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Alan Rockefeller
Mycologist

Registered: 03/10/07
Posts: 48,266
Last seen: 11 hours, 23 minutes
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Free DNA barcoding for wild mushrooms is now available 11
#28479937 - 09/23/23 12:35 PM (4 months, 2 days ago) |
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ITS DNA barcoding is revolutionizing mushroom identification. It doesn't always tell you exactly what you have found, but it does tell you which other finds are probably the same species. When the name of species isn't known, a provisional name is assigned, so at least we have a name for everything.
Here is an example of a Hygrocybe which was sequenced - it is probably a new species, but it is possible that an old name applies and will be associated with this barcode in the future. It has been given the code name Hygrocybe "sp-IN10", which means that it was the tenth unknown Hygrocybe sequenced in Indiana. This one was found in Florida.
You can search for all of the observations with a certain code name with a URL like this: https://www.inaturalist.org/observations?verifiable=any&place_id=any&field:Provisional%20Species%20Name=Hygrocybe%20%22sp-IN10%22
You can search iNaturalist for DNA barcoded fungi with the following URL: https://www.inaturalist.org/observations?field:DNA%20Barcode%20ITS=
I use this all the time when I want to see photos of a certain species without all the misidentifications. For example Pluteus hongoi is common in the eastern USA, but is often misidentified for Pluteus cervinus.
Here are the DNA verified observations of Pluteus hongoi:
https://www.inaturalist.org/observations?place_id=any&subview=map&taxon_id=516992&field:DNA%20Barcode%20ITS=
It is now possible to get all of your finds DNA barcoded for free! They can be from anywhere in the world, you just need an iNaturalist observation #.

Collecting mushrooms and getting them barcoded is a really great way to add to the knowledge of which species exist, and to figure out what you are finding.
Stephen Russell has a goal of sequencing 100,000 mushroom collections from North America in the next ten years - when this is done we will have a much better idea of the fungal biodiversity that exists, and all the sequence data gets added to Genbank so it is available for free to everyone forever.
ITS sequencing is really good at species discrimination, but it doesn't give much insight into strains, so don't just send in your cubes. Full genome sequencing is good at this - for more information on that see https://entheome.org.
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veggie

Registered: 07/25/04
Posts: 17,501
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Re: Free DNA barcoding for wild mushrooms is now available [Re: Alan Rockefeller] 1
#28480487 - 09/23/23 10:52 PM (4 months, 1 day ago) |
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What a great tool to have access to. And it is all free. Awesome! Thanks for the info.
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Alan Rockefeller
Mycologist

Registered: 03/10/07
Posts: 48,266
Last seen: 11 hours, 23 minutes
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Re: Free DNA barcoding for wild mushrooms is now available [Re: veggie] 2
#28482240 - 09/25/23 10:55 AM (4 months, 11 hours ago) |
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nakadash1
Stranger
Registered: 11/02/22
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Re: Free DNA barcoding for wild mushrooms is now available [Re: Alan Rockefeller]
#28484099 - 09/26/23 06:56 PM (3 months, 30 days ago) |
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Would they have any problems barcoding actives? It would be interesting to submit samples of various strains, like B+, Tidal Wave, and Enigma to see if the story behind Enigma (a mutated cross of B+ and Tidal wave) is accurate.
Edit: Also, Yoshi Amano claims that he made an entirely new strain(Yellow umbo), by crossing natalensis with a cubensis exhibiting yellow caps. If one were to submit this strain for barcoding would there be any interesting results?
-------------------- #1 Tek With utmost care and precision,I work to achieve my fungal mission. Sterilizing all my tools and space,to ensure not a single spore is out of place. I carefully select the fungal strain and onto the agar, I make it rain. With a steady hand and gentle touch, I inoculate the plate without a hitch. Success is sweet when it's pure and true, and my agar plates are a testament too. A job well done, with no contamination, my fungi inoculation, a thing of admiration. JK NO --Bacteriological Virtuoso aka Master of Mold
Edited by nakadash1 (09/26/23 06:58 PM)
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Alan Rockefeller
Mycologist

Registered: 03/10/07
Posts: 48,266
Last seen: 11 hours, 23 minutes
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Re: Free DNA barcoding for wild mushrooms is now available [Re: nakadash1]
#28484173 - 09/26/23 07:52 PM (3 months, 30 days ago) |
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Quote:
nakadash1 said: Would they have any problems barcoding actives? It would be interesting to submit samples of various strains, like B+, Tidal Wave, and Enigma to see if the story behind Enigma (a mutated cross of B+ and Tidal wave) is accurate.
Edit: Also, Yoshi Amano claims that he made an entirely new strain(Yellow umbo), by crossing natalensis with a cubensis exhibiting yellow caps. If one were to submit this strain for barcoding would there be any interesting results?
No problems with submitting actives, but DNA barcoding will tell you a cube is a cube, and no more. Full genome sequencing is needed to get insight into strains, and that is expensive.
Psilocybe natalensis will show up as different than cubensis. It would be interesting to see how a hybrid sequence looks, it might show one parent, or the other parent, or a mix of both.
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Carnonos
The Horned Wanderer

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Re: Free DNA barcoding for wild mushrooms is now available [Re: Alan Rockefeller]
#28496039 - 10/07/23 11:42 PM (3 months, 18 days ago) |
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Read through the doc and am thinking of submitting some samples, but I didn't see a sample size listed anywhere. Is there a minimum g/mg amount needed for genetic sequencing?
-------------------- All that is gold does not glitter, Not all those who wander are lost; The old that is strong does not wither, Deep roots are not reached by the frost. J.R.R. Tolkien
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Alan Rockefeller
Mycologist

Registered: 03/10/07
Posts: 48,266
Last seen: 11 hours, 23 minutes
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Re: Free DNA barcoding for wild mushrooms is now available [Re: Carnonos]
#28497383 - 10/09/23 08:46 AM (3 months, 17 days ago) |
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Quote:
Carnonos said: Read through the doc and am thinking of submitting some samples, but I didn't see a sample size listed anywhere. Is there a minimum g/mg amount needed for genetic sequencing?
A few milligrams is all that is needed for DNA barcoding. Larger collections are nice so they can be a holotype of a new species, but any size collection is very useful.
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murderlabz
RIP Stoneman



Registered: 05/18/19
Posts: 550
Loc: The Multiverse
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Re: Free DNA barcoding for wild mushrooms is now available [Re: Alan Rockefeller] 1
#28510902 - 10/19/23 06:24 PM (3 months, 7 days ago) |
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Soloist
Indigenous Human

Registered: 02/10/22
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Re: Free DNA barcoding for wild mushrooms is now available [Re: murderlabz]
#28546735 - 11/17/23 04:13 PM (2 months, 9 days ago) |
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That is really really cool! I definitely want to help!
This makes me want to go out and hunt for Psilocybe graveolens, Iβve seen some of the observations on MO and am actually familiar with the habitat. Living on Long Island I know Iβm close to where the type species was collected. Maybe this coming year I could get off my ass and give it a go.
-------------------- Embrace your darkness, For without it, Your light can never truly exist. πππππππππ The Earth And I 89g fresh Gymnopilus subspectibilis RapΓ©h Crafters Trade and wish list ππMOππ Itβs time to ghost this placeβπ»
Edited by Soloist (11/17/23 04:17 PM)
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