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leschampignons
Biochemistry + Mycology


Registered: 08/30/13
Posts: 1,583
Loc: NY/NJ/ME
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Cryptotrama sp. Can't find much of anything about this genus
#23429870 - 07/10/16 05:16 PM (7 years, 6 months ago) |
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http://mushroomobserver.org/243855?q=2nPPM
I saved a sample and could throw it under the scope if people are interested. Doesn't look like C. asprata to me. No fuzziness on the cap.
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leschampignons
Biochemistry + Mycology


Registered: 08/30/13
Posts: 1,583
Loc: NY/NJ/ME
Last seen: 4 days, 6 hours
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Re: Cryptotrama sp. Can't find much of anything about this genus [Re: leschampignons]
#23429873 - 07/10/16 05:17 PM (7 years, 6 months ago) |
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I'd love to hear anyone's opinion about the ID of this mushroom or just any general info about the genus including monographs and other references.
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ToxicMan
Bite me, it's fun!


Registered: 06/28/02
Posts: 6,722
Loc: Aurora, Colorado
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Re: Cryptotrama sp. Can't find much of anything about this genus [Re: leschampignons]
#23430225 - 07/10/16 07:42 PM (7 years, 6 months ago) |
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They do look reasonably close. Here's a quick link to the most obvious place:
http://www.mushroomexpert.com/cyptotrama_asprata.html
I would be tempted to attribute a lack of the granular stuff to having it wash off in rain. I frequently find Cystoderma that way.
A look at the spores and hymenocystidia should help confirm an ID.
-------------------- Happy mushrooming!
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leschampignons
Biochemistry + Mycology


Registered: 08/30/13
Posts: 1,583
Loc: NY/NJ/ME
Last seen: 4 days, 6 hours
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Re: Cryptotrama sp. Can't find much of anything about this genus [Re: ToxicMan]
#23430261 - 07/10/16 07:51 PM (7 years, 6 months ago) |
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Ok cool thanks for the response. does hymenocystidia just mean any cystidia on the gills/spore bearing surface of the mushroom? So cheilocystidia and Pleurocystidia
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Alan Rockefeller
Mycologist

Registered: 03/10/07
Posts: 48,276
Last seen: 2 hours, 25 minutes
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Re: Cryptotrama sp. Can't find much of anything about this genus [Re: leschampignons]
#23430314 - 07/10/16 08:03 PM (7 years, 6 months ago) |
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Right, hymenocystidia are any of the cystidia on the hymenium.
You have one of the things that is being called Cyptotrama asprata, I heard that there were at least three species going under that name. Not sure if the others have been named.
I wouldn't spend too much time with the microscopy, it's going to match. If you are curious about it, get the DNA sequenced (ITS gene) and then see if the sequence you have turns up in a location similar to where it was described from. I haven't read the paper that described it but I suspect it is European.
You could also do some GenBank work without sequencing it, check to see if sequences from the midwest/east of North America match sequences from nearer to where it was described. The best thing to do would be to make a phylogenetic tree of the 100 closest BLAST matches that includes locations on each sequence, that way you have all the data in front of you in a visual format so you don't need to be comparing individual base pairs or staring at alignments.
Let me know if you need any help with the bioinformatics.
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leschampignons
Biochemistry + Mycology


Registered: 08/30/13
Posts: 1,583
Loc: NY/NJ/ME
Last seen: 4 days, 6 hours
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Re: Cryptotrama sp. Can't find much of anything about this genus [Re: Alan Rockefeller]
#23430487 - 07/10/16 08:52 PM (7 years, 6 months ago) |
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Ok so if I go on genbank and search this mushroom I get 78 matches and it appears that only #42 to #69 have info about ITS genes. So about 28 entries of ITS sequences total.
So I clicked the FASTA link below #42 on genbank and it gave me the DNA sequence in GTGTGTGAAATCC format. Then I plugged that into BLAST and I see a bunch of C. asprata and then farther down some other species that are less closely related. How do I restrict the search results to collections/sequences that include the location where the sample was taken? Also what software would I use to create a phylogenetic tree? Is it part of the BLAST website or a separate program?
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Alan Rockefeller
Mycologist

Registered: 03/10/07
Posts: 48,276
Last seen: 2 hours, 25 minutes
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Re: Cryptotrama sp. Can't find much of anything about this genus [Re: leschampignons]
#23430597 - 07/10/16 09:36 PM (7 years, 6 months ago) |
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I don't know of any way to restrict matches to ones with location data. It's complicated because while there is a Country field in the sequence data that often has location data, sometimes that field is left blank and you can get the location from the name of the paper - for example sometimes the paper is something like "A study of fungi in French Polynesia". Sometimes you have to read the paper to find the location - they often will have a table that lists the collections and locations. Sci-hub.bz is really helpful for getting papers.
What I do is download the nearest 50 or 100 or 250 BLAST matches in FASTA format, then run that through a perl script I wrote that looks up the location field for each sequence and replaces the long name with just the Genbank #, species name and location. For close matches I manually look up the locations that the script doesn't get, if I care enough about the locations to do that. Locations for the really close matches are a lot more important than locations for closely related species.
You can make a tree through BLAST, but I usually use phylogeny.lirmm.fr/phylo_cgi/simple_phylogeny.cgi to make a quick tree. If I want to make a good tree for publication I use RaxML (via https://www.phylo.org/portal2/login!input.action) and FigTree. The quick trees pretty much always turn out the same as the high quality trees, but you get a lot more configuration and display options.
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