Talk:List of sequenced eukaryotic genomes

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|- | |An entry from List of sequenced eukaryotic genomes appeared on Wikipedia's Main Page in the Did you know? column on 11 September 2006.

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Suggestion: Could this list be orderered by date of completion?

Contents 1 Dating 2 Common names 3 Order 4 Mitochondrial Genomes 5 To add photosynthetic "cabozoan" chloroplast genomes 6 Archea 7 Linking the headings? 8 Updates 9 What is a gene? 10 Genome size 11 TODO: Chlamy

[edit] Dating

This list claims to be up-to-date, but since it is manually maintained it will temporarily become out of date, until edited, every time a new genome is sequenced. It badly needs a "Last updated xxxx" or "as of xxxx" date specification. --mglg_(talk) 21:35, 11 September 2006 (UTC)

[edit] Common names

Since this is a public encyclopedia, common names of each species (or broader group description, such as "fruit fly") should be added. --mglg_(talk) 21:35, 11 September 2006 (UTC)

Redirects let people know the common name easily. I was thinking of having a field to describe the type of organism - which I will propably add soon.--Peta 22:16, 11 September 2006 (UTC)

Thanks - that is exactly what I am looking for - mglg_(talk)

Thanks Peta for adding the "Relevance" column. I took the liberty to separate the "Type of organism" (say, "Mosquito") from the "Relevance" ("Vector of malaria"). Feel free to check my entries. --mglg_(talk) 22:33, 21 September 2006 (UTC)

Looks great, thanks. --Peta 00:02, 25 September 2006 (UTC)

[edit] Order

Is alphabetical order by genus name really the best approach to organisation? I would suggest that taxonomic order or order by date woud make more sense. This list is going to get really long soon and might be easier to resort now. --Aranae 00:42, 10 November 2006 (UTC)

Oh, yes, it should be sorted by plant, animal, protist, fungi, bacteria, etc., etc., as even now the list of organisms is overlong for an unsorted or alphabetically sorted list to be usable. KP Botany 00:45, 10 November 2006 (UTC)

Yeah, dividing the list in plants, animals, fungi and protists should make it more readable. Tycho 03:08, 14 November 2006 (UTC)

I will try doing it --Kupirijo 16:48, 27 December 2006 (UTC)

Thanks, and good luck. I am looking into the other matter. KP Botany 18:56, 27 December 2006 (UTC)

[edit] Mitochondrial Genomes

I think organisms which have only their mitochondrial genome sequenced should not be listed since it is misleading to list such a small genome for the whole organism. --Kupirijo 19:51, 29 December 2006 (UTC)

There's nothing misleading about it, simply note that it's the mitochondrial genome. It's correct terminology to refer to the mitochondrial genome, and it's by definition, a eukaryotic genome, so it belongs. Again, just make sure it's clear that that is what has been sequenced. KP Botany 21:15, 29 December 2006 (UTC)

I did so for the Cryptomonad. It was its nucleomorph genome. Let me know if it is OK with you. Cheers. --Kupirijo 23:14, 29 December 2006 (UTC)

Oh, I didn't even notice, I simply searched for mitochondrial and chloroplast. Yes, of course it's okay, as it accomplishes what it intends, the indication that it is not nuclear DNA that has been sequenced. Particularly important with funky DNA, I would think. Thanks for taking the time to do this, sort by kingdom/division/whatever, and for working with other editors to make the article usable and accurate for readers. KP Botany 23:41, 29 December 2006 (UTC)

I strongly discourage the addition of organelle genomes to this list as it will make the size of the article unmanageable. The lead text clearly describes this as a list of fully sequenced eukaryote genomes, which in my mind clearly excludes organisms with organelle only information.--Peta 00:10, 31 December 2006 (UTC)

That's fine with me that is why I started this section. KP Botany what is your opinion? Happy new year to everybody --Kupirijo 08:54, 31 December 2006 (UTC)

That's fine, but they are rather important in plant genomics and phylogenetic systematics, some studies and classifications based on research on what is available in the line of chloroplast genomes, rather than deciding which plants to use in analyses based on characteristics. So, where should they go? Also, I point out that if "fully sequenced eukaryote genomes" then means nuclear genome only, this isn't "fully sequenced eukaryotic genomes," but, rather "fully sequenced eukaryotic nuclear genomes." KP Botany 19:49, 31 December 2006 (UTC)

I think the title of the page is ok. I think "eukaryote" necessarily refers to an organism as a whole; I wouldn't call a chloroplast itself a eukaryote, I'd call it part of a eukaryotic cell. (You can type "define:eukaryote" in Google to see what others think.) So I think when users scanning this list see an organism listed on this page, they would assume the organism's full genome has been sequenced, and we shouldn't rely on a note to indicate otherwise. As for where to put them, maybe we need a new page for sequenced organelle genomes? –Adrian J. Hunter 13:43, 1 January 2007 (UTC)

But what about a nucleopmorph? Isn't that misleading? There is a chromist listed that has only its nucleomorph genome sequenced. Kupirijo 18:47, 1 January 2007 (UTC)

I think you're misunderstanding me. "Fully sequenced eukaryote genomes" seems to mean that ALL of the genomes of the eukartyote in question have been sequenced. Does it mean this, or does it mean that the nuclear genome has been sequenced? For a plant, fully sequenced sounds like it means nuclear, plastid and mitochondrial genomes have been sequenced, but actually, you seem to be saying it means the nuclear genome has been sequenced. If the latter is the case, the article should explicitly state that it is about nuclear genomes only. KP Botany 20:25, 1 January 2007 (UTC)

When I started this page I intended for it to be a list of completed nuclear genomes (or whatever weird equivalent the organism may have) - the list did not include organisms that have organelle sequences but lack nuclear sequence, since many plants and animals have organelle sequences - but don't have fully sequenced nuclear genomes. I think a list of fully sequenced organelles by organism might be interesting - but it'd be too long to include in this page. I should add (although I haven't checked) that I'd be very surprised if any organism with a full nuclear genome sequence didn't also have organelle sequences available. --Peta 01:39, 2 January 2007 (UTC)

[edit] To add photosynthetic "cabozoan" chloroplast genomes

The two major photosynthetic "cabozoan" chloroplast genome sequences are available. Euglena gracilis (1993) and Bigelowiella natans (2007). The article by the Keeling group (C-S's nemesis) claims to disprove Cavallier-Smith's cabozoan theory since the chloroplast genomes of the green algae that were phagocytosed by these two organisms are not the same. This means that there were two independent endosymbiosis events of green algae, one for the class Euglenoidea and the other for the class Chlorarachniophyta. See my latest table in algae. I guess C-S was wrong, but I am waiting for his rebuttal. --Kupirijo 01:22, 30 December 2006 (UTC)

• As above, I don't think this list should include organelle only sequences. Heaps of organisms have full organelle sequences available, which don't really fit here as this is a list of complete genomes. Add the info to the species pages.--Peta 00:18, 31 December 2006 (UTC)

[edit] Archea

I started a list of sequenced archeal genomes, I don't have much time to finish it, so if anyone wants to move it to the main namspace and finish it, it's here. --Peta 00:27, 31 December 2006 (UTC)

• The incomplete list is now in the main namespace. --Peta 02:05, 8 January 2007 (UTC)

[edit] Linking the headings?

A non-expert who comes to this page will very likely not know what type of organisms Chromista or Alveolata are, and may be curious to learn. It is, of course, central to Wikipedia's intent that such a curious visitor should be able to just click a wikilink and find out. In January I therefore wikilinked the clade headings on this page. This was promptly reverted, because on the surface it conflicts with the recommendation of the Wikipedia Manual of Style to avoid wikilinks in headings. However, the motivation in the MoS for avoiding wikilinks in headings is that "Depending on settings, some users may not see them clearly. It is much better to put the appropriate link in the first sentence under the heading." In other words, putting a link in a heading instead of in the plain text that follows might make a few users (with unusual display preferences) unable to notice that it is a link, and thus deprive them of the utility of the link. The problem is that on this page there is no following plain text, and no other occurrences of these main clade names: the word protist for example never occurs in the table of sequenced protists. Thus the heading is our only opportunity to link to Protist, and the obvious place to do so. I fail to see how having no link, thus depriving every user of the utility of the link, helps further the intent of the MoS, which was to avoid depriving even a small subset of users of the utility of the link. If we link, most people will see a link; if we don't, nobody will. Therefore I argue that on this particular page we link all the clade headings. Comments? --mglg_(talk) 23:50, 11 February 2007 (UTC)

I think it looks really bad, thats why they MoS says don't do it; why don't we just add a sentence or two before the table explaining (and linking) what the organism is and why it is interesting. --Peta 00:00, 12 February 2007 (UTC)

Nice work, Peta. Thanks! --mglg_(talk) 23:40, 12 February 2007 (UTC)

Thanks, I don't know much about protists, so it'd be great if you could improve the text in any way.--Peta 23:48, 12 February 2007 (UTC)

[edit] Updates

This page really needs some updates. The horse genome has been completed, and i suspect many more - can someone add the horse info, i didn;t know how to edit a table like that. This website - http://www.genome.ucsc.edu lists the rhesus, the cat, the cow and the opossum as all completed, and has lots of information on them. can someone put this into a table, please.

This page is now very seriously out of date. The "animals list" only includes 6 mammals. By Jan 2008 some 24 full Mammal genomes have been sequenced. According to the genome lists on the web http://www.ncbi.nlm.nih.gov/projects/WGS/WGSprojectlist.cgi, with some help from http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Search&db=genomeprj&term=%22Mammalia%22%5BOrganism%5D and http://www.broad.mit.edu/mammals/ the current list of sequenced whole genomes for mammals is: Cow, Dog, Guinea Pig, Nine-banded Armadillo, Horse, European Hedgehog, Cat, Human, African Elephant, Mouse Lemur, Mouse, Pika, Rabbit, Rhesus Macaque, Bushbaby, Chimpanzee, Orangutan, Rat, European Shrew, Squirrel, Northern Tree Shrew, Little Brown Bat, Platypus, Tenrec-Hedgehog Despite announcements in the press, only about 10% of the genome for the Opposum is available. And Entrez is wrong in saying that the Gorilla sequence is complete. (Mollwollfumble (talk) 23:15, 14 January 2008 (UTC))

[edit] What is a gene?

There is no consensus from the leading researchers in a field. I think putting "estimated genes" is pointless and this column should be removed since there is no clear definition to the word. Perhaps 'estimated loci' is more accurate. —Preceding unsigned comment added by 130.113.111.210 (talk) 15:27, 18 January 2008 (UTC)

[edit] Genome size

To the lay reader (me), the value of "551 Kb" for a genome size is ambiguous. I assume that kilobit is intended here, but the kilo- prefix is ambiguous in this context. Does it mean 551*1000 bits or 551*1024 bits? Thunderbird2 (talk) 12:33, 17 February 2008 (UTC)

Looking at Ref. [1] (Douglas et al 2001), I see that Kb actually means kilobase, not kilobit. My question now becomes, what is a kilobase? Thanks in advance Thunderbird2 (talk) 15:03, 17 February 2008 (UTC)

Never mind. I found this, which seems to answer my question. Thunderbird2 (talk) 15:07, 17 February 2008 (UTC)

[edit] TODO: Chlamy

We should add the Chlamydomonas reinhardtii genome. --Kupirijo (talk) 17:55, 8 June 2008 (UTC)