Talk:List of sequenced plastomes

	This article is within the scope of WikiProject Lists, an attempt to structure and organize all list pages on Wikipedia. If you wish to help, please visit the project page, where you can join the project and/or contribute to the discussion.ListsWikipedia:WikiProject ListsTemplate:WikiProject ListsList articles
???	This article has not yet received a rating on the project's importance scale.

Plants Mid‑importance

	Plants portal This article is within the scope of WikiProject Plants, a collaborative effort to improve the coverage of plants and botany on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.PlantsWikipedia:WikiProject PlantsTemplate:WikiProject Plantsplant articles
Mid	This article has been rated as Mid-importance on the project's importance scale.

Scope

Whether nucleomorph and Paulinella cyanelle genomes are plastomes is at best debatable, but since they are too few (unlike, say, mitomes) to justify a separate list, it is convenient to append them to this list. Lavateraguy (talk) 10:42, 1 August 2008 (UTC)[reply]

Section headers

Two of these were unfamiliar to me. The first was Cyanophytes, which I see is the group which I would know as cyanobacteria (most likely) or blue-green algae. The second is Metalgae, a word which seems to appear nowhere on wikipedia and only 5 places on google. Is this misspelled? I see it includes Euglenids, Cryptomonads, and I don't know what Odontella sinensis is. Perhaps just make section headers for each of those groups and rename "other" to Apicomplexa (and add new sections as needed for dinoflagellates and the others)? Kingdon (talk) 04:46, 1 August 2008 (UTC)[reply]

Cyanophyte was a slip of the brain; I meant glaucophyte, which are those few species with primarily endosymbiotic photosynthesis which are neither green nor red algae. Metalgae seems to be a misrecollection on my part of meta-algae, which are species which have secondary or tertiary endosymbiotic photosynthesis. Dinoflagellates are meta-algae. Apicomplexans are the biggest group of others, but there's the question as to where you draw the line with secondarily aphotosynthetic euglenoids and chlorarachniophytes and related species. (Cf. Epifagus virginiana is still a plant.) Lavateraguy (talk) 09:55, 1 August 2008 (UTC)[reply]

I guess I would include non-photosynthetic euglenoids and chlorarachniophytes along with their photosynthetic relatives, I guess just because it seems a bit odd to classify the page phylogenetically everywhere else and then fall back to a definition based on photosynthetic vs not. This would imply a definition similar to the one we now have for "meta-algae" but without the word "photosynthetic" (so "other" would go away). It is possible that the best term is something like "eukaryotes with secondary and tertiary plastids" and the best definition is just to list the 7 groups. Another term in the literature is "eukaryote-eukaryote chimaeras" but that seems less common than "secondary plastid". Kingdon (talk) 14:45, 1 August 2008 (UTC)[reply]

Notes column

On some of the tables, i put in a column for notes. For the ferns, lycophytes, and gymnosperms, i put family names in this column. I am considering family and order names for the flowering plants. Does anyone think that this extends the table excessively? I would appreciate some comment before i go ahead with this. 128.171.106.243 (talk) 00:27, 5 May 2010 (UTC)[reply]

Not sure I have a strong opinion, but it strikes me as a bit more natural to organize the list by family (or perhaps order or monocot/eudicot/magnoliid/etc), with headings for each group. Kingdon (talk) 00:07, 17 May 2010 (UTC)[reply]

Number of genes

The NCBI list does not correlate with the numbers shown here. Does anyone have a strong opinion on whether we should use the original publication or the current number on NCBI? I'd prefer to use the NCBI data, and to list protein coding genes to separately to RNA genes. If there are no complaints, I'll start in a week or so. Aaadddaaammm (talk) 01:58, 2 January 2012 (UTC)[reply]

Red Algae

There a paywalled article in Current Biology with 6 new rhodophyte plastomes. Judging by the abstract it will also give citations to more than the current 5 plastomes listed on the page. Lavateraguy (talk) 09:43, 13 July 2017 (UTC)[reply]

External links modified

Hello fellow Wikipedians,

I have just modified one external link on List of sequenced plastomes. Please take a moment to review my edit. If you have any questions, or need the bot to ignore the links, or the page altogether, please visit this simple FaQ for additional information. I made the following changes:

Added archive https://archive.is/20061004083557/http://www.expasy.ch/sprot/hamap/plastid.html to http://www.expasy.ch/sprot/hamap/plastid.html

When you have finished reviewing my changes, you may follow the instructions on the template below to fix any issues with the URLs.

This message was posted before February 2018. After February 2018, "External links modified" talk page sections are no longer generated or monitored by InternetArchiveBot. No special action is required regarding these talk page notices, other than regular verification using the archive tool instructions below. Editors have permission to delete these "External links modified" talk page sections if they want to de-clutter talk pages, but see the RfC before doing mass systematic removals. This message is updated dynamically through the template {{source check}} (last update: 5 June 2024).

If you have discovered URLs which were erroneously considered dead by the bot, you can report them with this tool.
If you found an error with any archives or the URLs themselves, you can fix them with this tool.

Cheers.—InternetArchiveBot (Report bug) 08:54, 2 January 2018 (UTC)[reply]

What to do with this page?

The number of published plastomes is now increasing at a great pace. (There are now 244 for Malvaceae alone, though with some species replicated several times over.) Extremely large lists (e.g. list of minor planets, list of placental mammals) are not without precedent in Wikipedia, but it might be worth having a discussion about the way forward for this page. Lavateraguy (talk) 19:53, 8 May 2021 (UTC)[reply]

There are 29 thousand plastomes of 12 thousand species could be found in Genbank, accounting for almost 4% of known plant species. https://www.ncbi.nlm.nih.gov/nuccore/?term=%22chloroplast%2C+complete+genome%22 ——🦝 The Interaccoonale ^{Will be the raccoon race}_{(talk・contribs)} 06:20, 3 November 2022 (UTC)[reply]

I think it would be a good idea to list the number of sequenced species by family or genus. ——🦝 The Interaccoonale ^{Will be the raccoon race}_{(talk・contribs)} 06:32, 3 November 2022 (UTC)[reply]

Perhaps we should move to Plastome sequence and talk about most salient or earliest sequences, methods and applications. Invasive Spices (talk) 3 November 2022 (UTC)

But I think applications should be in chloroplast DNA, for example, plastome as a phylogenomic marker.——🦝 The Interaccoonale ^{Will be the raccoon race}_{(talk・contribs)} 03:30, 7 November 2022 (UTC)[reply]

@Interaccoonale @Lavateraguy @Invasive Spices Since 3 November 2022, the number of plastomes has increased by more than 50%, with just shy of 20,000 species. I think the idea of a manually curated comprehensive table is not going to work, and would also not be very helpful to the reader. As is, the page is hopelessly outdated and therefore misleading, so I think if we keep it we should decide what its role should be.

I suppose my idea would be merging some of the most salient information of general interest into Chloroplast DNA, but I'd be open to any other ideas. Felix QW (talk) 09:22, 17 October 2024 (UTC)[reply]

How about list some earliest sequenced plastomes and some special ones (for example, some parasitic plants with significant structural variations)? ——🦝 The Interaccoonale ^{Will be the raccoon race}_{(talk・contribs)} 23:20, 17 October 2024 (UTC)[reply]

I think that would make sense, but I also think that might be more useful in prose than as a list. For instance, Chloroplast DNA currently includes

More than 5000 chloroplast genomes have been sequenced and are accessible via the NCBI organelle genome database. The first chloroplast genomes were sequenced in 1986, from tobacco (Nicotiana tabacum) and liverwort (Marchantia polymorpha). Comparison of the gene sequences of the cyanobacteria Synechocystis to those of the chloroplast genome of Arabidopsis provided confirmation of the endosymbiotic origin of the chloroplast. It also demonstrated the significant extent of gene transfer from the cyanobacterial ancestor to the nuclear genome.

I think that such text is a lot more helpful than a short table listing the species and dates. Of course, it would be more work to find actual secondary literature supporting such prose, but the effort could be worth it. Then one can still see whether it is better on a separate page or as a section in Chloroplast DNA. Felix QW (talk) 13:19, 19 October 2024 (UTC)[reply]

I created this article in 2008, as I was putting together a list for my own purposes, and thought that it might as well be publicly available. I failed to foresee the explosive growth in DNA sequencing, which has led to the list being vastly incomplete. In principle it could be split into smaller lists (cf minor planets, placental mammals, ...) - perhaps by order for flowering plants and phylum for everything else - but in the absence of interest in doing the work I think that the way forward is to save what is worth saving, and then take the article to AfD.

The nucleomorph genome table can go to nucleomorph. Lavateraguy (talk) 22:33, 19 October 2024 (UTC)[reply]

The apicomplexan table can go to apicoplast (with the addition of a genome section).

I have some issues with the naming and content of the chloroplast DNA page (not all plastids are chloroplasts; the material protein synthesis and trafficking is not about chloroplast DNA - I suggest a split to plastid proteome. I'll start a discussion at TALK:chloroplast DNA. Lavateraguy (talk) 22:39, 19 October 2024 (UTC)[reply]