Talk: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). 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

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

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)