[Coral-List] Coral holobiome sequencing
david.miller at jcu.edu.au
Tue Jul 29 03:45:23 EDT 2008
Sequencing the Acropora millepora holobiome
As you are aware, as yet there are no whole genome data for any coral – the sequence of the genome of the sea anemone Nematostella vectensis has proven a really useful resource for many of us, but a coral genome sequence would be much more useful. Indeed, many members of the coral research community believe that the availability of the whole genome sequence for a coral would greatly enhance their research. In a recent open online survey, Acropora millepora was the coral of first choice for whole genome sequencing, and this decision was endorsed during a session of the recent Symposium of the International Society for Reef Studies.
A group of us who have a long standing interest in either this specific coral or particular aspects of coral biology are pursuing ways of bringing about the sequencing the Acropora millepora genome. One means to this end is a competition recently announced by Roche, who now own 454, for access to massive parallel sequencing technology. We intend applying for a Roche grant, and seek your support and feedback in making the strongest possible application on behalf of the coral biology community.
The idea central to the Roche application is the need to establish a molecular profile of the coral organism that is as complete as possible – we need not just the genome sequence of the coral, but also the transcriptome of its zooxanthellae and the metagenome of the bacteria and viruses associated with the coral. Together, these will enable many aspects of coral function to be understood, and provide a platform for investigating how the association responds to environmental variables and various kinds of disturbance. The availability of one coral genome sequence will make obtaining others much simpler – it will be possible to assemble the genomes of other corals based on much lower coverage, because the Acropora genome can be used as a scaffold.
As indicated above, we seek comments on and constructive criticism of the proposal. To enable this, the full text of the proposal is available on the following URL:
Please note that tight length restrictions apply – the abstract must be <250 words, and the main text <1500 – hence the brevity of the draft. The deadline for applications is August 8th.
Letters of support would be really useful in convincing Roche that this is an application on behalf of the coral biology community, rather than a specific interest group. Send letters of support (ideally as pdfs) and comments to:
David Miller (david.miller at jcu.edu.au), Monica Medina (mmedina at ucmerced.edu), Mikhail Matz (matz at mail.utexas.edu) or any of the other applicants (but be aware that Denis Allemand is away until August 25).
We look forward to hearing from you.
on behalf of the coral holobiome consortium
Prof David J Miller
Comparative Genomics Centre
Molecular Sciences Building 21
James Cook University
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