[Coral-List] coral genome
capman at augsburg.edu
capman at augsburg.edu
Wed Sep 17 14:07:03 EDT 2003
I'd like to add to Julian's endorsement of Pocillopora damicornis as
a potentially good model system:
1. P. damicornis is a fast growing coral in aquaria, and very
adaptable to varying conditions. Not quite as fast growing as the
fastest Acropora species I have grown, but very fast nonetheless.
2. P. damicornis (at least the clones I have grown, which are
commonly available clones from the aquarium trade) has a finer
branching structure than most of the Acropora species, which means
even a modest-sized colony can be fragmented into many very
uniform-sized branch-tips for starting replicate, genetically
identical colonies for lab work. Within a year, each of these new
colonies could be fragmented into at least a dozen (or more likely
*dozens*) of new colonies.
3. Following up on point 2 above, even very small fragments of P.
damicornis (with as little as just a few polyps) can be used to start
a new colony, and attachment to new surfaces is rapid (typically
resulting in sheeting growth to anchor the colony before substantial
branch growth occurs). In contrast, most Acropora species have
thicker branches, fewer branch tips, and much larger fragments
(longer fragments) are usually necessary in order to start a
successful new colony.
4. P. damicornis has a high density of large (for a small-polyped
stony coral) long polyps, giving the colonies a very fuzzy
appearance. What is important here is that these polyps are almost
always well extended. In addition, P. damicornis colonies are
relatively unbothered by handling, or vibrations. With many (most?)
corals, if you pick up a colony and put it into a dish of water for
viewing under a low-power microscope, the polyps retract and don't
extend well for some time...and even when they do extend again
vibrations from working with them on the microscope will cause them
to contract again. In contrast, P. damicornis will retract only
partially if handled gently, but then within minutes the polyps will
be fully extended again, and will typically stay extended even while
being worked with on the microscope. For this reason, P. damicornis
is the absolute star performer in my teaching labs (where we have
about 50 species of growing corals to choose from) for demonstrations
and other activities where I want students to be able to work with
live, fully extended coral polyps. I can even break fragments off of
large colonies just before class and usually have extended polyps
5. Following up on point 4 above, the long, nearly always extended
polyps of P. damicornis are very transparent except for their
zooxanthellae (and the pale polyps from lower shaded portions of
healthy growing colonies are almost completely unobscured by
zooxanthellae, and the polyps from the most intensely illuminated
branch tips are relatively low in zooxanthellae as well). I would
think that these polyps would be perfect for studies of gene
expression in which genes of interest have been linked, for example,
to genes for bioluminescence, so that cells expressing a given gene
will glow. Live healthy colonies of such genetically modified P.
damicornis could be viewed under low-power microscopes, with very
clear complete views (both top views and side views) of fully
extended polyps, so it should be possible to not only see when genes
are turned on and off, but also see precisely where in the polyps
this is happening.
>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.
>>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
>> 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.
>>> >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!
>>> >>Mike Matz
>>> >>Whitney lab, University of Florida
> >> >>
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