[Coral-List] coral genome

[Tonya Shearer]

Having sequenced DNA from many Caribbean scleractinian 
species, I thought I would add a couple of comments.  One 
consideration when choosing a species is the availability of 
zooxanthella-free tissue (ideally sperm).  In my experience, DNA 
from the zoox is often amplified (and subsequently sequenced) in 
addition to the coral DNA, unless the tissue is free from zoox or the 
primers are specific to cnidarians.  Obtaining gametes from 
broadcasting species is relatively easy, whereas brooded larvae 
often already have zoox from the maternal colony.  I'm not sure 
how easy it is to get sperm from brooding species.

My personal preference is for a Porites species, one because I 
have developed microsatellites for P. astreoides (unfortunately a 
brooder), and two, because there are several representatives in 
the Indo-Pacific and Caribbean.  Thus this genome can be used 
as a model for efficiently developing genetic markers for several 
Porites species.  Three, conducting molecular analysis on Porites 
(at least Caribbean species) is very easy = high amplification and 
sequencing success (not the case for some other species).  
Finally, as brooders that release larvae multiple times throughout 
the year, molecular biologists can take advantage of breeding 
experiments without having to hope for good weather conditions 
on the couple of evenings of mass spawning.

I have also developed microsatellites for Montastraea cavernosa. 
Although technically easier to work with as far as eliminating the 
concern for zoox contamination by using sperm, I think 
sequencing a Montastraea genome would on the whole, be less 
useful for molecular biologists than a species from a more 
widespread genus.

No matter which species is chosen, this information is extremely 
useful for those of us that are interested in the genetic structure 
and gene flow (larval transport) of coral species.  For those of you 
that don't know the struggles of doing molecular work on corals, 
standard molecular markers used for population genetics on 
other organisms (mitochondrial genes) cannot be used in corals 
due to a slow rate of evolution in the mitochondrial genome.  
Therefore we have to develop other markers, which can take 
years.  Having a model genome available to develop these 
markers will save time, money and the sanity of those doing the 
work.

Tonya (Snell) Shearer

tlsnell at buffalo.edu

109 Cooke Hall
University at Buffalo
Buffalo, NY  14260