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OfflineLongtimenosee
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Registered: 12/05/22
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Gene sequencing
    #28084774 - 12/05/22 01:55 PM (1 year, 1 month ago)

I was wondering how people on here go about sequencing mushroom samples. At home kits? Send away tests? Also what is the typical coast per sample? Thanks!


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Invisiblecooleko
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Registered: 08/15/22
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Re: Gene sequencing [Re: Longtimenosee]
    #28084823 - 12/05/22 02:43 PM (1 year, 1 month ago)

Sequencing the whole genome is expensive. Unless you know someone who will slide it in for free or as part of an ongoing project with a university, it will likely exceed your desired threshold by a zero or three.

If you just want to use a smaller assay to identify the genus you can use a send away kit for $50 to a few hundred.

I can't speak to which test kits are best to use but google lists several.


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InvisibleIcyurmt
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Re: Gene sequencing [Re: cooleko]
    #28084903 - 12/05/22 03:51 PM (1 year, 1 month ago)

This place does ITS extraction/sequencing for a little less than $20 a sample http://alvalab.es/

The cost per sample can be brought down if you set up a home pcr lab for the extraction/amplification portion, but that requires more upfront investment (around 1k iirc). If you search on here, Alan Rockefeller provides a lot of great info and advice on it all.


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Hunt for the habitat not the mushroom.


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OfflineAlan RockefellerM
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Re: Gene sequencing [Re: Longtimenosee]
    #28085570 - 12/06/22 12:34 AM (1 year, 1 month ago)

Quote:

Longtimenosee said:
I was wondering how people on here go about sequencing mushroom samples. At home kits? Send away tests? Also what is the typical coast per sample? Thanks!





What are the questions that you hope to be able to answer with the sequencing?    This will determine which type of sequencing you need to do and which genes you need to look at.

Here is a webpage I wrote that shows how to do DNA barcoding at home:  https://wiki.counterculturelabs.org/wiki/DNA_sequencing

McLab sequences PCR products for $3 each.


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OfflineLongtimenosee
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Registered: 12/05/22
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Re: Gene sequencing [Re: Alan Rockefeller]
    #28086064 - 12/06/22 01:46 PM (1 year, 1 month ago)

I am looking to sequence a Psilocybe sp. that I believe to be a currently undescribed species. Probably going to send out the sample to be tested seams easier.


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OfflineAlan RockefellerM
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Re: Gene sequencing [Re: Longtimenosee]
    #28106587 - 12/20/22 08:31 PM (1 year, 1 month ago)

Quote:

Longtimenosee said:
I am looking to sequence a Psilocybe sp. that I believe to be a currently undescribed species. Probably going to send out the sample to be tested seams easier.




It sounds like you want to sequence the barcode gene(s) then - ITS is the first one you should do because that will have the most matches.  If you want more complete sequencing you could add LSU, RPB1, RPB2 and TEF1 genes, but that will be unlikely to tell you anything that ITS doesn't.  It would allow you and future researchers to build a phylogenetic tree with good bootstrap support, to accurately place it in a section and figure out which species it evolved from.

You could send a sample to http://alvalab.es - they charge about 20 euros to do sequencing.  For unusual Psilocybe you could also send them to me - I sequence a lot of obscure Psilocybe and don't charge people because it's a genus I am working on.


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