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Alan Rockefeller
Mycologist

Registered: 03/10/07
Posts: 48,312
Last seen: 3 days, 4 hours
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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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psylosymonreturns
aka Gym Sporrison



Registered: 10/16/09
Posts: 13,948
Loc: Mos Eisley,
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I wish I knew what this meant! Great work non the less .
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Alan Rockefeller
Mycologist

Registered: 03/10/07
Posts: 48,312
Last seen: 3 days, 4 hours
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What are the mushroomobserver links for the Psilocybe cyanescens, P. pelliculosa and P. stuntzii collections that you sent her?
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MachineElf1.618
4-PO-Dimethyltryptamine



Registered: 06/27/11
Posts: 1,911
Loc: Miðgarðr
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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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Alan Rockefeller
Mycologist

Registered: 03/10/07
Posts: 48,312
Last seen: 3 days, 4 hours
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Whole genomes have not been sequenced.
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psylosymonreturns
aka Gym Sporrison



Registered: 10/16/09
Posts: 13,948
Loc: Mos Eisley,
Last seen: 3 years, 6 months
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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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MachineElf1.618
4-PO-Dimethyltryptamine



Registered: 06/27/11
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Quote:
Alan Rockefeller said: Whole genomes have not been sequenced.
Why the heck not!? 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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Alan Rockefeller
Mycologist

Registered: 03/10/07
Posts: 48,312
Last seen: 3 days, 4 hours
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Yes please do!
Now that the sequences are in genbank, the pics are super important!Quote:
mtlmike90 said: Why the heck not!? 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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MachineElf1.618
4-PO-Dimethyltryptamine



Registered: 06/27/11
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Loc: Miðgarðr
Last seen: 3 years, 2 days
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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!? 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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The Lightning
Mycology Enthusiast


Registered: 09/06/11
Posts: 3,889
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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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MachineElf1.618
4-PO-Dimethyltryptamine



Registered: 06/27/11
Posts: 1,911
Loc: Miðgarðr
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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) |
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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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Joust
Mycotographer




Registered: 10/13/11
Posts: 13,392
Loc: WA
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damn im not on this list...
-------------------- ~~~~~~***Psilocybin Mushrooms***~~~~~~ _________A Practical Guide To Psilocybin Mushrooms_________ "Think about the species, not your scale". -NeoSporen "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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suchen
Once and Future Noob



Registered: 06/28/11
Posts: 8,841
Loc: Shangri-la
Last seen: 3 years, 2 months
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Re: New Psilocybe sequences in Genbank [Re: Joust]
#19269293 - 12/13/13 03:47 AM (10 years, 2 months ago) |
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So subcubensis is actually a thing? Interesting.
-------------------- Rod Tulloss said: The bulb is the bulb. The volva is the volva. They have a very long term realtionship, but they’re “just friends.”
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Joust
Mycotographer




Registered: 10/13/11
Posts: 13,392
Loc: WA
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Re: New Psilocybe sequences in Genbank [Re: suchen]
#19269296 - 12/13/13 03:49 AM (10 years, 2 months ago) |
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Quote:
suchen said: So subcubensis is actually a thing? Interesting.
-------------------- ~~~~~~***Psilocybin Mushrooms***~~~~~~ _________A Practical Guide To Psilocybin Mushrooms_________ "Think about the species, not your scale". -NeoSporen "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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Ran-D



Registered: 12/19/10
Posts: 16,315
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Re: New Psilocybe sequences in Genbank [Re: Joust]
#19269728 - 12/13/13 08:11 AM (10 years, 2 months ago) |
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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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The Lightning
Mycology Enthusiast


Registered: 09/06/11
Posts: 3,889
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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) |
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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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Alan Rockefeller
Mycologist

Registered: 03/10/07
Posts: 48,312
Last seen: 3 days, 4 hours
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Re: New Psilocybe sequences in Genbank [Re: suchen]
#19270830 - 12/13/13 01:45 PM (10 years, 2 months ago) |
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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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MachineElf1.618
4-PO-Dimethyltryptamine



Registered: 06/27/11
Posts: 1,911
Loc: Miðgarðr
Last seen: 3 years, 2 days
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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) |
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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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maynardjameskeenan
The white stipes



Registered: 11/11/10
Posts: 16,391
Loc: 'Merica
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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.
Edited by maynardjameskeenan (12/14/13 03:56 PM)
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MarcusFreeman



Registered: 09/16/13
Posts: 376
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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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