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Just slap my name on there somewhere as image credit and you can definitely use the photos.
It is less than 0.4% distant form a previous sequence from a specimen of magniverrucata in our herbarium. Looks like we’ll need to look at another several samples of magnivelaris to get some idea of the amount of variation in the “proposed barcode gene.”
Thank you for sending this material.
It might be easy to make some, align all the Amanitas and look for 20 or so bases that they all have. Maybe it would be possible to make primers that amplify Amanita and nothing else.
Ben Wolfe ran into the problems that you mention and did have to use the dilution method and create some primers for specific species. I don’t know if it applies in the present case, but there is also the unhomogenized state of the nuclear ribosomal repeat in quite a few amanitas. Sequencing some amanitas (e.g., the lavendula look-alike found by Karen Hughes) is chaotic because you are simultaneously reading sequences with not only simple differences in specific bases, but indels as well which throw the sequences out of synch with each other. I have not had time to get an analysis of the specific problem in this case.
I wonder if the problem is PCR inhibitors or insertions in the primer binding site. If it is PCR inhibitors, diluting the template or doing a more complicated DNA extraction will help. If there is an insertion at the binding site, some new Lepidella primers could be really useful.
No positive results to report.
This material has been received and accessioned to Rod’s herbarium. We have scheduled it for DNA sequencing.
Created: 2015-03-03 23:57:59 PST (-0800)
Last modified: 2017-12-28 13:15:22 PST (-0800)
Viewed: 151 times, last viewed: 2018-01-19 23:15:39 PST (-0800)