[Coral-List] Re: Coral model for functional genomics

Morgan, Michael B. mbmorgan at berry.edu
Thu Jan 5 14:01:43 EST 2006

To those interested in coral genomic investigations:
I would respectfully disagree with item #6 in the list of reasons given why Porites should be the model for molecular work.  As for RNA extractions and subsequent cDNA synthesis, it has been the experience of my collaborators and myself that Porites sp are the most difficult to work with due to pigments.  These pigments co-precipitate with the RNA and can inhibit reverse-transcription reactions.  I have found that even if you want to isolate mRNA by using a column, these pigments can still carry over.  I not saying that Porites is impossible, but Acroporids or Favids are definitely much easier to extract RNA from.
Mike Morgan

Michael B. Morgan, PhD.
Assistant Professor of Biology
Berry College
364A Science Building
P.O. Box 430
Mount Berry, GA 30149-0430
Tel:  706-290-2148
Fax:  706-238-7855
Email: mbmorgan at berry.edu

-----Original Message-----
Message: 1
Date: Thu, 05 Jan 2006 08:51:07 -0500
From: Mikhail Matz <matz at whitney.ufl.edu>
Subject: [Coral-List] Re: Coral model for functional genomics
To: coral-list at coral.aoml.noaa.gov
Message-ID: <43BD244B.3090203 at whitney.ufl.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

The major argument against Porites that still remains is the notable 
absense of any genomic resourses for this coral, whereas there are 
already some ESTs for others  - Acropora palmata (4017), Montastraea 
faveolata (2156) and Acropora millepora (promised to be made available 
soon  from David Miller's lab). Also, there are already some microarrays 
developed for A. millepora.  Those corals have a head-start and seem to 
be favorites, so why betting on a dark horse?..

The arguments in favor of Porites which I recall from the previous 
discussion are:

1. Porites as a genus is an important reef builder both in Caribbean and 
2. It is not considered particularly endangered anywhere, so there is 
minimal concern about field sampling (quite unlike A. palmata, for example)
3. grows rapidly
4. easy to handle and keep in the lab
5. transmits its symbionts vertically, so there must be minimal genetic 
and gene expression variation due to zooxanthellae (I think this one is 
really important for genomics)
6. is easier for biochemistry and molecular work that Acropora and 
Monstastrea (according to Craig Downs).

Another concern that I received is that since Porites lobata is not a 
branching type it will be difficult to separate pieces (nubbins) for 
experiments; but here I was simply unfortunate to encounter a reviewer 
who did not try it with Porites and does not know how easy it is to saw 
its soft skeleton into neat chunks of any size required (as well as to 
saw off a larger piece in the field, for that matter). Let's disregard 
this one.


Michel Pichon wrote:

> Misha,
>  Before one can go any further, if would be useful  (indeed 
> necessary)  to know on what grounds/ Porites lobata/ is deemed 
> unsuitable for coral genomics. Have you got such a piece of information  ?
>  Cheers,
>  Michel
>         Professor Michel PICHON, Directeur d'Etudes
>      Laboratoire des Ecosystemes aquatiques tropicaux & mediterraneens
>        Ecole Pratique des Hautes Etudes
>         Universite de Perpignan
> 66860 PERPIGNAN Cedex
>    Ph: 33 (0)4 68 66 21 94  Fax  : 33 (0)4 68 50 36 86
>      email : pichon at univ-perp.fr    
> -- 
> Ce message a été vérifié par *MailScanner* <http://www.mailscanner.info/>
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> CRI Université de Perpignan 

Mikhail V Matz, Ph.D

Research Assistant Professor
Whitney Laboratory for Marine Bioscience
University of Florida
9505 Ocean Shore Blvd
St Augustine, FL 32080, USA
phone 904 461 4025
fax   904 461 4008
matz at whitney.ufl.edu


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