[Coral-List] coral model for functional genomics

[Zac Forsman]

Dear Jakie and Coral-list,
  I agree that Porites species are indeed among the
most difficult to identify, however there has been
some progress resolving relationships in the genus. 
There are morphometric and genetic methods that have
successfully resolved species-level relationships. 
There is even a preliminary phylogeny available for
Atlantic and E. Pacific species (my dissertation work,
and 10th int. coral reef proceedings paper in press;
available here: http://www2.hawaii.edu/~zac/ ).  We
are currently working on adding Hawaiian species to
that phylogeny and including two mitochondrial genes. 

In my opinion, P. lobata could very well interbreed
with other morphotypes, or be part of a flock of
incipient species –but I view that as a double-edged
sword; on one hand it’s a great opportunity to study
hybridization, speciation, and geographic variation,
on the other hand there is potential for
misidentification.  In my view, the opportunities far
outweigh the pitfalls, and once the genomic
information is gathered, rapid means for
identification and comparison will emerge, yielding a
wealth of information about the nature of the ‘coral
species problem’ itself.

 P. lobata has a unique combination of characters
(such as geographic ubiquity and abundance,
cultivability, annual growth bands, corallite-level
taxonomic characters, excellent fossil record, and a
foundation of previous work), that make it an
excellent candidate as a model organism.  There are
significant challenges, but there are equally
significant rewards.

I should also mention that we have been growing small
nubbins of P. lobata in large outdoor tanks with as
high as 90% survivorship (n=72) for some colonies,
nearly doubling in area in 6 weeks (paper submitted to
Aquaculture).  It may therefore be possible to grow
and distribute a reference strain of P. lobata (as is
done for most model organisms). 

All the best!  -Zac Forsman


PS.  I also initially had some difficulty extracting
good quality DNA as Michael Morgan mentioned earlier,
however I was able to find alternate protocols that
worked quite well for me.


--- j.wolstenholme at student.qut.edu.au wrote:

> Dear Misha and Coral-List
> 
> My main concern about the species selected relates
> to whether samples would be collected from more than
> one colony. If so, the issue of consistent
> identification of different colonies needs to be
> considered - both in terms of species and subspecies
> (i.e. incipient species, morphotypes, etc). This
> problem exists for many species of corals, but is
> definitely an issue for most species of Porites as
> they are so difficult to identify.
> 
> But then, a positive of selecting P. lobata is that
> large colonies are discrete - in contrast to e.g.
> species of Acropora that form thickets. So, provided
> that you could be sure of returning to the same
> colony, subsequent samples could be collected
> without the concern of consistent identification.
> 
> cheers
> Jackie
> 
> Master of Information Management Candidate
> Faculty of Information Technology
> Queensland University of Technology
> Brisbane QLD 4001
> Australia
> 
> 
> 
> ---- Original message ----
> >Date: Wed, 04 Jan 2006 13:07:24 -0500
> >From: Mikhail Matz <matz at whitney.ufl.edu>  
> >Subject: [Coral-List] coral model for functional
> genomics   
> >To: coral-list at coral.aoml.noaa.gov
> >
> >
> >Hello listers,
> >
> >I'd like to re-initiate the discussion about what
> would be an 
> >appropriate coral species (singular or plural) for
> genomics and 
> >functional genomics (such as studies of stress
> related gene expression 
> >changes). Some time ago we managed to reach a
> consensus that Porites 
> >lobata would be a good model; and it was that
> species that went into the 
> >white paper for genome sequencing (Gary Ostrander
> sent an update about 
> >that some time ago, I attached it below just in
> case). However, just now 
> >my grant proposal was critisized (and effectively
> killed) by two of the 
> >four reviewers who felt that P. lobata is
> inappropriate as a functional 
> >genomics model. I am afraid I lost the track of
> things - apparently P. 
> >lobata is falling out of fashion again. Would
> anybody be willing to 
> >comment?..
> >
> >cheers
> >
> >Misha
> >
> >--------------------
> >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
> >www.whitney.ufl.edu/research_programs/matz.htm
> >
> >------------------------
> >message from Gary Ostrander:
> >------------------------
> >
> >Update on Coral Genome Sequencing Project (November
> 3, 2005).
> >
> > 
> >In late 2003 we prepared a white paper for NHGRI
> for the sequencing of the genome of Porites lobata. 
> This document included letters of support from about
> 50 investigators from around the world and reflected
> the prevailing wisdom that P. lobata was the
> preferred species for sequencing.
> >
> >The review of our white paper was slowed
> considerably by introduction of a new review process
> at NHGRI.  Moreover, in mid-2004 I was asked to
> provide further justification for the selection of
> P. lobata over Acropora palmata.  Though this had
> been discussed in the white paper, I did provide
> further justification.
> >
> >In August of 2004 I was notified that initially two
> species, P. lobata and A. millepora had been chosen
> for pilot sequencing.  This came as a surprise as A.
> millepora had only been advanced by one group when
> the white paper was being developed.  Following
> subsequent discussions I was informed by NHGRI that
> they would conduct pilot sequencing of three coral
> species, P. lobata, A. palmata, and A. millepora and
> based on the sequencing they would select one coral
> species for full-scale sequencing.  Over the next
> few months I was able to obtain HM DNA for each of
> these species from Monica Medina (A. palmata),  
> David Miller (A. millepora) and Craig Downs, Teresa
> Lewis and I (P. lobata).  These samples were
> processed and shipped to the Sequencing Center at
> Washington University in St. Louis, MO (USA).  
> Please see:
> http://www.genome.wustl.edu/genome_index.cgi for
> details of the analysis.
> >
> >After our analysis of the resulting data we
> prepared a sequencing plan for P. lobata and
> submitted this to NHGRI for consideration in early
> 2005.  We were notified in August 2005 that the
> working group had recommending P. lobata to the
> coordinating committee.  Unfortunately, after the
> Council met to consider these recommendations, I
> received the following email from NIH/NHGRI:   
> >
> >Hello Gary,
> >
> >I am sorry to say that, in the end, sequencing the
> coral genome was not seen
> >as being a high priority for NHGRI. As you know,
> the original working group
> >discussion was very positive, and continued to be
> up until the time that it
> >forwarded the specific recommendation this round.
> But the Coordinating
> >Committee had significant concerns. They did think
> that Coral sequence would
> >be valuable for basic biology, and that Porites was
> probably the right
> >choice. However, the committee did not think that
> sequencing the coral
> >genome was of direct enough significance or
> relevance for the general NIH
> >mission. 
> >
> >There was specific discussion of some of the
> features of coral discussed in
> >the original white paper that could have importance
> for human health, such
> >as long life span, or understanding/identifying
> genes underlying biological
> >functions characteristic of organisms at that
> evolutionary position.
> >However, the committee thought that the arguments
> were too indirect. It is
> >important to note that the Coordinating Committee
> members did agree about
> >the ecological significance of coral, and the
> problem of coral bleaching,
> >but they thought that these issues were not within
> the NIH purview. They
> >also thought that it was unclear how sequence
> information would lead to a
> >better understanding of these significant issues,
> compared to other avenues
> >of research. 
> >
> >Our Council concurred with these conclusions. 
> >
> >>From a personal perspective, it is important to
> note that our sequencing
> >program is changing as we continually evaluate what
> we do. In the past year,
> >more emphasis is being put on problems of more
> direct medical relevance,
> >though certainly not to the exclusion of
> investigating significant
> >biological problems, or sequencing model organisms.
> In addition, there is a
> >sense that the general goal of filling in the nodes
> of the tree leading to
> >humans has mostly been done, and that arguments
> based on that concept alone
> >are no longer sufficient. Finally, this discussion
> comes at a time of
> >decreasing NIH budgets, and as you might expect
> that forces us to look more
> >carefully at everything, and to refine our
> priorities. 
> >
> >I am sorry that the outcome was not more positive. 
> If you have any
> >questions, please don't hesitate to contact me. 
> 
=== message truncated ===


'How inappropriate to call this planet Earth, when it is clearly Ocean.' 
  -Arthur C. Clarke

Zac Forsman, Ph.D.
University of Hawaii
Dept. of Biology
2450 Campus Road, Dean II Bldg
Honolulu Hawai'i 96822


		
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