[Taxacom] RES: DNA contamination

Fri Apr 1 09:13:52 CDT 2011

Hi, Paul,

Yes, the fungal ITS sequences resulted from a contaminated plant DNA
extraction are a common issue when working on rDNA.

That is in part caused by applying the so-called universal primers
originally developed from fungal sequences. 

See this paper: 

<http://www.scielo.br/scielo.php?pid=S1516-89132010000100018&script=sci_artt
ext>
http://www.scielo.br/scielo.php?pid=S1516-89132010000100018&script=sci_artte
xt

Best wishes,

Vitor Miranda

De: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] Em nome de Paul Kirk
Enviada em: sexta-feira, 1 de abril de 2011 10:48
Para: bti at dsmz.de; taxacom at mailman.nhm.ku.edu
Assunto: Re: [Taxacom] DNA contamination

I've got some nice BLAST results for fungal ITS with various plants (Datura
stramonium) in the 100% matched category. Perhaps more correctly 100%
matches to sequences 'tagged' as Datura stramonium. If this happens for
organism which are clearly different is there any confidence in what we get
from GenBank?

Have a good weekend,

Paul

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of bti at dsmz.de
Sent: 01 April 2011 08:35
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] DNA contamination

This only deals with one aspect with the other major problem being "the
sequence deposited", "the name associated with it" and "what it really was".
The other one to read is:

http://journals.sfu.ca/sigen/index.php/sigen/article/viewArticle/sigs.972221

Brian

Quoting Lynn Raw <lynn at afriherp.org>:

> I presume that most people on the Taxacom list are aware of this paper
> -
> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.001
> 6410
> .
>
> I was wondering if contamination is a more general problem affecting
> molecular phylogenies. It might explain one that I saw with an African
> species nested within a set of apparently unrelated North American
> species.
>
> Lynn Raw
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