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This specimen has been accessioned to the UT fungarium with the following number:
not take so much time. Finding the coding region takes time as it is manual. If I were you I would consider using the portal for your ITS and LSU submissions and Bankit for the others that way you get them on GB quickly and take your time with the others.
One hour for a single TEF-1 submission is not particularly thrilling, but one should encourage himself to think it’s time well spent for the sake of the science effort. :-) What’s so complex and time-consuming about it apart from removing introns and doing a protein translation?
Well, looks like BankIt it is for me, though I doubt the tutorial/webinar is going to walk me through every nuance of the submission process. I know I am not going to enjoy this at all! :D
It takes well over an hour. Very complex. You could search for Alan’s tutorial on YouTube or just email him tho I doubt that you’ll need it for the Submission Portal.
I found two BankIt webinars on YouTube. Each video is almost 1 hr long- that’s not too bad, but my eyes will eventually be glazing over. Probably would make sense to learn that rather than the GB Submission Portal because I already have a substantial number of TEF-1 sequences and plan to continue using protein-coding genes in the future… On the other hand, do you have a link to Alan’s video handy?
The easiest by far is the Submission Portal on GenBank which guides you through the process step by step. It’s about 5-10 minutes this way especially if you have your MO obs handy to access voucher/MO numbers, isolation source, host, country, collection date, collector and other features. Also Alan Rockefeller has a tutorial on You Tube I think in which he uses the portal. Rod uses Sequin or Bankit which is more complicated to use. Actually GenBank is pushing the use of the portal for ITS and LSU. It can’t be used for TEF, RBP1, RBP2 and others.
I’ve been wanting to learn how to submit my sequences to GB, but I heard it wasn’t trivial. Recently, I came into possession of Rod Tulloss’ presentation on this topic, but haven’t had a chance to peruse it yet (at the first glance it looked rather daunting)… Is there an online tutorial for dummies? :-)
as Boletus atkinsonii as it will represent the only correctly labeled specimen of it on GenBank. Now that GenBank makes it so easy to submit and update sequences it is too bad they’re not corrected once a determination is made.
was sent to Dr. B.T.M. Dentinger at UMNH in March 2018.
> A clean and contiguous nrITS sequence of the last 796 bps was obtained from this collection. The sequence starts from toward the end of ITS1 primer. There are no ambiguous characters present.
> A BLASTn search of this sequence gave the following 3 top-scoring hits:
: Boletales sp. voucher RL045 = 783/783 = 100% similar
: Boletales sp. voucher RL009 = 783/783 = 100% similar
: Boletales sp. voucher B3208 = 795/796 = 99.9% similar
> Since all three GB accessions are linked to vouchers originating from Canada, I contacted Renee Lebeuf for help with getting additional information on these collections. Here is what I was able to find out (thank you, Renee!)…
—> Voucher RL045 was collected in Grenville-sur-la-Rouge in 2013. There are 3 photographs representing the same collection consisting of multiple fruiting bodies:
—> Voucher RL009 was collected by Renee under red oaks in Arboretum Morgan in 2011. Unfortunately, I don’t know how to upload the two jpeg files from Renee to this observation. However, Renee also sent me links to photographs of her 2015 collections that came from the same spot where she found RL009 (incidentally, these are the same pics found in Bessettes’ BENA, p. 88):
—> Finally, voucher B3208 is actually B3202 (a typo in GenBank), collected by Y. Lamoureux:
According to Renee, these 3 GenBank collections represent the current species concept of Boletus atkinsonii in the minds of her esteemed colleagues:
“We have several pictures of what we call B. atkinsonii, including the pictures illustrating the species in the last Bessettes’ book on Boletes. The best distinguishing character is the cracked cap, even in young specimens. The color of the cap is variable and can range from dark brown to yellowish brown to pale brown. The stipe length is also variable, shorter or larger than the cap diameter.”
> The current concept of B. atkinsonii is almost certainly that of a member of the porcini sensu stricto lineage of Boletus section Boletus, based on its morphological gestalt as well as the nrITS BLASTn profile. The porcini s.s. lineage currently consists of three main clades as per the phylogenetic treatment of Feng et al. (2012): “Edulis-clade”, “Variipes-clade” and “Aereus-clade”. It’s possible B. atkinsonii falls into the “Aereus-clade”.
The magenta reaction to ammonia lends more credence to the atkinsonii proposal. It’s nice of you to have saved this collection for further study.
Iron salts =greenish
You can see the last photos
All my woods are mixed
I have all the existing trees growing in N. Americas
To 20 square meters
Samples are redy for you
Did you do the ammonia test on the cap?
What was the habitat like — any conifers around?
Created: 2017-06-21 13:24:53 PDT (-0700)
Last modified: 2018-10-10 12:32:53 PDT (-0700)
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