Talk:Genome

Organism or species?

The introduction to the articles says "The genome for several organisms have been sequenced and genes analyzed, ...". This reflects the usage of the word "organism" established earlier in the paragraph. This seems quite odd, as if the organisms perhaps are me and my auntie Sarah. Is there a good reason for not using the word "species" instead? --Willbown (talk) 11:04, 10 September 2021 (UTC)

Number of genes in that STD example might me incorrect

The number of genes stated in the article about that organism said that its 17000 genes while page said that it has 60,000 genes. —Preceding unsigned comment added by 70.171.42.135 (talk) 00:13, 29 May 2008 (UTC)

According to Wikipedia, the genome is the entirety of an organism's hereditary information, which includes the genes. And, information is uncountable. tosendo (talk) 08:09, 9 December 2010 (UTC)

LIBRARY analogy: Extremely helpful, but possibly erroneous

Could someone correct/clarify the library example? For instance, it claims the genes/pages range from (400-3340), but supposedly Chromosome 11 has only 379, and Chromosome 1 has 4220, (379-4220) according to: http://en.wikipedia.org/wiki/Chromosomes —Preceding unsigned comment added by 98.234.218.46 (talk) 21:23, 21 June 2010 (UTC)

Request for improvement

This page really needs to be improved. Is anyone planning on taking on the job? Right now it is very basic, disjointed, and even repetitious. Not trying to crticize what has been done, but to look forward to what still needs to be done.Evolver 13:17, 4 September 2005 (UTC)

Definition debate

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). 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") 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. 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? 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?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? 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? 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. 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

I'm concerned with the article's opening definition: "the genome of an organism is it's whole hereditary information." This is flatly wrong. In eucaryotes, of course, mitochondrial DNA (not part of the genome) is also heritable from mother to daughter. And then there is that whole category of epigenetic information that is also heritable, but isn't encoded in DNA at all. The concept of "whole hereditary information" is changing rapidly, and it's now quite clear that it goes beyond the genome. RobPol 21:53, 29 June 2007 (UTC)

Request for improvement - If possible, could the number of mutations be added to the list of gene size? Comparing gene size to mutation might show a correlation. 99.235.162.164 (talk) 21:44, 19 March 2013 (UTC)

"Number of mutations" unfortunately isn't really a quantifiable single value. We can compare genome sequences or genes and infer how they might be related, but the number of mutations must be defined in relation to another genome or gene or an ancestral genome or gene. Even that value is always an estimate (and often a difficult estimate to make, especially with sequences from distantly related species.) §everal⇒|Times 18:11, 20 March 2013 (UTC)

book promotion

Somebody stuck the following on the front of the genome article.

":Genome 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

Fair enough, but some people may come to Wikipedia looking for information about Ridley's book, which was quite well known.70.31.67.60 19:54, 3 September 2005 (UTC)

Ridley's book should be mentioned in the human genome page, not here. Although he called it "Genome", it was specifically about humans. It is also not a primary reference work but a popular discussion. If someone wants to make a separate new page about the book to avoid confusion with this page, that's fine, but I don't think the book needs to be cited on this page.Evolver 21:03, 3 September 2005 (UTC)

Looks like a standard Wikipedia:Disambiguation link to me. If Einstein's biography is called "Relativity" and there is a Wikipedia article about it, the Relativity page should have a disambiguation link to it. Joe D (t) 00:28, 4 September 2005 (UTC)

I agree with that. Evolver 01:13, 4 September 2005 (UTC)

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. - 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.--Doucher 23:34, Jun 21, 2005 (UTC)

Heh. "Pairs." Yeah, I, um, didn't notice that. - Omegatron 01:07, Jun 22, 2005 (UTC)

Since it is a base "pair", the genome size (of a given organism) is the same whether one refers to one strand or both. One usually refers to genome size in base pairs (bps) or in the number of nucleotides from a single strand. So, "# bps" = "# of nucleotides from one strand". --Thorwald 05:18, 30 June 2007 (UTC)

It seems HIV genome (single stranged RNA) has 9,749 bases, NOT bp, isn't it?Terlu (talk) 13:05, 26 January 2012 (UTC)

Reference Book Removed

I am removing (again) the book added as a reference by 70.31.67.60. Please explain why this book, as opposed to many others out there, should be added as a reference, considering that 1) the text was written well before the reference was added, 2) the addition is coming from an anonymous user, 3) the link goes to an Amazon page to help people buy the book, 4) the history of 70.31.67.60 shows that not only has the user created a page on the book, but is inserting it as a reference in other pages on Wikipedia as well (example one) (example two) Turnstep 19:30, September 3, 2005 (UTC)

1) it is the most recent and comprehensive book that covers all the (previously, and now again, unreferenced) statements made, 2) who cares who added it -- it is referenced so you can check it yourself, 3) no it doesn't now, 4) indeed, because it provides summaries -- in some cases the ONLY ones available -- of the topics discussed, but those pages also include LOTS of other references as well. 70.31.67.60 19:53, 3 September 2005 (UTC)

Incidentally, if you think B chromosomes, ancient genome duplications (now merged with polyploidy), and other topics are not worthy of inclusion in Wikipedia, may I ask why not? It so happens that I noticed these were all missing, and added brief articles plus LOTS of references, including to the book in question (since again, it contains the most detailed and up to date reviews I am aware of -- please by all means feel free to expand these articles and add more references if you are an expert). In your example one, the book is one of five references, and in example two it is three of 13 references. I also considered making links to every journal I cited, but I was not sure if it was worthwhile adding so many external links. It occurred to me that linking to Amazon was not really appropriate, so I created a summary page for the book within Wikipedia. I did not realize it was an issue to create a summary page about a book. Initially I included everything I could find about it (including the back cover copy), but was told that was too promotional and might be a copyright issue, so I removed everything except a short summary. I hope this is satisfactory now.70.31.67.60 20:13, 3 September 2005 (UTC)

There is obviously nothing wrong with creating a book page. And once made, it makes perfect sense to inject references to it where appropriate (including in new pages that are created by the same user). I don't understand what the criticism is about.Evolver 01:13, 4 September 2005 (UTC)

References

This page is sorely lacking in references and links to further published material. I have added some in the section discussed above, but we need to insert more throughout. Hopefully as this page grows, we will incorporate citations of primary sources as much as possible, as this is one area where people will definitely need to look for more detail than Wiki pages can ever provide. Note that I have included a link to the book discussed above -- I think that is appropriate since a page exists. If people make pages for the other books, I will link to them also. However, I agree that linking to Amazon is not a good move. Note: please only put references cited in the text in the "References" section. Relevant but uncited publications could be provided in a "Further reading" section if need be. Evolver 15:48, 4 September 2005 (UTC)

Human genome is Wikipedia:Science_collaboration_of_the_week

Just to let you know that Human genome has been voted Science Collaboration of the Week. - Samsara _contrib ^talk 10:32, 27 January 2006 (UTC)

Genomes Stability

I think this article could use a section on genome stability, as I don't think the subject as a whole warrants it's own article. It's not exactly my area of expertease hence why I am mentioning here rather than doing it myself! Million_Moments 16:11, 16 October 2007 (UTC)

OED

The OED citation is a conjecture onto what went through the mind of an individual, and cannot be cited as more reliable than any other linguistic conjecture. The OED has been known to be wrong on such issues, and does offer corrections. The citation provided is enough to shine reasonable doubt. Ottava Rima (talk) 15:51, 21 March 2008 (UTC)

Definition of genome seems wrong

The definition given by this page is:

                       In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information.

But the article on Common_misunderstandings_of_genetics says:

                       Epigenetic inheritance. In the widest definition this includes all biological inheritance mechanisms that do not change or involve the genome. 

They can't both be right. Ethyr (talk) 23:15, 9 September 2010 (UTC)

Definition of the genome seems the definition of DNA

The first paragraph of this article says:

In modern molecular biology and genetics, the genome is the genetic material of an organism. It consists of DNA (or RNA in RNA viruses). The genome includes both the genes and the non-coding sequences of the DNA/RNA.[1]

Considering the fact that DNA is a genetic material and a gene is a segment of DNA (according to the Wikipedia article), the above sentence can be rewritten as:

.., the genome is DNA.  It consists of DNA.  DNA includes both DNA segments and non-coding sequence of DNA/RNA.

Well, it is intentionally made weird a bit, but the meaning of the definition really is as such.

So far I remember, the definition here used be like:

.., the genome is a heredity unit of genetic material of an organism. (snip)

It can be rewritten as

.., the genome is a heredity unit of DNA of an organism. (snip)

I think this instance is more reasonable. Why was the definition rewritten?

BTW, isn't there an expression of Genomic DNA any more? If it is still alive, it would mean DNA's DNA. Uh-oh.

In my opinion genome is not DNA itself, rather it is the information contained. This is much simpler to explain. Wordmasterexpress (talk) 09:31, 8 April 2016 (UTC)

This sounds like a lot of hairsplitting. The current definition in the intro is perfectly fine. I wouldn't change it. Your statements have some issues. E.g. the genome is DNA sounds like genome = DNA which is not exactly true. I would argue that DNA describes the chemical nature of the genome while genome emphasizes the biological nature (genetics, including the integrity and order of genes etc.). It's similar to transcriptome which is not just RNA, but also includes the timing and ralative amounts of RNA etc. Does that make sense? Peteruetz (talk) 14:16, 8 April 2016 (UTC)

@Wordmasterexpress: I agree with Peteruetz on this one. I think the current definition is actually both clearer and more accurate than "the genome is a heredity unit of DNA of an organism", which excludes RNA genomes, doesn't explicitly link to genes, and the word "unit" is misleading. T.Shafee(Evo﹠Evo)^talk 05:52, 9 April 2016 (UTC)

@Peteruetz & T.Shafee(Evo﹠Evo) Thanks for comments. I do not argue that molecular biologists consider DNA (or RNA) as the carrier material of genomic information. I question whether genome is the set of instructions to develop and maintain life, or merely the container material. It would be analogous to a CD-ROM containing useful computer program. Is this CD-ROM the program or not? I believe not, because the carried instruction set shall be the program, not the media itself, however it appears to be. When two people independently execute the program the appearance would be more or less the same with some environmental effect such as personal settings. This analogy always keeps me questioning the appropriateness of the definition of genome. Well, I might be crazy if no one can share this naiive and intuitive question.Wordmasterexpress (talk) 17:58, 9 April 2016 (UTC)

Yes, the genome is the set of instructions to develop and maintain life, as well as the container material. The concept of the genome can best be understood in the context of evolution, as evolution shapes the organization of the genome. As with a computer program, you could envision many different genomes achieving the same goal (an organism) but by contrast, genomes are not "intelligently designed". Bacteria are good examples: two species can look almost identical but have very different genomes. Similarly, organisms can look very different but their genomes may be almost identical (think of males and females). Thus genome is as much a functional term as it is a structural concept.Peteruetz (talk) 22:22, 9 April 2016 (UTC)

Thank you for reply, but it is still unclear to me. What you are talking about seem to me that genome is material and the instruction set is a function or attribute it bears, not genome itself. I am afraid, but your explanation of evolution didn't seem to clarify my question. Wordmasterexpress (talk) 00:16, 11 April 2016 (UTC)

Not sure what the question is... Yes, the genome is the material containing the instruction set. A CD is probably a bad analogy because all CDs are standardized and just carriers for information. DNA is the carrier but it cannot be rewritten at will (well, not exactly true, today we can do that, but "natural" genomes are not "designed"). Genomes carry a history that determines their sequence. That's why evolution is critical, at least if you want to understand the structure of a genome. That's also the reason why genomes contain junk (some of them LOTS), information that is NOT relevant for the function of genes or genomes.Peteruetz (talk) 00:35, 11 April 2016 (UTC)

@Peteruetz: Thank you for reply. I regret that my words were not clear enough.

Genomes are also standardized in a sense, such that they can behave as instruction sets for life. In other words, only a certain kind of DNA can be genomes, not all of them. Consider what kind of DNA can be a genome. Say a dinucleotide. Nobody would agree that a dinucleotide is a genome, nonetheless it can be a DNA. How about a DNA of 1000 bases? What about one gigas of random DNA sequence? Evolution can solely occur through the narrow paths of astronomical space of DNAs to facilitate living activities. It emphasizes that the instruction set, or information, is the main body of the genome, not material.

There is a very strict rule on DNA to be a genome by natural selection, which is analogous to the standards for the specification of CD-ROM. Of course, the time scales differ, but it is nothing to do with definition. The difference in layout among genomes are mentioned, but it also applies to CD-ROM. That is, the layout can be completely different among CD-ROMs as long as the functions are the same.

While the codes on CD are selected by human to follow the standard, the codes on genomic DNA are selected by nature to follow the rule of natural selection. Thus the criticism on the analogy does not seem to make much sense. --Wordmasterexpress (talk) 02:51, 11 April 2016 (UTC)

What are included on genome?

Recent edits by IP user (sorry I'm using mobile device and uneasy to refer) states genome includes genes and non-protein-coding information. Though agreed partly, I feel it a bit misleading because it implies any gene is protein-coding. Unsure, but some expression like non-genic information might cause less misunderstanding. Does anybody know more appropriate expression? --Wordmasterexpress (talk) 00:16, 14 April 2016 (UTC) Wordmasterexpress (talk) 00:16, 14 April 2016 (UTC)

Reference to human genome size

Looking into the actual references for the human genome size, the Science paper estimate the size to 2.91 Gbp (Table 11), and the Nature paper to 3.289 Gbp (Table 8). Note what matters is genome size, not length of what was sequenced. The table of this page has a single value for the estimated human size.

Anyway, the problem is on the reference to the Nature paper. It's referencing a FAQ at ornl.gov which no longer exists and I had to check on web.archive.org. That website had the, incorrectly rounded, value of 3.2 Gbp and reference the Nature paper. Could someone that understands references on mediawiki fix it? Specially for papers with a thousand authors? The reference should be for this paper http://www.nature.com/nature/journal/v409/n6822/full/409860a0.html

Also, those were estimates for the draft of the human genome, there's likely better estimates nowadays.

--Carandraug (talk) 16:10, 18 August 2016 (UTC)

@Carandraug: The Nature paper says, in a note below Table 8, that the value 3.289 Gbp is an overestimate and that a better estimate is 3.2. But you're right that there are probably better estimates now. The Human genome article gives about 3.088 Gbp. Eric Kvaalen (talk) 09:59, 26 September 2020 (UTC)

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Why Genome compression?

What is the importance of the section on genome compression? As it's currently presented without context, it seems like a technical topic without broad appeal. ThokozileA (talk) 21:30, 1 November 2017 (UTC)

Archaea

In the list of genome sizes, there should be some Archaea as well.--Solomonfromfinland (talk) 20:42, 20 April 2021 (UTC)

Student at Uskudar university

I am shadha alghurbani i want to edit this article ,because i am assigned this to my course in istanbul,Turkey. Shadha AlGhurbani (talk) 15:02, 29 December 2022 (UTC)

Remove Composition of the human genome pie chart

Composition of the human genome

The composition of the human genome pie chart was added to this article on Nov. 9, 2017. It was inaccurate then and it's even more inaccurate today. It's time to remove this figure. If there are no objections from people who are monitoring this article, I will remove it in a few days.

Here are some of the major inaccuracies.

1. There's no mention of important functional regions such as regulatory sequences and noncoding genes.

2. The chart perpetuates the common confusion between coding regions and protein-coding genes. The coding region occupies about 1% of the genome (not 2%) but protein-coding genes (exons + introns) take up almost 40%.

3. The chart doesn't mention virus-related DNA sequences (~4%).

4. There is considerable overlap between introns and repetitive DNA; they are not separate categories as implied in the chart. (About 40% of intron sequences is transposon-related.)

5. Segmental duplications are not a separate category.

6. Heterochromatin is not a separate category.

Genome42 (talk) 14:37, 25 February 2023 (UTC)

Remove Prokaryotic Cell Diagram

A label diagram explaining the different parts of a Prokaryotic genome

The prokaryotic cell diagram was created by Ulissesrp and inserted into this article on May 29, 2020.

The label under the diagram says, "A label diagram explaining the different parts of a prokaryotic genome" but the diagram does not explain the different parts of a prokaryotic genome. Instead it describes different parts of prokaryotic cell but some of those labels are incorrect.

The prokaryotic cell diagram stacks on top of the Genetics series banner, which should normally be at the top of the article.

I propose deleting the prokaryotic cell diagram in a few days unless anyone objects.

Genome42 (talk) 15:20, 25 February 2023 (UTC)

Genome, genotype and genes of an entire population

The definitions in the respective Wikipedia pages do not appear to differ between genotype and genome. This is also evident in most definitions I found. Is there a difference? Clarification would help - and perhaps a mention in the Introduction to Genetics article (https://en.m.wikipedia.org/wiki/Introduction_to_genetics). “The genotype of an organism is its complete set of genetic material”(https://en.m.wikipedia.org/wiki/Genotype). There is a somewhat different definition of genotype from the NHGRI at NIH (https://www.genome.gov/genetics-glossary/genotype). “a genome is all the genetic information of an organism” (https://en.m.wikipedia.org/wiki/Genome) It would also be informative to discuss the genetic information of the entire population of an organism. Does it have a name? How many more genes are present in the population of an organism than in a single individual? Presumably unknown but the current academic thoughts (or lack of) would be interesting. QuietJohn (talk) 16:39, 14 June 2023 (UTC)

Centimorgans

If you know and you think the article should discuss it: how big is the (haploid) human genome, as measured in centimorgans? —Quantling (talk | contribs) 23:43, 15 August 2023 (UTC)