[Coral-List] Coral genome

David J Miller david.miller at jcu.edu.au
Sun Sep 28 21:07:43 EDT 2003

Dear All

I very recently became aware of this discussion forum, hence my late 
entry to the coral genomics debate. I thought Mike Matz did a good 
job in raising some of the pros and cons of the various proposed 
model corals, but there are a few things that maybe should be more 
widely known than they appear to be.

First, there seems to be the misapprehension out there that a coral 
genome would be the first cnidarian genome to be sequenced. This is 
not the case; it is extremely likely that a current bid to sequence 
the genome of the sea anemone Nematostella vectensis will be 
successful. All of the cnidarian evo-devo community has strongly 
supported this application, and I would be very surprised if it is 
not funded. This animal has special advantages for evo-devo studies, 
hence the universal support for the Nematostella sequencing 

Second, as Mike previously pointed out, it's really important that 
the 'homework' is done before a coral genome proposal goes forward. 
By this I mean that it is essential that parameters such as the 
approximate genome size are known; note in the case of Hydra species, 
H. viridis has a genome that is one quarter the size of the more 
widely studied H. vulgaris and H. magnipapillata. Note also that 
genome size is not a function of the number of chromosomes - it's 
just that the chromosomes of H. viridis are smaller than those of the 
other species. No one should seriously consider using H. vulgaris for 
a sequencing project, despite its popularity otherwise; a bid to 
sequence H. viridis will go forward very soon. Similar criteria 
should apply in the case of a coral.

Mike also pointed out the requirement or desirability of technology 
and tools for the coral selected. Please consider the advantages of 
the coral that we work on, Acropora millepora, in this respect. 
Acropora is the second best represented cnidarian in the databases 
(behind Hydra). Indirect estimates put the genome size as small - 
comparable with the fruit fly and roundworm, and therefore at the low 
end of cnidarian genome sizes. Most corals have the same number of 
chromosomes, but those of A. millepora are particularly small. Also, 
most of the molecular tools are there for A. millepora - genome 
libraries in lambda and cosmid vectors, cDNA libraries for six 
different embryonic and larval stages (as well as adult colonies), 
and an extensive EST dataset. Microarrays featuring 3,000 ESTs of 
known sequence are presently available (mail me if you want details 
of this), and the sequences of these clones will be available 
shortly; note that we have been holding off releasing these until the 
first paper is accepted, and that we expect to hear that this has 
happened within two weeks. The first batch of ESTs was from planulae, 
and at present we are generating ESTs from other libraries. In 
addition, thanks to Eldon Ball's efforts, in situ hybridisation 
technology works wonderfully on A.millepora, whereas I do not believe 
this method has been established for any other coral. Therefore in 
terms of the molecular basics being in place, Acropora is a much more 
advanced system than is any other coral, and I am quite sure that the 
evo-devo community would strongly support a proposal to sequence the 
genome of this coral. Before putting forward such a proposal, 
however, we intend to accurately determine the genome sizes of a 
range of Acropora and other coral species. It should be possible also 
to do this for any coral for which zooxanthellae-free cells can be 

I don't wish to discount the Porites lobby but, for a coral 
sequencing initiative to be successful and useful, the molecular 
parameters outlined above are particularly important.


David J Miller
Comparative Genomics Centre
Molecular Sciences Building
James Cook University
Queensland 4811

Phone (61)-747-814473
Fax    (61)-747-816078
Email david.miller at jcu.edu.au

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