Observation 185697: Amanita argentea Huijsman

When: 2014-10-26

Collection location: Serra de São Mamede, Portugal [Click for map]

Who: zaca

Specimen available

Notes:
Growing under oaks.

Images

474492
Sp.3
474493
Sp.1-Sp.2
474494
Sp.1-Sp.2
474495
Sp.1-Sp.2
474496
Sp.1-Sp.2
474497
Sp.3
474498
Sp.3
474499
Sp.3
474500
Sp.3
484116
Microscopy: Spores and Basidia.
484117
Microscopy: Spores and Basidia.
484118
Microscopy: Spores and Basidia.

Proposed Names

29% (1)
Recognized by sight
ret
54% (1)
Eyes3
Based on microscopic features: zaca’s spore data

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

Eye3 = Observer’s choice
Eyes3 = Current consensus

Comments

Add Comment
Yes, zaca, it was very helpful.
By: R. E. Tulloss (ret)
2018-02-27 06:06:39 PST (-0800)

I feel like the illustration in a Dickens novel in which the child hero hold’s out a bowl saying, “Please, sir. May I have some more?”

The difficulties are of a sort that is not uncommon in Amanita. Usually, we start studying the genetics of a new sample by trying to obtain sequences of two commonly sequenced genes. There are many sequences from these genes already in worldwide data bases; so we can see if we have sequences similar to what other people have found. It appears that argentea has not been previously sequenced. So we can’t get confirmation for our results.

The difficulties within the sequences are probably attributable to the genetic history of the organism itself. The genes in question are represented many, many times in a single nucleus of a cell. So sequencing these genes is like recording a chorus singing. If they all have the same sheet of music, you get a nice clear, clean recording of their song. If the sheets of music differ, then there is a chance that you will get chaos instead of music or you will have only fragments of the song interrupted by chaos.

Sometimes, it can be due to an error in the process or damage to the DNA during storage of the dried specimen. In my experience, however, most often the problem is variation among the multiple copies of the gene. In Amanita, this is not uncommon. Hence, it is necessary to do further work and look at genes for which the sequencing process is analogous to recording a solo singer instead of a chorus. :) I hope this helps a bit.

Very best,

Rod

Continuing…
By: R. E. Tulloss (ret)
2018-02-25 08:23:57 PST (-0800)

I then BLASTED fragment 3 against my internal database that includes sequences not posted to GenBank. There were 12 sequences with less than 2% genetic distance (sequences sorted by “grade”…percent of overlap with the submitted sequence). Eleven of these were sequences from Amanita rooseveltensis (nom. prov.) with genetic distances ranging from 1.2% to 1.6%. This is not “close” given the current data on section Vaginatae. On the other hand, perhaps a coincidence, A rooseveltensis is, like, A. argentea a species with average spore Q value more or less around 1.3. The remaining sequence of the 12 is from A. coprinopsoides (nom. prov.).

I then BLASTED fragment 2 against the same LSU sequence database for the Vaginatae. Remember that the two fragments have no overlap. They represent different regions within the nrLSU locus. The smaller fragement gave less resolution as one might expect. Again, the “match” data was ordered by grade.
The highest rated matches with genetic distance less than 2% again included rooseveltensis (genetic distances 1.4-1.7%) as well as "__sp-GSM04__ “(1.0-1.1%),”__ sp-N52__" (1.2%), an undetermined specimen from Louisiana (MO #204749) (1.7%) and an undetermined David Lewis specimen from Texas (1.0%).

I conclude there is nothing in my database that is close to the sequence from the present observation.

For completeness, the 75 characters of nrITS produced matches in my local nrITS data base for the Vaginatae only with “sp-GSM04” with a range of genetic distance of 4.6-5.8%. Probably this is not meaningful because of the very small size of the fragment.

Since the two larger fragments are trimmed for quality and do not fit the form of the contaminations that I sometimes see, I conclude that the species probably has not been previously sequenced. Searches in UNITE and GenBank were no more successful in finding matches.

Very best,

Rod

thanks Rod
By: Debbie Viess (amanitarita)
2018-02-25 07:58:21 PST (-0800)

for answering my question.

not always possible to get useable DNA, even from the most interesting examples! I do see fragmented DNA posted on Genbank; perhaps your idea is a good one … to post what we already have rather than wait to maybe get more, better material someday.

Thank you very much, Rod,
By: zaca
2018-02-25 03:24:48 PST (-0800)

for the clarifications about this material. Unfortunately my knowledge of DNA Sequences is very limited, so I can not achieve all that would be desirable from your comments. I just wish it was useful to send you this material.
Best regards, zaca

More about the fragments, zaca.
By: R. E. Tulloss (ret)
2018-02-24 14:49:24 PST (-0800)

There are three fragments of the LSU sequence.

They are all separated from each other and cannot be connected to produce a longer sequence. The “barcode” fragment and its attached piece of LSU are too distant form LSU fragment 2 to be attached to LSU fragment 2. Fragment 2 does not overlap Fragment 3. Hence, the ITS fragment can’t be posted to GenBank. Fragments 2 and 3 may be of sufficient quality to be posted to GenBank separately. That is the next thing to consider. In this situation, I would like to request additional collections of possible A. argentea in order to see if a better understanding could be obtained.

Zaca, thank you very much for sending this interesting collection. It certainly raises a lot of questions.

Very best,

Rod

The DNA results are fragmentary, zaca.
By: R. E. Tulloss (ret)
2018-02-24 13:35:41 PST (-0800)

This was supposed to be posted earlier. I just found it waiting for me to hit the “create” button.

The nrITS fragment is 75 characters from the “right hand end” of the ITS2 locus followed by the first 61 initial characters the nrLSU locus. This is too short to deposit in GenBank on its own But it is enough to show that the species is not in the penetratrix grouping.

The fragmentary situation may be associated with failure of the nuclear ribosmal RNA to homogenize. As readers probably know by now, this prevent on from getting a “barcode” simply by using the basic Sanger sequencing process.

I’ll report on the LSU gene later. I want to make sure that I can’t join it to the ITS fragement and deposit them together (because that would not violate the length of sequence limit).

I’d really like to have a second specimen to use so that we could try to get a better understanding of the partial results we’ve gotten. If we have the same problems that will suggest that we are probably correct in suggesting that the nrRNA failed to homogenize in this species. On the other hand if we cannot combine nrITS and nrLSU sequences in this case, we might do better on a second try.

Very best,

Rod

where are the DNA results, Rod?
By: Debbie Viess (amanitarita)
2018-02-24 10:05:04 PST (-0800)

not up on your webpage nor on Genbank.

it would be interesting to compare with our somewhat similar NA form: “stannea.”

Material received and accessioned to the herbarium in December 2014.
By: R. E. Tulloss (ret)
2018-02-24 09:54:38 PST (-0800)

DNA sequences raw data received and processed in December 2017.

I’m trying to catch up on reporting back on results, but I think I will always be behind.

Very best,

Rod

Thank you very much.
By: R. E. Tulloss (ret)
2014-11-28 14:50:34 PST (-0800)

Very best,

Rod

2014-11-28 – Material sent.
By: zaca
2014-11-28 14:05:48 PST (-0800)
You’re very welcome.
By: R. E. Tulloss (ret)
2014-11-22 14:10:17 PST (-0800)

Thanks in advance for the material. It will be very interesting.

Very best,

Rod

Thanks, Rod, for …
By: zaca
2014-11-22 09:18:37 PST (-0800)

your kindness and disposal to analyze the sample that I will send you next week.
Kind regards,
zaca

Your measurements make a sporograph…
By: R. E. Tulloss (ret)
2014-11-21 17:45:51 PST (-0800)

That fits inside my sporograph for argentea. Because of the physial appearance and the ellipsoid spores, I’d suggest A. argentea for this collection.

Do you have enough dried material to spare me a piece? I’m interested to see if (and how) our spore measurements differ. Part of it is that my measurements are a composite of spores from many collections in different states of preservation and conservation. But I don’t think that that is the whole story.

Very best,

Rod

I almost forgot the existence of …
By: zaca
2014-11-21 15:15:04 PST (-0800)

dried material from this observation. I uploaded some photos of the microscopy.
Thanks for your comment, Rod.
Kind regards,
zaca

The squat stature of the mushroom in the first image reminded me of dried…
By: R. E. Tulloss (ret)
2014-11-21 04:58:25 PST (-0800)

material that I borrowed in the past from European herbaria…Amanita argentea. It is still the case that this species is mistakenly identified with A. mairei in some books. They both have unusually narrow spores for European Vaginatae, but they are far from identical.

If you should find this creature again, spore measurements would be very useful in finding if you have argentea.

Very best,

Rod

Created: 2014-10-26 14:23:33 PDT (-0700)
Last modified: 2018-02-27 06:06:40 PST (-0800)
Viewed: 164 times, last viewed: 2018-03-22 03:53:16 PDT (-0700)
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