specific genes that were significantly different from those found in Neanderthals and Denisovans, and could be the distinguishing factor between modern humans and their ancestors.

There is no gene we can point to and say, This accounts for language or some other unique feature of modern humans, Slatkin said. But from this list of genes, we will learn something about the changes that occurred on the human lineage, though those changes will probably be very subtle.

[UC Berkeley] [Nature]

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Neanderthal genome reveals inbreeding and interbreeding

Dec. 18, 2013 The most complete sequence to date of the Neanderthal genome, using DNA extracted from a woman's toe bone that dates back 50,000 years, reveals a long history of interbreeding among at least four different types of early humans living in Europe and Asia at that time, according to University of California, Berkeley, scientists.

Population geneticist Montgomery Slatkin, graduate student Fernando Racimo and post-doctoral student Flora Jay were part of an international team of anthropologists and geneticists who generated a high-quality sequence of the Neanderthal genome and compared it with the genomes of modern humans and a recently recognized group of early humans called Denisovans.

The comparison shows that Neanderthals and Denisovans are very closely related, and that their common ancestor split off from the ancestors of modern humans about 400,000 years ago. Neanderthals and Denisovans split about 300,000 years ago.

Though Denisovans and Neanderthals eventually died out, they left behind bits of their genetic heritage because they occasionally interbred with modern humans. The research team estimates that between 1.5 and 2.1 percent of the genomes of modern non-Africans can be traced to Neanthertals.

Denisovans also left genetic traces in modern humans, though only in some Oceanic and Asian populations. The genomes of Australian aborigines, New Guineans and some Pacific Islanders are about 6 percent Denisovan genes, according to earlier studies. The new analysis finds that the genomes of Han Chinese and other mainland Asian populations, as well as of native Americans, contain about 0.2 percent Denisovan genes.

The genome comparisons also show that Denisovans interbred with a mysterious fourth group of early humans also living in Eurasia at the time. That group had split from the others more than a million years ago, and may have been the group of human ancestors known as Homo erectus, which fossils show was living in Europe and Asia a million or more years ago.

"The paper really shows that the history of humans and hominins during this period was very complicated," said Slatkin, a UC Berkeley professor of integrative biology. "There was lot of interbreeding that we know about and probably other interbreeding we haven't yet discovered."

The genome analysis will be published in the Dec. 19 issue of the journal Nature. Slatkin, Racimo and Jay are members of a large team led by former UC Berkeley post-doc Svante Pbo, who is now at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

In another analysis, Jay discovered that the Neanderthal woman whose toe bone provided the DNA was highly inbred. The woman's genome indicates that she was the daughter of a very closely related mother and father who either were half-siblings who shared the same mother, an uncle and niece or aunt and nephew, a grandparent and grandchild, or double first-cousins (the offspring of two siblings who married siblings).

Further analyses suggest that the population sizes of Neanderthals and Denisovans were small and that inbreeding may have been more common in Neanderthal groups than in modern populations.

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Neanderthal genome shows early human interbreeding, inbreeding