Acropora millepora frags for genomics

[victoly]

you'd have to find people who originally brought them in "fresh: and then had a relatively well documented chain of owners. It might be worth contacting some of the old school, high-visibility reefers (e.g., sanjay joshi, mike paletta, richard ross) to see if they can help source some older frags. "Newer" frags could just be brought in strait from the reef. Something worth noting might be that there may be a distinction between a frag from the reef as opposed to a mariculture. Is there any degradation while still in-situ before they even reach a hobbyist?
 

[Gig 'em @ NDstructible]

Ty has the most "old school" frags in austin, just get 10 frags from him! [emoji38]

[Timfish]

How would an aquarist get their corals genotyped like you've done in your other research and are doing with the millie you got from John?   

[Robb in Austin]

Cool stuff.

[Mikhail Matz]

Sorry for the radio silence:

On genotyping: so far we were just talking about measuring DNA integrity, no actual genotyping involved. A very easy procedure for us, but sadly you cannot do this at home. Let me know if you want to do this for your corals - if we amass enough old and new frags to make it scientifically interesting (like 15 of each kind?) we will do it for you gratis.

Genotyping, as in identifying a specific genotype/clone your frag is coming from, would be more involved and expensive, but again, can be done for a total of $1200 for 100 frags (just not worth it doing it for less fragments; plus we need to make sure we sample enough frags so we would actually start getting matches between different aquarists). I am not sure what purpose this information would serve, though - the genotype itself does not really tell you anything about biology. Still, you can expect all frags of the same genotype behave in the same way across all y'alls tanks.

cheers

Misha

[Timfish]

I realized over a decade ago our systems should live centuries (in my maintenance business I've had systems be inherited and go through multiple owners).   I was under the impression though that most corals lived indefinitely so long term propagation by fragging was a viable method to maintain a clone line.  I've known some corals like Fungiids had life expectancies of 30 to 40 years but was thinking they were more an exception than the rule.  It was quite a surprise when you confirmed Acroporiids also had life a life expectancy when the question of scenesence came up as an explanation for the degraded DNA in Ty's coral.  It seems obvious now we really we need to be focusing on sexual reproduction.  Fragging does not look viable long term for propagating a species.  We're already selecting for genotypes that are highly adaptable but knowing what genotypes we have and track them ideally would help eliminate some of the guesswork when dealing with problems (besides being able to develop new colors ).   Correct me if I'm wrong but it's my understanding a clone line can't self fertilize.   Additionally some species look very similar and hybridization is not necessarily viable (or desired if it is).  If we're going to be successful we need to be able to identify both genotype and clone line.  Picking different colors or chain of custody might work as a surrogate for identifying a clone line but it seems knowing the genotype is still essential. 

 

How large of a frag is needed?   Are we talking a 5mm piece or a 3 cm piece?  Can the sample of 100 be a range of species or does it all have to be, ideally, a single species?

[Mikhail Matz]

Senescence is seen in old Acropora colonies in older parts of the colony - the branches and polyps become misshapen and sometimes develop blobs of tissue that looks very much like tumors. In the same time, the newer parts - outskirts of a table colony A. hyacinthus, for example - look perfectly fine. This suggests to me that asexual propagation might not necessarily lead to senescence, as old corals seems to be still capable of making new nice-looking branches. Lack of sexual reproduction, however, might relax constraints of DNA integrity possibly leading to fragmentation - interesting idea to test.

Frag size for genotyping: 5 mm.

Sample of 100: the whole study will only become interesting if we start finding the same clones. If every frag is a different clone, we are not really learning anything. So these 100 frags better be the same species (and specifically, A.millepora, our genomic model!) 

[Timfish]

Dam*, this thread is just raising more and more questions and I don't have nearly enough tanks or time.

 

So if we just limited it to Palmer's Blue or maybe just blue A. millie colonies?  I've got a Palmer's Blue from Juiceman and another blue but I don't know where the 2nd came from.

 

I know colonies from other families have been shown to have an environmental memory, has any research suggested that for Acroporiids?  I certainly see differences between my tanks but I don't have two tanks I would consider identical so I don't really expect the same results.

[Mikhail Matz]

I would take 5-7 different blues just to test the hypothesis that they are all in fact the same clone (feels highly likely for some reason); but once we establish that there is not much interest to genotype more blues. Are there any other distinctive A. millepora color types perhaps?

[Timfish]

Yeah, it's a bit concerning.  If all blue millies turn out to be the same clone line and they all show the degraded DNA Ty's sample did worst case scenario we may not be able to breed them in captivity and end up losing the clone line in the future.

 

Definitely but there's the issue of variation in color due to environmental factors, mostly light intensity but nutrition plays a role too.

 

Funding.   We need to send money to your lab c/o UT, correct?  Is there a research or job #?  And am I safe in thinking it'll be tax deductible?

[Gig 'em @ NDstructible]

Correct me if I'm wrong, but it sounds like senescence really only occurs in the older part of a coral where there has been no new growth in a while. The actively growing parts of a coral where new polyps are being developed don't appear to portray senescence. If that's the case, then as long as growing colonies are kept then there's not too much to worry about. The only risk is low genetic diversity of only maintaining one strain, which leaves it vulnerable to a complete wipe out if a disease is introduced in the aquarium trade that it is prone to.