Notes:
Overall – 17.1cm
Cap – 4.4cm W
Stipe – .8cm W
Volva – 3.5cm

Images

Habitat

Proposed Names

54% (3)
Recognized by sight
Based on chemical features: Partial ITS\LSU
ret
27% (1)
Based on chemical features: incomplete sequence fragment

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= Observer’s choice
= Current consensus

Comments

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The voucher material for this observation has been accessioned in our herbarium.
By: R. E. Tulloss (ret)
2018-07-15 21:21:43 EDT (-0400)

Thank you for your sending this material and for the interaction we had over the DNA of from the voucher. I found it very interesting.

Very best,

Rod

Going back for another look at ITS…
By: R. E. Tulloss (ret)
2018-07-10 14:30:03 EDT (-0400)

If we take the segment of pretty good quality including the last 13 characters of 18S (SSU) followed by the opening 80 characters of ITS1 and BLAST these 93 characters against GenBank we find that there are several justicei sequences and one sp-A03_ sequence that match precisely with this string. I wouldn’t try to stretch this information out by interpreting the read to be something less similar over a greater length. That’s my view. You’d need 200 characters to make the string minimally submittable to GB on the grounds of its length. I can be done, but what is the quality (hence, value) of the result?

Very best,

Rod

The character that differs is the 525th character of your sequence.
By: R. E. Tulloss (ret)
2018-07-05 18:41:18 EDT (-0400)

R

The LSU sequence only differs in one character from the overlapping region…
By: R. E. Tulloss (ret)
2018-07-05 18:32:16 EDT (-0400)

in the longer LSU sequences that Dr. Kudzma and I have deposited for justicei. Since that difference is persistent, I again agree with Alan that you should try to extend the length of your LSU by picking a reverse read primer that will take you up to 900 or more characters. Maybe you will find that you have some differentiation in both ITS and LSU and that you have something different from justicei … or not.

Very best,

Rod

My previous comment relates to basic quality control checks that can be…
By: R. E. Tulloss (ret)
2018-07-05 18:24:07 EDT (-0400)

performed to see if you have an ITS sequence and how much of it that you have. The motifs for the beginnings and/or ends of the subloci of ITS have been studied in hundreds of Amanita sequences. A paper is nearly finished peer review that addresses the subject in a tutorial mode directed particularly at citizen scientists and students.

Very best,

Rod

I concur with Alan that there is a problem with the ITS sequence.
By: R. E. Tulloss (ret)
2018-07-05 18:14:28 EDT (-0400)

It does begin with something that looks like the 3’ terminus of 18S (SSU), but several characters are missing or wrong in what is a very highly conserved region. Your usable sequence begins with only the last five characters of 18S (“catta”). It is very plausible that “ttg” is the opening of ITS1; however, things soon go wrong. One test to apply is whether you can find the beginning of 5.8S. I cannot find it. Another test is to see if you can find the opening characters of the 5’ end of 28S (LSU). I can’t find them.

Very best,

Rod

What is up with the ITS sequence?
By: Alan Rockefeller (Alan Rockefeller)
2018-07-04 06:33:09 EDT (-0400)

Did it come back dirty?

That’s what it looks like, but without the chromatogram data it’s hard to be certain.

Sometimes that happens – when it happens to me I load up the chromatogram and the closest BLAST match. In the spots that my sequence differs from the chromatogram I look and see if the peak of the closest BLAST match is there in the spot it should be. If the peak is there, but there are also other peaks confusing the base caller, I assume that the reference sequence has the correct base and change it – leaving a lower case letter so I can later see what I changed. If the peak is completely missing, I assume this is a real difference.

In this way you can turn a dirty sequence into a good one. The lower case letters give an indication that it wasn’t a clean sequence but had to be worked on, to distinguish it from clean sequences which are slightly less error prone. Takes 5 – 20 minutes depending on how dirty it is.

If you email me the chromatogram I would be happy to work on it.

You might want to do a reverse read on the LSU sequence
By: Alan Rockefeller (Alan Rockefeller)
2018-07-03 21:25:19 EDT (-0400)

Looks like there is some enzyme slippage after a repeated string of a’s, and that is the only reason this isn’t matching A. justicei 100%. You could also probably pull the data out of the chromatogram by analyzing the spots where it differs from BLAST matches.

Very sympathetic regarding lack of time. It only disappears faster as…
By: R. E. Tulloss (ret)
2017-08-22 12:42:25 EDT (-0400)

one gets older…or so it seems to this old bird.

Thanks for retaining the material.

Very best,

Rod

Rod,
By: Ryan Patrick (donjonson420)
2017-08-22 11:59:18 EDT (-0400)

I saved this one it was too unique to leave behind. Ill include it with the others coming your way. I updated the notes with some measurements and may get a look at the spores tonight. Time has not been on my side lately and I’ve been blasting through my observations forgetting key details.

Quite a glorious species, Ryan.
By: R. E. Tulloss (ret)
2017-08-22 09:29:59 EDT (-0400)

I’m very sorry to hear there is no dried material.

This seems to be a very good year for previously unphotographed (?undiscovered) amanitas in sect. Vaginatae.

Very best,

Rod

Created: 2017-08-21 21:57:26 EDT (-0400)
Last modified: 2018-07-16 08:50:26 EDT (-0400)
Viewed: 205 times, last viewed: 2018-12-06 04:36:54 EST (-0500)
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