:Genome (book) ''is also a popular science book by Matt Ridley...'' In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). This includes both the gene and the Junk DNA. The term was first coined, in 1920, by Hans Winkler, Professor of Botany at the University of Hamburg. More precisely, the genome of an organism is a complete DNA sequence of one set of chromosomes; for example, one of the two sets that a diploid individual carries in every somatic cell. When people say that the genome of a sexual reproduction species has been "sequencing," 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 from the chromosomes of various individuals. In general use, the phrase genetic makeup is sometimes used conversationally to mean 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. ==Types of genomes== Most biological entities more complex than a virus (biology) sometimes or always carry additional genetic material besides that which resides in their chromosomes. In some contexts, such as sequencing the genome of a pathogenic microbe, "genome" is meant to include this auxiliary material, which is carried in plasmids. In such circumstances then, "genome" describes all of the genes and non-coding DNA that have the potential to be present. In vertebrates such as humans, however, "genome" carries the typical connotation of only chromosomal DNA. So although human mitochondria contain genes, these genes are not considered part of the genome. In fact, mitochondria are sometimes said to have their own genome, often referred to as the "mitochondrial genome". ==Genomes and genetic variation== Note that a genome does not capture the genetic diversity or the genetic polymorphism (biology) of a species. For example, the human genome sequence in principle could be determined from just half the DNA of one cell from one individual. To learn what variations in DNA underlie particular traits or diseases requires comparisons across individuals. This point explains the common usage of "genome" (which parallels a common usage of "gene") to refer not to any particular DNA sequence, but to a whole family of sequences that share a biological context. Although this concept may seem counter intuitive, it is the same concept that says there is no particular shape that is the shape of a cheetah. Cheetahs vary, and so do the sequences of their genomes. Yet both the individual animals and their sequences share commonalities, so one can learn something about cheetahs and "cheetah-ness" from a single example of either. ==Minimal genomes== Since genomes and their organisms are very complex, one research strategy is to reduce the number of genes in a genome to the bare minimum and still have the organism in question survive. There is experimental work being done on minimal genomes for single cell organisms as well as minimal genomes for multicellular organisms (see Developmental biology). The work is both ''in vivo'' and ''in silico''. By understanding the functioning of minimal organisms one hopes to add complexity incrementally leading to the understanding of multicellular diseases such as Cancer.(see #References) ==Genome projects== ''Main article:'' Genome project The Human Genome Project was organized to physical map and to sequencing the human genome. Other genome projects include mus musculus, rice, the plant Arabidopsis thaliana, the puffer fish, bacteria like E. coli, etc. Many genomes have been sequenced by various genome projects. The cost of sequencing continues to drop, and it is possible that eventually an individual's genome could be sequenced for around several thousand dollars (US). ''Compare:'' proteome ==Comparison of the sizes of different genomes==
''Note:'' The DNA from a single human cell has a length of ~1.8m.
==Genome evolution==
Genomes are more than the sum of an organism's genes and have traits that may be measured and studied without reference to the details of any particular genes and their products. Researchers compare traits such as chromosome number, chromosome size, gene order, codon usage bias, and GC-content to determine what mechanisms could have produced the great variety of genomes that exist today.
Duplications play a major role in shaping the genome. Duplications may range from extension of short tandem repeats, to duplication of a cluster of genes, and all the way to duplications of entire chromosomes or even entire genomes. Such duplications are probably fundamental to the creation of genetic novelty.
Horizontal gene transfer is invoked to explain how there is often extreme similarity between small portions of the genomes of two organisms that are otherwise very distantly related. Horizontal gene transfer seems to be common among many microbes. Also, eukaryotic cells seem to have experienced a transfer of some genetic material from their chloroplast and mitochondrial genomes to their nuclear chromosomes.
== Other Omics & Ome pages ==
* Genome, Proteome, Expressome, Metabolome, Regulome, Functome, Phenome, Textome
* Mitochondriomics, Golgiome, Ligandomics, Eukaryome, Bacteriome, Archaeome
== Subfields of Genome ==
* Human genome, Mitochondriome, Eukaryome
==References==
* (2005) [http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371%2Fjournal.pbio.0030025 Genome Sequencing: Using Models to Predict Who's Next.] PLoS Biol 3(1): e25.
* (2003) Werner, E., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14678738&query_hl=3 In silico multicellular systems biology and minimal genomes], DDT vol 8, no 24, pp 1121-1127, Dec 2003. (Paradigm for research on minimal multicellular systems with references to other literature)
==See also==
*Developmental biology, evolution, molecular systematics, molecular evolution, gene family, gene
== External links ==
*[http://www.genomesize.com/ Animal genome size database]
*[http://www.rbgkew.org.uk/cval/homepage.html/ Plant genome size database]
*[http://www.genomenewsnetwork.org/ The Genome News Network]
Genetics
Here's what the Oxford Dictionary of Biology says about genomes: http://www.xrefer.com/entry.jsp?xrefid=461212&secid=.-&hh=1 That definition, while brief, supports my idea of genome (and that of the molecular geneticist sitting next to me), which is that plasmids don't count (b/c they aren't chromosomes and they're optional). User:168... Then again, opinions seem to differ. This is from a FAQ at the Web site of TIGR ''What place do microbial plasmids have in defining the genome of microbes? It seems as though the term "microbial genome" refers solely to the microbial chromosome. How are plasmid genes, that often define key traits, included, or are they not included?'' By definition, a genome is all the DNA contained in an organism or a cell. A chromosome is the main DNA structure that contains the genes required for life. In microbial genomes, most often there is a single circular or linear chromosome and there are may be many extra-chromosomal, self-replicating, linear or circular DNA known as plasmids. In eukaryotic genomes, the chromosomes are within the nucleus and the extra chromosomal DNA is in the mitochondria as well as plastids in plants. In our genome projects of organisms that contain plasmids, ei. Borrelia borgdorferi, Methanococcus jannaschii, and Deinococcus radiodurans, the sequencing, finishing and annotation are done for the entire genome, chromosome and plasmids. http://www.tigr.org/about/faq.shtml But to me the question, which was expressed in words that don't sound naive, proves that the traditional sense of genome is that it's the chromosomes. The definition in the answer above disagrees with the usage of "genome" in humans and other eukaryotes: "All the DNA" would include mitochondrial DNA, which is typically considered its own genome (the "mitochondrial genome") User:168... Plus there's the issue that it's really only half of the chromosomal DNA in diploid cells. I guess the article needs work. Not tonight from me though. User:168... :I was under the impression that genome, when applied to an entire species, does refer to the generic sense, without encompassing any of the genetic diversity of the species, and so can be reduced to just one of the sets of chromosomes, but that genome, when applied to an individual, refers to the specific set of allelles that individual possesses, and so cannot be so reduced. Hence references to chimeras being "multiple genomes in one individual." Am I mistaken in this? User:Geoff 22:46 18 Jun 2003 (UTC) I've never encountered "chimera" being used like you used it (in the uses I know, people talk about two "genes" being spliced together, which proves there's some looseness in the use of the word "gene," [strictly I guess it's "alleles" that are spliced], but that doesn't mean people are equally loose with "genome"). I suppose I can imagine I've read news stories that say things like "once doctors have your own genome sequence" (even though nine times out of ten it's "THE human genome" the stories talk about). But that imagined or remembered phrase has the words "your own" in it, which I think is because you have to overcome the natural sense of genome as something general and impersonal. Is your chimera quote an actual excerpt from a magazine article, or just your recollection of the kind of thing you've read or heard?User:168... 00:38 19 Jun 2003 (UTC) :I've heard "chimera" described this way in at least a few places. I was paraphrasing, not quoting exact text (otherwise I would have given a citation), but I'm fairly sure that it was phrased in roughly those terms, although you're right, I could be mistaken. I believe the first place I read of chimeras was in Science News. We seem to have different ideas of what the term refers to, so I'll give my understanding of it. :In the ''very'' early stages of embryonic development (I hesitate to quote exact stages since I'm freely recalling this, not refering to anything, but I think it's prior to blastulation) two seperately fertilized embryos may come into contact and fuse. If it's early enough, the fused embryo will continue developing normally, with the result that the chromosomal DNA in a cell in one part of the body is only as similar to the chromosomal DNA in a cell another part of the body as one would normally expect the chromosomal DNA between siblings to be. This is uncommon in humans, since usually there's only one egg present during fertilization at a time, but more common in, for example, dogs, which commonly have many eggs present simultaneously. :Thinking about it more, actually, I think the first place I heard of chimeras was in my high school AP Biology course; my teacher may have been the one to describe chimeras as multiple genomes in a single individual. I'll be the first to admit that information taught in high school science classes is not always to be trusted, but I have a great deal of respect for the knowledge and integrity of my particular biology teacher. :Anyway, I'm not sure what bearing, if any, this has to the way one should interpret the word "genome." It could be that from a scientific standpoint, the only proper usage is, as you say, in reference to the general species-wide genome, and its usage in reference to an individual's set of chromosomal DNA is only a colloquialism, but it still seems to me that there would be a gray area. What about cases of speciation in progress? Do subspecies have seperate genomes? Also, if the word can be used colloqiually, if "incorrectly," to refer to an individual's set of DNA, shouldn't we acknowledge that? Language does reflect usage, after all. Maybe we should make a few of these issues clearer in the article? User:Geoff 22:09 19 Jun 2003 (UTC) O.K., I remember now this other context of chimeras. I think it's related to how they make transgenic mice--manually combining embryoes. Also I was confused before and thought you were talking about spliced genomes, not about individuals who are genetic "mosaics" (which I think is the more common way people talk about this kind of chimera-ness). Your subspecies question sounds reasonable to me, though I'm not sure it's a problem for the "genome" concept (my hunch is that subspecies would be spoken about as having different versions of the same genome, b/c they are the called the same species, and one species has one genome, I believe). I can't disagree with your philosophy of usage and how the article should accomadate it, but I'm just not sure we aren't talking about an idiosyncratic usage. e.g. If it were only your biology teacher who talks about mosaics having two genomes, I don't think it would be time yet to update the dictionary. I guess according to that usage regarding mosaics, it takes two sets of chromosomes to make a genome, and in a mosaic it takes at least four. Hmmm. I guess a reasonable person could hold that view. But besides your biology teacher, is anyone out there publishing it? User:168.150.238.72 00:58 20 Jun 2003 (UTC) :Your argument sounds good to me. Unless someone else disagrees, I'm willing to let the point be settled. User:Geoff 22:03 21 Jun 2003 (UTC) :Not so clear on what you're saying.. but a genome does not represent two sets of chromosomes. It does in humans, and most animals, but in plants, fungi etc. a genome may have only one set of chromosomes or many. Wheat is octoploidy, seedless watermellons are triploid. -adenosine == book promotion == Somebody stuck the following on the front of the genome article. ":''Genome (book) is also a popular science book by Matt Ridley.''" Looked like shameless book promotion to me, so I took it out. Would one start an article on relativity by a reference to the latest Einstein Biography? I would hope not. If somebody is still convinced of the importance of Ridley's contribution, perhaps mention of his book could be added further down. Hate mail to: Nickthompson@earthlink.net == Genome v. Gene Pool == I have heard and read the word geneOME used as a synonym for gene pool, meaning all the possible variants of all the genes carried by all the organisms in a population, rather than referring to all the genes carried by an individual. I am pleased to see the narrower usage defended here. However, I am wondering if there is any significant body of opinion out there that the term ought to have the broader meaning. If so I would like to hear it. nickthompson@earthlink.net == base pairs == does the genome count include base pairs from both strands or just one side? Since both would be mirror images of each other. - User:Omegatron 23:13, Jun 21, 2005 (UTC) The genome count is of basepairs, pairs of course being plural. Thus, a basebair is both individual bases. However, often people will just refer to a genome size in terms of bases, but what they really mean is baispairs.--User:Doucher 23:34, Jun 21, 2005 (UTC) :Heh. "Pairs." Yeah, I, um, didn't notice that. - User:Omegatron 01:07, Jun 22, 2005 (UTC)
See other meanings of words starting from letter:
Words begining with Genome:
Genome
Genome
Genome@home
Genomeceutical
Genomes
Genome_(book)
Genome_(genetic_algorithm)
Genome_(Matt_Ridley)
Genome_annotation
Genome_assembly
Genome_at_home
Genome_degradation
Genome_Project
Genome_project
Genome_project
Genome_projects
Genome_projects
Genome_reduction
Genome_screen
Genome_sequencing
Genome
:Genome (book) ''is also a popular science book by Matt Ridley...'' In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). This includes both the gene and the Junk DNA. The term was first coined, in 1920, by Hans Winkler, Professor of Botany at the University of Hamburg. More precisely, the genome of an organism is a complete DNA sequence of one set of chromosomes; for example, one of the two sets that a diploid individual carries in every somatic cell. When people say that the genome of a sexual reproduction species has been "sequencing," 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 from the chromosomes of various individuals. In general use, the phrase genetic makeup is sometimes used conversationally to mean 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. ==Types of genomes== Most biological entities more complex than a virus (biology) sometimes or always carry additional genetic material besides that which resides in their chromosomes. In some contexts, such as sequencing the genome of a pathogenic microbe, "genome" is meant to include this auxiliary material, which is carried in plasmids. In such circumstances then, "genome" describes all of the genes and non-coding DNA that have the potential to be present. In vertebrates such as humans, however, "genome" carries the typical connotation of only chromosomal DNA. So although human mitochondria contain genes, these genes are not considered part of the genome. In fact, mitochondria are sometimes said to have their own genome, often referred to as the "mitochondrial genome". ==Genomes and genetic variation== Note that a genome does not capture the genetic diversity or the genetic polymorphism (biology) of a species. For example, the human genome sequence in principle could be determined from just half the DNA of one cell from one individual. To learn what variations in DNA underlie particular traits or diseases requires comparisons across individuals. This point explains the common usage of "genome" (which parallels a common usage of "gene") to refer not to any particular DNA sequence, but to a whole family of sequences that share a biological context. Although this concept may seem counter intuitive, it is the same concept that says there is no particular shape that is the shape of a cheetah. Cheetahs vary, and so do the sequences of their genomes. Yet both the individual animals and their sequences share commonalities, so one can learn something about cheetahs and "cheetah-ness" from a single example of either. ==Minimal genomes== Since genomes and their organisms are very complex, one research strategy is to reduce the number of genes in a genome to the bare minimum and still have the organism in question survive. There is experimental work being done on minimal genomes for single cell organisms as well as minimal genomes for multicellular organisms (see Developmental biology). The work is both ''in vivo'' and ''in silico''. By understanding the functioning of minimal organisms one hopes to add complexity incrementally leading to the understanding of multicellular diseases such as Cancer.(see #References) ==Genome projects== ''Main article:'' Genome project The Human Genome Project was organized to physical map and to sequencing the human genome. Other genome projects include mus musculus, rice, the plant Arabidopsis thaliana, the puffer fish, bacteria like E. coli, etc. Many genomes have been sequenced by various genome projects. The cost of sequencing continues to drop, and it is possible that eventually an individual's genome could be sequenced for around several thousand dollars (US). ''Compare:'' proteome ==Comparison of the sizes of different genomes==
| Organism | Genome size (base pairs) |
|---|---|
| Virus, Phi-X174 phage | 5387 - First sequenced genome |
| Virus, lambda phage | 5×104 |
| Bacterium, ''Escherichia coli'' | 4×106 |
| Plant, ''Fritillary Fritillary assyriaca'' | 13×1010 - Largest known genome |
| Fungus,''Saccharomyces cerevisiae'' | 2×107 |
| Nematoda, ''Caenorhabditis elegans'' | 8×107 |
| Insect, ''Drosophila melanogaster'' | 2×108 |
| Mammal, ''Homo sapiens'' | 3×109 |
Genome
Here's what the Oxford Dictionary of Biology says about genomes: http://www.xrefer.com/entry.jsp?xrefid=461212&secid=.-&hh=1 That definition, while brief, supports my idea of genome (and that of the molecular geneticist sitting next to me), which is that plasmids don't count (b/c they aren't chromosomes and they're optional). User:168... Then again, opinions seem to differ. This is from a FAQ at the Web site of TIGR ''What place do microbial plasmids have in defining the genome of microbes? It seems as though the term "microbial genome" refers solely to the microbial chromosome. How are plasmid genes, that often define key traits, included, or are they not included?'' By definition, a genome is all the DNA contained in an organism or a cell. A chromosome is the main DNA structure that contains the genes required for life. In microbial genomes, most often there is a single circular or linear chromosome and there are may be many extra-chromosomal, self-replicating, linear or circular DNA known as plasmids. In eukaryotic genomes, the chromosomes are within the nucleus and the extra chromosomal DNA is in the mitochondria as well as plastids in plants. In our genome projects of organisms that contain plasmids, ei. Borrelia borgdorferi, Methanococcus jannaschii, and Deinococcus radiodurans, the sequencing, finishing and annotation are done for the entire genome, chromosome and plasmids. http://www.tigr.org/about/faq.shtml But to me the question, which was expressed in words that don't sound naive, proves that the traditional sense of genome is that it's the chromosomes. The definition in the answer above disagrees with the usage of "genome" in humans and other eukaryotes: "All the DNA" would include mitochondrial DNA, which is typically considered its own genome (the "mitochondrial genome") User:168... Plus there's the issue that it's really only half of the chromosomal DNA in diploid cells. I guess the article needs work. Not tonight from me though. User:168... :I was under the impression that genome, when applied to an entire species, does refer to the generic sense, without encompassing any of the genetic diversity of the species, and so can be reduced to just one of the sets of chromosomes, but that genome, when applied to an individual, refers to the specific set of allelles that individual possesses, and so cannot be so reduced. Hence references to chimeras being "multiple genomes in one individual." Am I mistaken in this? User:Geoff 22:46 18 Jun 2003 (UTC) I've never encountered "chimera" being used like you used it (in the uses I know, people talk about two "genes" being spliced together, which proves there's some looseness in the use of the word "gene," [strictly I guess it's "alleles" that are spliced], but that doesn't mean people are equally loose with "genome"). I suppose I can imagine I've read news stories that say things like "once doctors have your own genome sequence" (even though nine times out of ten it's "THE human genome" the stories talk about). But that imagined or remembered phrase has the words "your own" in it, which I think is because you have to overcome the natural sense of genome as something general and impersonal. Is your chimera quote an actual excerpt from a magazine article, or just your recollection of the kind of thing you've read or heard?User:168... 00:38 19 Jun 2003 (UTC) :I've heard "chimera" described this way in at least a few places. I was paraphrasing, not quoting exact text (otherwise I would have given a citation), but I'm fairly sure that it was phrased in roughly those terms, although you're right, I could be mistaken. I believe the first place I read of chimeras was in Science News. We seem to have different ideas of what the term refers to, so I'll give my understanding of it. :In the ''very'' early stages of embryonic development (I hesitate to quote exact stages since I'm freely recalling this, not refering to anything, but I think it's prior to blastulation) two seperately fertilized embryos may come into contact and fuse. If it's early enough, the fused embryo will continue developing normally, with the result that the chromosomal DNA in a cell in one part of the body is only as similar to the chromosomal DNA in a cell another part of the body as one would normally expect the chromosomal DNA between siblings to be. This is uncommon in humans, since usually there's only one egg present during fertilization at a time, but more common in, for example, dogs, which commonly have many eggs present simultaneously. :Thinking about it more, actually, I think the first place I heard of chimeras was in my high school AP Biology course; my teacher may have been the one to describe chimeras as multiple genomes in a single individual. I'll be the first to admit that information taught in high school science classes is not always to be trusted, but I have a great deal of respect for the knowledge and integrity of my particular biology teacher. :Anyway, I'm not sure what bearing, if any, this has to the way one should interpret the word "genome." It could be that from a scientific standpoint, the only proper usage is, as you say, in reference to the general species-wide genome, and its usage in reference to an individual's set of chromosomal DNA is only a colloquialism, but it still seems to me that there would be a gray area. What about cases of speciation in progress? Do subspecies have seperate genomes? Also, if the word can be used colloqiually, if "incorrectly," to refer to an individual's set of DNA, shouldn't we acknowledge that? Language does reflect usage, after all. Maybe we should make a few of these issues clearer in the article? User:Geoff 22:09 19 Jun 2003 (UTC) O.K., I remember now this other context of chimeras. I think it's related to how they make transgenic mice--manually combining embryoes. Also I was confused before and thought you were talking about spliced genomes, not about individuals who are genetic "mosaics" (which I think is the more common way people talk about this kind of chimera-ness). Your subspecies question sounds reasonable to me, though I'm not sure it's a problem for the "genome" concept (my hunch is that subspecies would be spoken about as having different versions of the same genome, b/c they are the called the same species, and one species has one genome, I believe). I can't disagree with your philosophy of usage and how the article should accomadate it, but I'm just not sure we aren't talking about an idiosyncratic usage. e.g. If it were only your biology teacher who talks about mosaics having two genomes, I don't think it would be time yet to update the dictionary. I guess according to that usage regarding mosaics, it takes two sets of chromosomes to make a genome, and in a mosaic it takes at least four. Hmmm. I guess a reasonable person could hold that view. But besides your biology teacher, is anyone out there publishing it? User:168.150.238.72 00:58 20 Jun 2003 (UTC) :Your argument sounds good to me. Unless someone else disagrees, I'm willing to let the point be settled. User:Geoff 22:03 21 Jun 2003 (UTC) :Not so clear on what you're saying.. but a genome does not represent two sets of chromosomes. It does in humans, and most animals, but in plants, fungi etc. a genome may have only one set of chromosomes or many. Wheat is octoploidy, seedless watermellons are triploid. -adenosine == book promotion == Somebody stuck the following on the front of the genome article. ":''Genome (book) is also a popular science book by Matt Ridley.''" Looked like shameless book promotion to me, so I took it out. Would one start an article on relativity by a reference to the latest Einstein Biography? I would hope not. If somebody is still convinced of the importance of Ridley's contribution, perhaps mention of his book could be added further down. Hate mail to: Nickthompson@earthlink.net == Genome v. Gene Pool == I have heard and read the word geneOME used as a synonym for gene pool, meaning all the possible variants of all the genes carried by all the organisms in a population, rather than referring to all the genes carried by an individual. I am pleased to see the narrower usage defended here. However, I am wondering if there is any significant body of opinion out there that the term ought to have the broader meaning. If so I would like to hear it. nickthompson@earthlink.net == base pairs == does the genome count include base pairs from both strands or just one side? Since both would be mirror images of each other. - User:Omegatron 23:13, Jun 21, 2005 (UTC) The genome count is of basepairs, pairs of course being plural. Thus, a basebair is both individual bases. However, often people will just refer to a genome size in terms of bases, but what they really mean is baispairs.--User:Doucher 23:34, Jun 21, 2005 (UTC) :Heh. "Pairs." Yeah, I, um, didn't notice that. - User:Omegatron 01:07, Jun 22, 2005 (UTC)
See other meanings of words starting from letter:
G
GA | GB | GC | GD | GE | GF | GH | GI | GJ | GK | GL | GM | GN | GO | GP | GR | GS | GT | GU | GW | GX | GY | GZ |Words begining with Genome:
Genome
Genome
Genome@home
Genomeceutical
Genomes
Genome_(book)
Genome_(genetic_algorithm)
Genome_(Matt_Ridley)
Genome_annotation
Genome_assembly
Genome_at_home
Genome_degradation
Genome_Project
Genome_project
Genome_project
Genome_projects
Genome_projects
Genome_reduction
Genome_screen
Genome_sequencing
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