[Coral-List] coral model for functional genomics

Thu Jan 5 08:21:26 EST 2006

Acropora palmata is important for reef building in the Caribbean. Porites
lobata is probably the most important reef builder throughout the
Indo-Pacific. It is also listed by J. Veron as 'Probably the most common
Porites.' It is the most common coral forming microatolls, vital to
reef-height/sea surface studies. It has one of the most extensive fossil
records of any species, and a lot of data has been gathered on it via coring
for oil exploration.

Obviously, the two would be great, but P. lobata would make a lot of sense
as the one and only. Millepora is interesting, but not representative of
anything except Millepora, as it is not even a Scleractinian coral. 

I would be fascinated to learn what the reasoning was for criticizing your
choice of P. lobata. Perhaps it had something to do with technical
analytical difficulties? 

Perplexed,

John

John W. McManus, PhD
Professor, Marine Biology and Fisheries
Coral Reef Ecology and Management Laboratory (CREM Lab)
Director, National Center for Coral Reef Research (NCORE)
Rosenstiel School of Marine and Atmospheric Science
University of Miami, 33149
Office: 305-421-4814/4820, Fax: 305-421-4910, Website: www.ncoremiami.org

If I cannot build it, I do not understand it. -- Richard Feynman, Nobel
Laureate

-----Original Message-----
From: coral-list-bounces at coral.aoml.noaa.gov
[mailto:coral-list-bounces at coral.aoml.noaa.gov] On Behalf Of Mikhail Matz
Sent: Wednesday, January 04, 2006 1:07 PM
To: coral-list at coral.aoml.noaa.gov
Subject: [Coral-List] coral model for functional genomics 

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. 

Best regards,

Adam

Obviously, we are disappointed.  However, we have not been deterred.  We are
preparing to submit our request to sequence P. lobata the GJI and I have
also identified one private foundation that has expressed an interest in
picking up the 7 million dollar price tag for the sequencing project.  We
are looking at other options as well.  I suspect, in the end, we will have
to secure funding from multiple sources to finance this effort.  I am also
pursing this matter further with NHGRI as I respectfully disagree with some
of the conclusion expressed in their summary statement.

Do not hesitate to contact me with questions.

GKO

Gary K. Ostrander 

Professor of Biochemical Oncology &

    Marine Biology

University of Hawai

_______________________________________________
Coral-List mailing list
Coral-List at coral.aoml.noaa.gov
http://coral.aoml.noaa.gov/mailman/listinfo/coral-list