[Coral-List] coral genome

Julian Sprung julian at twolittlefishies.com
Wed Sep 17 20:10:48 EDT 2003

Dear Mike,

Regarding requirement 8, what about Pocillopora damicornis? It reproduces
prolifically (by asexual formation of planula larvae), and aquarium spawned
colonies can reproduce this way in a year or less. It is also very
widespread and easily cultured in aquariums.

Julian Sprung

>From: "Mike Matz" <matz at whitney.ufl.edu>
>To: "coral-list" <coral-list at coral.aoml.noaa.gov>
>Subject: [Coral-List] coral genome
>Date: Tue, Sep 16, 2003, 4:48 PM

> 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
> research.
> 8. Ultimately, the species should be reproducible in the lab, completing
> full life cycle in less than a year, and amenable for transgenic
> manipulations.
> Please add your requirements if you feel necessary.
> Discussion:
> 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
> wrong!)
> 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
> it.
> 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?..
> cheers,
> Mike
> Mike Matz
> Whitney Lab, University of Florida
> 904 461 4025
> http://www.whitney.ufl.edu/research_programs/matz.htm
> ----- 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,
> but
>> >I would side with Mikhail.  It seems to me that (if it is a Caribbean
> species)
>> >one of the  Caribbean Montastraea annularis complex species would be our
> first
>> >choice, given that this is the most important coral today on Caribbean
> reefs
>> >and it is affected by multiple diseases.  My second choice would be
> Acropora
>> >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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