Observation 154815: Melanoleuca Pat.

When: 2012-12-29

Collection location: Davis, California, USA [Click for map]

Who: Byrain

Specimen available

Found alongside a bike trail under some redwoods.



Proposed Names

57% (1)
Eye3 Eyes3
Recognized by sight

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Eye3 = Observer’s choice
Eyes3 = Current consensus


Add Comment
By: Alan Rockefeller (Alan Rockefeller)
2016-06-25 08:13:29 BST (+0100)

LSU costs the same as ITS, about $8. Some entries in GenBank have only LSU, so sometimes there are matches with that gene region where ITS doesn’t show matches. If this is going to be described as new, it is best to get as many gene regions as possible.

By: Byrain
2016-06-25 02:35:29 BST (+0100)

I do not know the LSU would help, but unless the price is exceptionally discouraging it would be best to collect as much data as possible. I understand a LSU sequence might eventually help in placing Melanoleuca better?

Ok, I put in a sequencing order for the reverse strand.
By: Alan Rockefeller (Alan Rockefeller)
2016-06-25 00:40:53 BST (+0100)

The data should arrive tomorrow morning. Should we do LSU as well?

By: Byrain
2016-06-24 23:36:36 BST (+0100)

These should be studied, its a nice collection and a relatively recognizable and interesting Melanoleuca. I can get microscopy on these eventually as well, I have not tried to do so yet because I did not have any good Melanoleuca literature to compare with.

ITS sequence, enzyme slippage
By: Alan Rockefeller (Alan Rockefeller)
2016-06-24 21:45:41 BST (+0100)

Matches 95% with three different Melanoleuca species. The sequence had a lot of noise towards the end due to enzyme slippage caused by 6 T’s in a row – if you are serious about studying this one I can have them read the reverse strand which will improve data quality of the last 200 bases. The lower case characters are the ones I changed – this was done by viewing the chromatogram with FinchTV and using the close BLAST matches to suggest what the base actually is in the cases of ambiguity. If the close BLAST match found a different base than I had and the chromatogram showed a peak of the suggested base, it was changed. If the chromatogram did not show any sign of the suggested base being present, it was considered a real difference between this sequence and the BLAST matches, and left alone. This sequence is probably over 99% accurate and may be 100% accurate.


Created: 2013-12-10 05:47:26 GMT (+0000)
Last modified: 2018-05-13 11:47:19 BST (+0100)
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