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OfflineAlan RockefellerM
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New Psilocybe sequences in Genbank
    #19266892 - 12/12/13 05:28 PM (10 years, 2 months ago)
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In the past few days, a whole lot of new Psilocybe sequences have shown up in Genbank from the Ramirez-Cruz paper.

The new sequences are attached.

Some of my friends in Mexico use PhyDE for editing, TnT - Tree Analysis using new technology for making trees and RAxML for maximum liklihood.

The new sequences include:


<AR> /home/alan <28> > cat sequence.fasta | grep Psilocybe | cut -c30-5599 | sort | uniq
Psilocybe caerulescens voucher Franco-Galvan 1 (IBUG) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
Psilocybe caerulescens voucher Franco-Galvan 1 (IBUG) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe caerulescens voucher Franco-Galvan 1 (IBUG) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe caerulipes voucher SAT09-216-06 (TENN) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
Psilocybe caerulipes voucher SAT09-216-06 (TENN) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe cubensis voucher RHP5203 (TENN) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
Psilocybe cubensis voucher RHP5203 (TENN) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe cubensis voucher V. Ramirez-Cruz 87 (XAL) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
Psilocybe cubensis voucher V. Ramirez-Cruz 87 (XAL) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe cubensis voucher V. Ramirez-Cruz 87 (XAL) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe cyanescens voucher J. Workman & P. Werner s.n. (XAL) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
Psilocybe cyanescens voucher J. Workman & P. Werner s.n. (XAL) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe cyanescens voucher J. Workman & P. Werner s.n. (XAL) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe cyanescens voucher Ower 257(F) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe cyanescens voucher Ower 257(F) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe cyanescens voucher Ower 257(F) internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
Psilocybe cyanescens voucher S. Chornick s.n. (IBUG) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe cyanescens voucher S. Chornick s.n. (IBUG) internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
Psilocybe cyanescens voucher S. Chornick s.n.(IBUG) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe fagicola voucher M.A. Gomez 22731 (IBUG) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
Psilocybe fagicola voucher M.A. Gomez 22731 (IBUG) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe fagicola voucher M.A. Gomez 22731 (IBUG) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe hispanica voucher R. Fernandez-Sasia s.n. (XAL) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
Psilocybe hispanica voucher R. Fernandez-Sasia s.n. (XAL) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe hispanica voucher R. Fernandez-Sasia s.n. (XAL) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe mescaleroensis voucher L. Field Walstad s.n. Holotype (XAL) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe mescaleroensis voucher L. Field Walstad s.n. Holotype (XAL) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe mescaleroensis voucher L. Field Walstad s.n. Holotype (XAL) internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
Psilocybe mexicana voucher M.R. Sanchez-Jacome 1038 (IBUG) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
Psilocybe mexicana voucher M.R. Sanchez-Jacome 1038 (IBUG) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe mexicana voucher M.R. Sanchez-Jacome 1038 (IBUG) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe neoxalapensis voucher M.A. Gomez 1883 (XAL) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe neoxalapensis voucher M.A. Gomez 1883 (XAL) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe pelliculosa voucher S. Chornick s.n. (IBUG) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
Psilocybe pelliculosa voucher S. Chornick s.n. (IBUG) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe samuiensis voucher Sihanonth & J. Allen s.n. (XAL) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe samuiensis voucher Sihanonth & J. Allen s.n.(XAL) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
Psilocybe serbica voucher I. krisai s.n. (WU) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
Psilocybe serbica voucher I. krisai s.n. (WU) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe serbica voucher I. krisai s.n. (WU) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe sp. 1 VRZ-2013 voucher V. Ramirez-Cruz 551 (IBUG) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
Psilocybe sp. 1 VRZ-2013 voucher V. Ramirez-Cruz 551 (IBUG) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe sp. 1 VRZ-2013 voucher V. Ramirez-Cruz 551 (IBUG) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe sp. 2 VRZ-2013 voucher V. Ramirez-Cruz 1328 (IBUG) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe sp. 2 VRZ-2013 voucher V. Ramirez-Cruz 1328 (IBUG) 5.8S ribosomal RNA gene and internal transcribed spacer 2, partial sequence
Psilocybe sp. 2 VRZ-2013 voucher V. Ramirez-Cruz 1328 (IBUG) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe sp. 3 VRZ-2013 voucher M. No-Line s.n. (IBUG) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
Psilocybe sp. 3 VRZ-2013 voucher M. No-Line s.n. (IBUG) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe stuntzii voucher S. Chornick s.n. (IBUG) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
Psilocybe stuntzii voucher S. Chornick s.n. (IBUG) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe subaeruginosa voucher L.Taylor (PDD) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
Psilocybe subaeruginosa voucher L.Taylor (PDD) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe subaeruginosa voucher PBM 3218 (TENN) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
Psilocybe subaeruginosa voucher PBM3218 (TENN) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe subcubensis voucher G. Guzman 35102 (XAL) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe subcubensis voucher G. Guzman 35102 (XAL) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe subcubensis voucher G. Guzman 35102 (XAL) internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
Psilocybe thaiaerugineomaculans voucher S.C. Karunarathna NTS-121, Holotype (XAL) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
Psilocybe thaiaerugineomaculans voucher S.C. Karunarathna NTS-121, Holotype (XAL) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe thaiduplicatocystidiata voucher S.C. Karunarathna NTS-120, Isotype (XAL) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
Psilocybe thaiduplicatocystidiata voucher S.C. Karunarathna NTS-120, Isotype (XAL) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe thaiduplicatocystidiata voucher S.C. Karunarathna NTS-120, Isotype (XAL) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe thaizapoteca voucher G. Guzman 38342, Holotype (XAL) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
Psilocybe thaizapoteca voucher G. Guzman 38342, Holotype (XAL) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe yungensis voucher A. Cortes-Perez 549 (XAL) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
Psilocybe yungensis voucher A. Cortes-Perez 549 (XAL) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe yungensis voucher A. Cortes-Perez 549 (XAL) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe zapotecoantillarum voucher S. Cantrell & Salgado s.n., Isotype (XAL) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
Psilocybe zapotecoantillarum voucher S. Cantrell & Salgado s.n., Isotype (XAL) 28S large subunit ribosomal RNA gene, partial sequence
Psilocybe zapotecoantillarum voucher S. Cantrell & Salgado s.n., Isotype (XAL) RNA polymerase II largest subunit (rpb1) gene, partial cds
Psilocybe zapotecorum voucher V. Ramirez-Cruz 1094 (IBUG) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
Psilocybe zapotecorum voucher V. Ramirez-Cruz 1094 (IBUG) 28S large subunit ribosomal RNA gene, partial sequence


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Offlinepsylosymonreturns
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Re: New Psilocybe sequences in Genbank [Re: Alan Rockefeller]
    #19267696 - 12/12/13 08:03 PM (10 years, 2 months ago)

I wish I knew what this meant! Great work non the less .:congrats:


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OfflineAlan RockefellerM
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Re: New Psilocybe sequences in Genbank [Re: psylosymonreturns]
    #19267717 - 12/12/13 08:06 PM (10 years, 2 months ago)

What are the mushroomobserver links for the Psilocybe cyanescens, P. pelliculosa and P. stuntzii collections that you sent her?


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OfflineMachineElf1.618
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Re: New Psilocybe sequences in Genbank [Re: Alan Rockefeller]
    #19267722 - 12/12/13 08:07 PM (10 years, 2 months ago)

This is awesome Alan. Are these only ribosomal RNA sequences though? I did a quick search on NCBI but I can't find any whole genome sequences only rRNA sequences. Have genomes been sequenced for P. cubensis or P. cyanescens?


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OfflineAlan RockefellerM
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Re: New Psilocybe sequences in Genbank [Re: MachineElf1.618]
    #19267729 - 12/12/13 08:08 PM (10 years, 2 months ago)

Whole genomes have not been sequenced.


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Offlinepsylosymonreturns
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Re: New Psilocybe sequences in Genbank [Re: Alan Rockefeller]
    #19267738 - 12/12/13 08:09 PM (10 years, 2 months ago)

Quote:

Alan Rockefeller said:
What are the mushroomobserver links for the Psilocybe cyanescens, P. pelliculosa and P. stuntzii collections that you sent her?




I never did make them. But i still have the pics so I can still do it.


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OfflineMachineElf1.618
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Re: New Psilocybe sequences in Genbank [Re: Alan Rockefeller]
    #19267756 - 12/12/13 08:11 PM (10 years, 2 months ago)

Quote:

Alan Rockefeller said:
Whole genomes have not been sequenced.




Why the heck not!?:mad2: Seriously though. I know you guys need the rRNA for taxonimic purposes but why haven't the genomes been sequenced? Is it against the law or something?


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OfflineAlan RockefellerM
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Re: New Psilocybe sequences in Genbank [Re: MachineElf1.618]
    #19267767 - 12/12/13 08:12 PM (10 years, 2 months ago)

Yes please do!

Now that the sequences are in genbank, the pics are super important!
Quote:



mtlmike90 said:
Why the heck not!?:mad2: Seriously though. I know you guys need the rRNA for taxonimic purposes but why haven't the genomes been sequenced? Is it against the law or something?




I can't think of any reason we would need the full genome.

It's also really expensive to sequence millions of base pairs.


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OfflineMachineElf1.618
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Re: New Psilocybe sequences in Genbank [Re: Alan Rockefeller]
    #19267826 - 12/12/13 08:22 PM (10 years, 2 months ago)

Quote:

Alan Rockefeller said:
Yes please do!

Now that the sequences are in genbank, the pics are super important!
Quote:



mtlmike90 said:
Why the heck not!?:mad2: Seriously though. I know you guys need the rRNA for taxonimic purposes but why haven't the genomes been sequenced? Is it against the law or something?




I can't think of any reason we would need the full genome.

It's also really expensive to sequence millions of base pairs.




There is a lot you can learn from the genome trust me. I'm actually quite surprised you don't think so. I know it can get expensive. I've had plasmids and bacterial genomes sequenced which is far cheaper than eukaryotic genomes. I'm really interested about this though. Do you know anyone doing any research on fungal genomes?


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InvisibleThe Lightning
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Re: New Psilocybe sequences in Genbank [Re: Alan Rockefeller]
    #19267842 - 12/12/13 08:25 PM (10 years, 2 months ago)

Quote:



I can't think of any reason we would need the full genome.

It's also really expensive to sequence millions of base pairs.




The full genome is being studied in human beings. It should also be sequenced in the genus Psilocybe and other active fungi.

When we compare phylogenies of the full ITS barcode with other regions (COI, etc), we do see different results.

The full genome may again give us a different tree with a different ancestor - and this is highly valuable and intriguing from all of our vantage points.

The cost cannot overcome the benefit of the knowledge obtained. I highly encourage you to explore this as one of your riffs.


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OfflineMachineElf1.618
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Re: New Psilocybe sequences in Genbank [Re: The Lightning]
    #19267850 - 12/12/13 08:26 PM (10 years, 2 months ago)

Quote:

The Lightning said:
Quote:



I can't think of any reason we would need the full genome.

It's also really expensive to sequence millions of base pairs.




The full genome is being studied in human beings. It should also be sequenced in the genus Psilocybe and other active fungi.

When we compare phylogenies of the full ITS barcode with other regions (COI, etc), we do see different results.

The full genome may again give us a different tree with a different ancestor - and this is highly valuable and intriguing from all of our vantage points.

The cost cannot overcome the benefit of the knowledge obtained. I highly encourage you to explore this as one of your riffs.




Yes, exactly!


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InvisibleJoust
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Re: New Psilocybe sequences in Genbank [Re: Alan Rockefeller]
    #19267857 - 12/12/13 08:27 PM (10 years, 2 months ago)

damn im not on this list...


--------------------
~~~~~~***Psilocybin Mushrooms***~~~~~~
_________A Practical Guide To Psilocybin Mushrooms_________

:sporedrop:                      "Think about the species, not your scale". -NeoSporen                      :sporedrop:

"Mr. Joust, I see you don't actually partake in the psilocin, but it looks like it may partake in you!" -Gojira


       


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Offlinesuchen
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Re: New Psilocybe sequences in Genbank [Re: Joust]
    #19269293 - 12/13/13 03:47 AM (10 years, 2 months ago)

So subcubensis is actually a thing? Interesting.


--------------------
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The volva is the volva.

They have a very long term realtionship, but they’re “just friends.”


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Re: New Psilocybe sequences in Genbank [Re: suchen]
    #19269296 - 12/13/13 03:49 AM (10 years, 2 months ago)

Quote:

suchen said:
So subcubensis is actually a thing? Interesting.



:header:


--------------------
~~~~~~***Psilocybin Mushrooms***~~~~~~
_________A Practical Guide To Psilocybin Mushrooms_________

:sporedrop:                      "Think about the species, not your scale". -NeoSporen                      :sporedrop:

"Mr. Joust, I see you don't actually partake in the psilocin, but it looks like it may partake in you!" -Gojira


       


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InvisibleRan-D
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Re: New Psilocybe sequences in Genbank [Re: Joust]
    #19269728 - 12/13/13 08:11 AM (10 years, 2 months ago)

What I want to know is how the hell do you guys go about learning what all this stuff means? Have you all taken classes on this kind of thing or what?


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InvisibleThe Lightning
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Re: New Psilocybe sequences in Genbank [Re: Ran-D]
    #19269787 - 12/13/13 08:35 AM (10 years, 2 months ago)

I learned almost everything I know from explicit, well-structured sentences from A.R.

A bit of supplemental reading was helpful and continues to help.


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OfflineAlan RockefellerM
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Re: New Psilocybe sequences in Genbank [Re: suchen]
    #19270830 - 12/13/13 01:45 PM (10 years, 2 months ago)

Quote:

suchen said:
So subcubensis is actually a thing? Interesting.






It does not need to be a real species to be listed in genbank.

Try downloading all the cubensis and subcubensis sequences, and make a tree using ovoideocystidiata as an outgroup.


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OfflineMachineElf1.618
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Re: New Psilocybe sequences in Genbank [Re: Ran-D]
    #19271864 - 12/13/13 05:58 PM (10 years, 2 months ago)

Quote:

Ran-D said:
What I want to know is how the hell do you guys go about learning what all this stuff means? Have you all taken classes on this kind of thing or what?




Yup 5 years of molecular biology and bioinformatics that and I do research in a Lab.


Edited by MachineElf1.618 (12/13/13 06:00 PM)


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Invisiblemaynardjameskeenan
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Re: New Psilocybe sequences in Genbank [Re: Alan Rockefeller]
    #19275243 - 12/14/13 03:38 PM (10 years, 2 months ago)

Quote:

Alan Rockefeller said:
Quote:

suchen said:
So subcubensis is actually a thing? Interesting.






It does not need to be a real species to be listed in genbank.

Try downloading all the cubensis and subcubensis sequences, and make a tree using ovoideocystidiata as an outgroup.





Although this isn't all the entries for subcubensis/cubensis, It looks like they could be a different sub-species. :shrug:


Edited by maynardjameskeenan (12/14/13 03:56 PM)


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Re: New Psilocybe sequences in Genbank [Re: maynardjameskeenan]
    #19275351 - 12/14/13 04:06 PM (10 years, 2 months ago)

Were any of the caerulescens from the US? Or were they all the Mexican variety?


--------------------
"The trick is to use the drugs once to get there, and maybe spend the next ten years trying to get back there without the drug." MJK

As one ends, another begins.



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