Observation 24776: Amanita “sp-N60”
When: 2009-08-28
Herbarium specimen reported

Notes: Under a large eastern white pine. In sandy type soil.

Images

55057
Copyright © 2009 Erlon Bailey
55058
Copyright © 2009 Erlon Bailey
55059
Copyright © 2009 Erlon Bailey
501203
Here is a tree with its closest relatives. http://www.ncbi.nlm.nih.gov/...#
501272
502332
A slightly different configuration with the RNA sequence.

Proposed Names

47% (3)
Recognized by sight
ret
30% (2)
Based on chemical features: nrLSU sequence from this material indicates placement in sect. Amanita.
29% (1)
Recognized by sight
ret
91% (2)
Eye3 Eyes3
Recognized by sight: The pale pink cap is distinctive in section Amanita in northeastern North America. http://www.amanitaceae.org?Amanita+sp-N60
Based on chemical features: An nrLSU sequence has been derived for this taxon.

Please login to propose your own names and vote on existing names.

Eye3 = Observer’s choice
Eyes3 = Current consensus

Comments

Add Comment
One of the interesting things about sp-N60…
By: R. E. Tulloss (ret)
2015-01-22 15:18:32 PST (-0800)

In the nrITS gene tree that Herbert has posted, you’ll notice that there are four leaves labeled “sp-N60.” These are four different sequences of the “proposed barcode gene” from one single fruiting body. The fact that the nrITS gene is not homogenized (all the copies identical) in sp-N60 was noted by Dr. Karen Hughes when she saw the first results from an attempt at sequencing. A process called “bacterial cloning” that utilizes useful properties of E. coli was employed to make copies of some of the distinct nrITS sequences from a small sample of gill (with spores) from Herbert’s collection.

Very best,

Rod

Poisonous?
By: Paul Derbyshire (Twizzler)
2015-01-22 14:15:49 PST (-0800)

From the sounds of it, most or all of the Amanitas in this clade would have ibotenic acid and muscimol, right?

I made a phylogenetic tree…
By: Erlon (Herbert Baker)
2015-01-22 12:21:37 PST (-0800)

Thank you, Rod. A. “sp-N60” appears in a closely related group with A. xylinivolva, A. stranella, A. rubrovolvata, A. breckonii, A. altipes, A. gemmata, A. parvipantherina, A. calochroa, and a few unknown/undescribed species. They all appear to descend from a common ancestor and are a neighbor to the Pantherina group. Amanita “sp-N60” appears very closely related to A. xylinivolva, A. stranella, and a species labeled A. praecox.

http://www.ncbi.nlm.nih.gov/...#
The LSU sequence and 4 bacterial clones of distinct ITS sequences have been…
By: R. E. Tulloss (ret)
2014-12-03 11:10:38 PST (-0800)

submitted to GenBank. We have received accession numbers, but it may take some time for the sequences to become publicly available in GenBank (a normal situation). The accession numbers are posted on the technical tab (in the “GenBank nos.” data field) here:

http://www.amanitaceae.org?Amanita%20sp-N60

When the sequence pages are publicly available, the GenBank accession numbers will be the active links to recover the corresponding sequences from GenBank.

Another step has been taken. Thanks again, Herbert.

Very best,

Rod

The typos are corrected.
By: R. E. Tulloss (ret)
2014-07-21 09:58:42 PDT (-0700)

Thank you for pointing them out.

Very best,

Rod

Hi
By: Erlon (Herbert Baker)
2014-07-21 09:54:24 PDT (-0700)

Thank you for your continued interest in this! Please compare with this observation: http://mushroomobserver.org/169619?q=24g6a Rod, I noticed on the Amanita studies page that the picture is labelled. “sp-N50” perhaps this is just a typo?

Now I got to go back and find more.

All the clones produce the same results as far as “nearest taxa” from nBLAST.
By: R. E. Tulloss (ret)
2014-07-21 09:11:09 PDT (-0700)

The closest ten taxa are:

1) pantherinoid (for example, A. subglobosa from east Asia and material from North America that was labeled simply “pantherina”)

2) not very close to sp-N60 in terms of percent difference of the characters (position by position) in the nrITS sequences.

So, it continues to be the case, that this material seems novel.

Very best,

Rod

We have obtained a set of raw data for as many as 8 clone sequences.
By: R. E. Tulloss (ret)
2014-07-21 08:49:41 PDT (-0700)

These have to be processed to remove probable errors and then to eliminated duplicates. I’ll report back on what results we obtain.

R

The isotype of Amanita breckonii from the New York Botanical Garden.
By: R. E. Tulloss (ret)
2014-07-21 08:33:55 PDT (-0700)

This was in my comment.

R

closest to breckonii??!
By: Debbie Viess (amanitarita)
2014-07-21 07:41:08 PDT (-0700)

which one?

the muscaroid taxa deposited in the SFSU herbarium or the “breckonii” that actually resembles this sp-N60, as depicted by Darvin DeShazer’s photo in Agaricales of California?

I assigned a temporary code for this species.
By: R. E. Tulloss (ret)
2014-07-21 05:07:06 PDT (-0700)

Herbert’s color images are distinctive.

The nrLSU sequence is closest to a sequence derived from the isotype of Amanita breckonii and to a sequence derived from material identified as A_. "praecox__" by B. E. Wolfe. The differences are small.

The proposed barcode gene (nrITS) is present in mutliple different copies in this species and a process called bacterial cloning is necessary in order to get samples of individual, distinct sequences of that gene. This distinguishes the present species from A. breckonii because an nrITS gene has been derived from its isotype (New York Botanical Garden) without the necessity of the cloning process. The two “praecox” nrITS sequences deposited in GenBank have quality problems from unknown cause(s) even in what should be relatively invariable portions of the gene.

At present, evidence indicates that “sp-N60” is probably an undescribed species.

What data I have is accumulating here:

http://www.amanitaceae.org?Amanita_sp-N60

Images will go up today.

Very best,

Rod

Hi Rod
By: Erlon (Herbert Baker)
2013-11-11 22:26:42 PST (-0800)

Oh I’m glad you have some of the sample left. Yes, I would like to suggest the name “persica” for this taxon if possible. Will you be getting the opportunity to look at some of the microscopic features soon? Any idea on subsection?

Are you suggesting the name “persica” for this material?
By: R. E. Tulloss (ret)
2013-11-11 05:35:33 PST (-0800)

R

Yes.
By: R. E. Tulloss (ret)
2013-11-11 05:33:08 PST (-0800)

Sequencing requires only a fragment of a gill.

Search for toxins requires about a gram of dried tissue.

Rod

Rod
By: Erlon (Herbert Baker)
2013-11-10 20:07:17 PST (-0800)

Is there anything left from the material I sent you for microscopic analysis?

When the sequence is posted to GenBank, the GenBank…
By: R. E. Tulloss (ret)
2013-09-22 20:16:02 PDT (-0700)

accession number will be posted in several places. I hope that it will be posted here, too.

R

That’s very interesting…
By: Erlon (Herbert Baker)
2013-09-22 18:20:53 PDT (-0700)

I’ve been continuing to look for it in the area I discovered it. Could you post the Genbank number? Thank you.

We have been able to obtain more information about this material.
By: R. E. Tulloss (ret)
2013-09-05 20:37:49 PDT (-0700)

A tree is a hypothesis of evolutionary history generated by a computer. It is not necessarily a true representation of evolutionary history. The more data (i.e., the more genes) available to build the tree, in principle, the more likely the tree represents a real history. A tree based on one gene is not very likely to provide a real history. However, experience of many people with whom I have collaborated in recent years, suggests that several genes are normally very good at placing amanitas into a section…as long as you have many examples of the same gene from amanitas in the seven sections of Amanita. Based on this experience and the fact that we have what appears to be a good quality nrLSU gene sequence from your collection, this material seems likely to belong in Amanita section Amanita.

If you find more material of this species, it would be very nice if you could take notes on the fresh fruiting bodies and try to encourage them to mature and drop spores. More material means more chances to get good morphological data and more chances to try to derive gene sequences.

This material is very interesting; I would be very glad to know more about this species.

Very best,

Rod

We have received some sequencing results for this observation.
By: R. E. Tulloss (ret)
2013-08-11 11:13:33 PDT (-0700)

It seems to have multiple different copies of the so-called “barcoding” gene; separation of them is a more complex process; so we don’t have any results there. The nrLSU gene gave no exact hits in GenBank. A direct hit of a possibly undescribed species in Amanita in North America would be an odd occurrence at present.

I hope we can move forward with this collection, but further work is probably not very likely in the nearest of futures.

Very best,

Rod

Status.
By: R. E. Tulloss (ret)
2013-07-12 12:39:10 PDT (-0700)

Material was sampled and sent for sequencing. But, because of a summer hiatus in sequencing, We will not find out if DNA can be extracted until this fall.

Very best,

Rod

who currently does your sequencing, Rod?
By: Debbie Viess (amanitarita)
2013-06-20 09:16:46 PDT (-0700)

Bojantchev is sending his to a commercial lab overseas, and our DNA analyzing fellas at UC Berkeley are (sob) moving on in their lives.

And what about all that micro work that you do so well? Are we no longer considering that the gold standard?

Doesn’t the DNA really just show relatedness, and the definition of what is a species (vs a close relative) just a human judgement call?

And then, of course, the human time constraints…no one person can possibly do everything. Best to spread the love and specimens around, don’t you think?

More amateur mycologists, trained to do the work, themselves.

And here comes the North American Mycoflora Project…to help fill the gaps.

We are scheduling the collection for sequencing today.
By: R. E. Tulloss (ret)
2013-06-20 08:50:45 PDT (-0700)

The answer to your question is “no.”

However, I’m no happier with that than anyone else.

At the very least, we will probably be able to tell which section the species belongs to from a sequence of the proposed barcode gene…if we can extract the sequence.

Rod

Rod
By: Erlon (Herbert Baker)
2013-06-19 23:11:39 PDT (-0700)

did you ever get a chance to work on these?

Since you have the specimen
By: Noah Siegel (Noah)
2009-12-17 17:28:12 PST (-0800)

I’m wasting time suggesting this because you will know what it is when you look at it. But… what about Amanita agglutinata?

specimen received
By: R. E. Tulloss (ret)
2009-12-17 09:56:34 PST (-0800)

R.

In the middle picture…
By: R. E. Tulloss (ret)
2009-08-31 13:45:03 PDT (-0700)

In the middle picture, it seems to me that the smaller button has a large patch of volva that is changing from white to gray; and the larger button has a ring of limbus internus circling the lower stem that is turning gray on its free edge. In addition to the strongly striate cap margin, I’d say that while I can’t offer a name for the specimen it belongs in the group with A. ceciliae, A. sororcula, and A. borealisorora Tulloss nom. prov. I’d guess it is a weak-volva’d, graying-volva’d member of sect. Vaginatae.

Very best,

R.

in stature, color and lack of partial veil, it reminds me of the western Amanita velosa.
By: Debbie Viess (amanitarita)
2009-08-28 19:58:24 PDT (-0700)

but I am NOT suggesting that as an ID. no idea, really.

Pink
By: Erlon (Herbert Baker)
2009-08-28 18:56:31 PDT (-0700)

To bad it isnt part of the Pantherina group, we could call it the “Pink Panther”. :)

Wow, a pink amanita
By: Paul Derbyshire (Twizzler)
2009-08-28 17:44:21 PDT (-0700)

Created: 2009-08-28 14:13:47 PDT (-0700)
Last modified: 2015-01-27 10:29:17 PST (-0800)
Viewed: 520 times, last viewed: 2016-10-22 08:54:31 PDT (-0700)
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