[Coral-List] coral genome

Mike Matz matz at whitney.ufl.edu
Tue Sep 16 16:48:12 EDT 2003

Hi all,

In responce to the questions from Bob Buddemeier, let me try to summarize
the two major benefits of sequencing a coral genome:

1. Coral genome would be the major bonus for evolutionary genomics, since
corals are representatives of the Cnidaria - sister group to all the
currently sequenced metazoans.

2. A basis will be created for molecular studies of how coral works. Of big
interest for conservation biology would be molecular mechanisms of stress
and resistance, and also molecular machinery of symbiosis between host and
algae. Immediate profit would be availability of microarrays to monitor
expression of thousands of genes, which would be a great tool for fine
characterization of various coral conditions and stresses.

For wide scientific community, the first benefit is definitely the most
interesting, while the second is more for the specialists in reef biology.

Main candidates nominated for genome sequencing:

Acropora sp (millepora?)
Montastraea sp (annularis/faveolata?)
Porites sp (lobata?)

Let's try to compare them, The model should have the following features:

1. should have small genome;

2. should be easy to work with basic molecular techniques such as RNA and
DNA isolation;

3. should be amenable to at least to in situ hybridization techniques and to
RNAi techniques - to study gene expression patterns and knock the genes
down, at least locally and temporarily.

4. Should be easily kept in the lab, preferrably growing.

5. Should be itself widely distributed and ecologically significant, or be a
representative of a closely related group of ecologically significant
species, so that sequence information from the genome project could be used
for studies in many places and many similar species.

6. Existence of other relevant molecular projects, such as EST sequences.

7. Popularity of the species in general as a model for various non-molecular

8. Ultimately, the species should be reproducible in the lab, completing
full life cycle in less than a year, and amenable for transgenic

Please add your requirements if you feel necessary.

1. Small genome: to my knowledge, most corals have genomes of similar or at
least comparable sizes, most common 2n number of chromosomes being 28. So
the first issue would not matter much for most candidates. Montastraea is
2n=28, as are most Acroporas, I wonder about Porites.

2. RNA-DNA isolation: Craig says Acroporas are difficult in this respect.
Montastraea and Porites seem to be OK. I have a feeling that generally, this
and the next issue (in situ hybridization and RNAi) would work the better
the meatier is the coral, so I favor Montastraea (especially cavernosa - the
fattest coral I ever worked with). Still, to my knowledge, nobody ever
attempted in situ hybridization or RNAi on coral (please let me know if I'm

4.  All the three candidates are nicely living in the lab, acropora grows
fastest, montatraea - slowest. Acropora seems to be more gentle than the
other two.

5. None of the candidates has a single species that is distributed
eveywhere. At least there is a limitation either to Caribbean or
Indo-Pacific. Still, at the generic level, all three genera - Acropora,
Porites and Montastraea - are distributed worldwide and are of the most
important reef-builders. Acropora model would represent the most
species-abundant genus (some 250 species), which is good. Porites comes
second in species numbers (some 50 species), and Montastraea - last, some 10
species. There is a slight downside of using representatives of species-rich
genera - there are more taxonomic difficulties there, but this would not
matter much for our situation, I quess.

6. Existence of supporting molecular projects is a Very Important Issue
indeed. We don't get too much money for coral molecular biology in general,
so it would be much better to stay focused. To my knowledge, there are some
EST projects going on Acropora millepora (although I don't know what the
status is) and another is just coming up on Montastraea annularis. I heard
nothing about molecular work on Porites. This was the main reason why I was
so skeptical about Porites candidate in the beginning.

7. Popularity: Acropora is definitely the star, Montastraea annularis comes
second. Porites seems to lag behind.

8. The ultimate requirement. I am not aware of any coral that would fulfill

Conclusion: there is no formally best candidate, so the choice would depend
on how one would weight the above considerations. I tend to put more weight
into general popularity and existence of other molecular projects, so, in my
view, Porites is not a good candidate. In all other respects, Acropora seems
better than Montastraea, except for the notion that it might be more
difficult to do molecular work, which would be very bad indeed. Could
anybody confirm this?..



Mike Matz
Whitney Lab, University of Florida
904 461 4025

----- Original Message -----
From: "Robert Buddemeier" <buddrw at kgs.ku.edu>
To: "Andy Bruckner" <Andy.Bruckner at noaa.gov>
Cc: <coral-list at coral.aoml.noaa.gov>; "Mikhail Matz" <mvmatz at yahoo.com>
Sent: Tuesday, September 16, 2003 12:44 PM
Subject: Re: [Coral-List] Porite genome 2

> I have been following this discussion with some interest.  Since I know
> relatively little about the potential application of genomics, this may
> be an ignorant question, but  ----
> What good will it do us, in the larger sense, to get the genome of a
> threatened or endangered or or regionally local  or endemic species?
> Wouldn't interpreting the significance of those results (in terms of
> vunerability or survival or distribution) require a lot of other genetic
> information before you could start to reap the benefits?
> It seems to me that a preferable strategy would be to go for a widely
> distributed, cosmopolitan species and than look for significant
> differences in the more specialized or localized or sensitive species.
> In that sense, Porites lobata  (or one of the widely distributed
> Indo-Pacific acroporids or pocilloporids) would seem to me to be as good
> a choice as any, although the thorny question of species identification
> in the morphological and environmental senses will certainly rear its
> head whatever you choose to look at.
> This would seem to me to put the project into a global, longer-term reef
> research and preservation framework.  I have pretty severe reservations
> about the short-term potential of  genome research to come up with a
> silver bullet that will fend off localized extinctions or reef collapses.
> What am I missing about the objectives and potential applications?
> Bob Buddemeier
> Andy Bruckner wrote:
> >Hi folks,
> >
> >I would like to add my 2 cents to this issue. Not sure if it is too late,
> >I would side with Mikhail.  It seems to me that (if it is a Caribbean
> >one of the  Caribbean Montastraea annularis complex species would be our
> >choice, given that this is the most important coral today on Caribbean
> >and it is affected by multiple diseases.  My second choice would be
> >palmata for the same reasons.
> >
> >
> >Andy
> >
> >Mikhail Matz wrote:
> >
> >
> >
> >>Dear Craig and all,
> >>
> >>The Porites candidate came as a surprize to me. My
> >>support would be for Montastraea (since my own
> >>molecular work is on M.cavernosa, and by the way, I
> >>never encountered the technical difficulties that
> >>Craig refers to), or Acropora. These two seem to me
> >>much more advanced in molecular terms than Porites.
> >>
> >>I do believe that having a coral genome sequenced
> >>would greatly benefit all of us and science in
> >>general, however, it is critical to select a proper
> >>species. I would be very glad to hear opinion of the
> >>list on this matter.
> >>
> >>In fact, I heard rumors of a couple other projects
> >>started that would lead to coral genomic studies, but
> >>nothing definite. Would be great to know for sure what
> >>is going on (or going to be going on) in this area!
> >>
> >>cheers
> >>
> >>Mike Matz
> >>
> >>Whitney lab, University of Florida
> >>http://www.whitney.ufl.edu/research_programs/matz.htm
> >>
> >>Note: forwarded message attached.
> >>
> >>__________________________________
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> >
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> --
> Robert W. Buddemeier, Ph.D.
> Kansas Geological Survey
> 1930 Constant Avenue
> Lawrence, KS 66047 USA
> ph 1-785-864-2112, fax 1-785-864-5317
> email  buddrw at ku.edu
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