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Thank you for agreeing to send us part of this material.
We are continuing to collaborate with Dr. Geml in Leiden on several groups within the Amanitaceae including many Western Hemisphere taxa and (without geographic limitation) species of all sections of Limacella and species of Amanita section Amanita. Since A. parcivolvata is in the latter section, it would be sampled for Dr. Geml and his colleagues in Leiden.
All handling of dried materials through the sampling process are done in the RET herbarium (New Jersey). Samples are shipped to Leiden in centrifuge tubes. All relevant herbarium information is supplied with each sample. The herbarium accession numbers are the unique identifiers used in communications concerning samples. I don’t always know the type of Sanger sequencing machine used for a given set of samples, and it may vary according to internal factors in Leiden.
Extensive bookkeeping to track the processes for each sample are implemented in spreadsheets. The New Jersey team tracks each sample from its creation to (if we’re lucky) a GenBank accession number.
The basic primers are standard ones. For nrLSU in the general case, LR0R is used for the forward read; and LR7, for the reverse read. For nrITS in the general case, ITS1F is used for the forward read; and ITS4, for the reverse read. If additional reads are necessary, these also utilize standard primers.
Usually, folks in New Jersey do the sequence quality checking, editing, BLASTing against GenBank and local sequence data bases (including data not yet submitted to GenBank), and submission to GenBank. We use geneious 7.1.7 as our basic tool. In some cases, we have started to use PeakTrace to help clarify peaks in the raw data.
I hope this is a sufficient summary. If not, please email me.
and cut this specimen in half in the dryer. Half of the specimen will be earmarked to be sent to you.
Do you have anything written up or available on the DNA protocols you are using? Is your primary target LSU or are you usually seeking out multiple regions. What are your primary primers (if you can do that to the English language)? Are there any recent papers out there where I could read up on your protocol overall?
and I see that we have not yet been successful in obtaining an nrLSU sequence.
Stephen, would you be willing for me to submit a sample from this material?
Created: 2015-06-29 19:31:25 PDT (-0700)
Last modified: 2015-06-29 20:46:27 PDT (-0700)
Viewed: 42 times, last viewed: 2017-02-19 15:34:49 PST (-0800)