Talk:CrAssphage
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genome lienar or circular
[edit]This article indicates the crAssphage genome as circular, but SIB crAssphage (ViralZone) shows and indicates it as linear. Please, can an expert clarify this? :-) Kind regards, Ernst.--Ernsts (talk) 09:51, 2 October 2019 (UTC)
- @Ernsts: Not an expert, but it looks like it was me who added the fact that it had a circular genome. I've checked the original 2014 paper and it definitely states circular. The 2018 paper by Shkoporov et al. states "circular or circularly permuted". ViralZone could simply be mistaken? Espresso Addict (talk) 06:08, 22 February 2021 (UTC)
- @Espresso Addict: Thanks for the message! I'm in contact with Philippe Le Mercier of SIB ViralZone since some time and just forwarded your note via email to Phil for clearifying. I'm afraid it might take a while as Phil was ooto last week. I'll hope to get an update on ViralZone if neccessary, so I could update the information provided here as well.--Ernsts (talk) 10:14, 22 February 2021 (UTC)
- Thanks! It is possible there's some explanation, or a later paper, that Dr Le Mercier might be able to provide. Espresso Addict (talk) 10:20, 22 February 2021 (UTC)
- BTW ViralZone tells about crAss-like phages comprise estimated 10 genera, NCBI lists them asd 'clade'. If the family was Podoviridae the clade rank must be higher than genus but lower than family, i. e. probably subfamily. However the Taxon Box here states crAss-like phages as single genus. I'm afraid I'm not very familiar with the english taxon box, so please could anyone correct it? Thanks--Ernsts (talk) 11:10, 22 February 2021 (UTC)
- @Espresso Addict:Philippe Le Mercier has updated https://viralzone.expasy.org/8496 -- crAssphage genome is circular. Just remaing a fix of the box here as we have a clade of about 10 genera. --Ernsts (talk) 21:49, 22 February 2021 (UTC)
- Thanks, Ernsts. I've hacked the infobox to better reflect my understanding of the current position, but we really need expert assistance here to create the proper virus taxobox, which I suspect needs work in Wikidata? It is possible that the virus taxobox only gets created when the entity is formally recognised by the ICTV, which I don't think (looking at the 2019 release) has yet happened. Espresso Addict (talk) 00:49, 23 February 2021 (UTC)
- @Espresso Addict:Philippe Le Mercier has updated https://viralzone.expasy.org/8496 -- crAssphage genome is circular. Just remaing a fix of the box here as we have a clade of about 10 genera. --Ernsts (talk) 21:49, 22 February 2021 (UTC)
- BTW ViralZone tells about crAss-like phages comprise estimated 10 genera, NCBI lists them asd 'clade'. If the family was Podoviridae the clade rank must be higher than genus but lower than family, i. e. probably subfamily. However the Taxon Box here states crAss-like phages as single genus. I'm afraid I'm not very familiar with the english taxon box, so please could anyone correct it? Thanks--Ernsts (talk) 11:10, 22 February 2021 (UTC)
- Thanks! It is possible there's some explanation, or a later paper, that Dr Le Mercier might be able to provide. Espresso Addict (talk) 10:20, 22 February 2021 (UTC)
- @Espresso Addict: Thanks for the message! I'm in contact with Philippe Le Mercier of SIB ViralZone since some time and just forwarded your note via email to Phil for clearifying. I'm afraid it might take a while as Phil was ooto last week. I'll hope to get an update on ViralZone if neccessary, so I could update the information provided here as well.--Ernsts (talk) 10:14, 22 February 2021 (UTC)
Espresso Addict crAss-like phages aren't yet officially classified but there is a proposal to have them be an order in Caudoviricetes. This proposal hasn't been approved by the ICTV and isn't in the list of proposals pending ratification, so it probably won't come with the upcoming taxonomy update and it may be changed significantly before approval/ratification. I can convert the taxobox to a virusbox for the proposed taxonomy of crAssphage, but maybe viruses that aren't yet classified shouldn't have virusboxes since the proposed taxonomy may change. Velayinosu (talk) 01:45, 23 February 2021 (UTC)
- Thanks, Velayinosu. That's interesting -- does it mean tailed phages are no longer considered monophyletic? Maybe hold off creating a virus taxobox until the ICTV ratifies, otherwise it might well just have to be redone? And in any case it would give the impression that the classification is fixed, when it isn't. In the meantime, not sure what exactly to do with the taxobox as I'm not sure the old format supports the new levels that were introduced recently. Espresso Addict (talk) 02:01, 23 February 2021 (UTC)
Wiki Education assignment: Microbial Symbiosis and Microbiomes
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This article was the subject of a Wiki Education Foundation-supported course assignment, between 16 August 2022 and 14 December 2022. Further details are available on the course page. Student editor(s): Jlmaier12 (article contribs).
— Assignment last updated by Jlmaier12 (talk) 19:51, 7 October 2022 (UTC) Hi everyone, I picked crAssphage as my topic for the Wikipedia assignment for my Microbial Symbiosis and Microbiomes course and have drafted some additions I'd like to make to this article. I would like to add more sections with information including crAss-like phage discovery, taxonomy, and replication strategy. I have tried to preserve the original authors' writing but have separated sentences into their respective sections. Please be kind if you don't agree with an edit I make and would like it changed :) — Preceding unsigned comment added by Jlmaier12 (talk • contribs) 17:01, 18 November 2022 (UTC)