Mikhail Matz Posted September 6, 2017 Share Posted September 6, 2017 Hi folks - I am looking to buy a few (2-3) small fragments of Acropora millepora. We need it for genome sequencing - so if you have your favorite A.millepora in your tank there is a chance to get its genome completely sequenced (for free). cheers Misha Link to comment Share on other sites More sharing options...
FarmerTy Posted September 6, 2017 Share Posted September 6, 2017 Hi folks - I am looking to buy a few (2-3) small fragments of Acropora millepora. We need it for genome sequencing - so if you have your favorite A.millepora in your tank there is a chance to get its genome completely sequenced (for free). cheers MishaDr. Matz,I'd be happy to donate a few mille frags in the name of science. I'll send you a message to coordinate.-Ty Link to comment Share on other sites More sharing options...
Mikhail Matz Posted September 6, 2017 Author Share Posted September 6, 2017 Hi Ty - many thanks!! I just need a twig with three branch tips. Can we meet this week? (I'll make sure your name is listed in Acknowledgements on the paper) Misha [email protected] Link to comment Share on other sites More sharing options...
FarmerTy Posted September 6, 2017 Share Posted September 6, 2017 Hi Ty - many thanks!! I just need a twig with three branch tips. Can we meet this week? (I'll make sure your name is listed in Acknowledgements on the paper) Misha [email protected]Absolutely. I'll email you to coordinate. Link to comment Share on other sites More sharing options...
Gig 'em @ NDstructible Posted September 6, 2017 Share Posted September 6, 2017 I have several strains of Mille in my tank. Red, green, and a little bit of both! Link to comment Share on other sites More sharing options...
Gig 'em @ NDstructible Posted September 6, 2017 Share Posted September 6, 2017 Email sent Link to comment Share on other sites More sharing options...
victoly Posted September 9, 2017 Share Posted September 9, 2017 I KNEW I SHOULD HAVE KEPT A TANK. UGHHHHHHHHHHHHHHHHHHHH. Link to comment Share on other sites More sharing options...
Mikhail Matz Posted September 10, 2017 Author Share Posted September 10, 2017 Man thanks for all the responses! The fragments issue is now solved, that was amazingly quick. Next, community project on sexual reproduction of corals in captivity (would massively help our research!), stand by for new forum topic. Link to comment Share on other sites More sharing options...
Mikhail Matz Posted September 16, 2017 Author Share Posted September 16, 2017 Reporting: Isolated genomic DNA from Ty's "Solomonian blue" and John Sorkness' "Indonesian green" (my own code name for the lack of better id). Ended up using John's sample - it yielded beautiful intact DNA. For some inexplicable reason "Solomonian blue" repeatedly yielded DNA with considerable degradation, even though the frag itself is thicker (and therefore looks kind of happier?) than John's. Both frags were looking good, putting tentacles out in my tank. Interesting. Maybe Solomonian coral goes through a lot of tissue remodeling? (something to research in the future) Anyway, sent "Indonesian green" DNA off for genome sequencing. We still need to establish the actual identity of this frag with John and Ty (this is going to be a rather famous coral individual after all). Thanks everybody for responses, and special thanks to Ty and John!! Will mention you both in the paper's acknowledgements section. cheers Misha Link to comment Share on other sites More sharing options...
FarmerTy Posted September 16, 2017 Share Posted September 16, 2017 Reporting: Isolated genomic DNA from Ty's "Solomonian blue" and John Sorkness' "Indonesian green" (my own code name for the lack of better id). Ended up using John's sample - it yielded beautiful intact DNA. For some inexplicable reason "Solomonian blue" repeatedly yielded DNA with considerable degradation, even though the frag itself is thicker (and therefore looks kind of happier?) than John's. Both frags were looking good, putting tentacles out in my tank. Interesting. Maybe Solomonian coral goes through a lot of tissue remodeling? (something to research in the future) Anyway, sent "Indonesian green" DNA off for genome sequencing. We still need to establish the actual identity of this frag with John and Ty (this is going to be a rather famous coral individual after all). Thanks everybody for responses, and special thanks to Ty and John!! Will mention you both in the paper's acknowledgements section. cheers MishaThat's great Misha! This is so exciting and I appreciate you keeping us and and club in the loop about it! Link to comment Share on other sites More sharing options...
Gig 'em @ NDstructible Posted September 17, 2017 Share Posted September 17, 2017 Reporting: Isolated genomic DNA from Ty's "Solomonian blue" and John Sorkness' "Indonesian green" (my own code name for the lack of better id). Ended up using John's sample - it yielded beautiful intact DNA. For some inexplicable reason "Solomonian blue" repeatedly yielded DNA with considerable degradation, even though the frag itself is thicker (and therefore looks kind of happier?) than John's. Both frags were looking good, putting tentacles out in my tank. Interesting. Maybe Solomonian coral goes through a lot of tissue remodeling? (something to research in the future) Anyway, sent "Indonesian green" DNA off for genome sequencing. We still need to establish the actual identity of this frag with John and Ty (this is going to be a rather famous coral individual after all). Thanks everybody for responses, and special thanks to Ty and John!! Will mention you both in the paper's acknowledgements section. cheers MishaWhat can I say? I produce quality corals [emoji12] haha. Totally joking, I'm just happy there were some good results and that we were able to help out. Hopefully we can be of further assistance to you. Don't be afraid to ask, we'll be happy to help in anyway we can! Link to comment Share on other sites More sharing options...
Isaac Posted September 17, 2017 Share Posted September 17, 2017 ty doesnt do water changes, maybe his corals adapt by having thick skin Link to comment Share on other sites More sharing options...
FarmerTy Posted September 17, 2017 Share Posted September 17, 2017 I was almost thinking that the Palmers Blue mille that I donated has been in captivity for over 10+ years and the green mille I grabbed from John's tank was a newer mariculture, probably just recently added in the last 6 months to his tank. So perhaps that may have affected the integrity of the DNA somehow? Link to comment Share on other sites More sharing options...
Gig 'em @ NDstructible Posted September 17, 2017 Share Posted September 17, 2017 I was almost thinking that the Palmers Blue mille that I donated has been in captivity for over 10+ years and the green mille I grabbed from John's tank was a newer mariculture, probably just recently added in the last 6 months to his tank. So perhaps that may have affected the integrity of the DNA somehow?I think it's just the acropower [emoji23] Link to comment Share on other sites More sharing options...
Mikhail Matz Posted September 18, 2017 Author Share Posted September 18, 2017 Nice hypothesis indeed! How shall we test it? Link to comment Share on other sites More sharing options...
FarmerTy Posted September 18, 2017 Share Posted September 18, 2017 Nice hypothesis indeed! How shall we test it?How about I drop you off another frag of a long-term captive kept coral and a frag of a newly added mariculture and see if we see the same DNA degradation? Since both frags will be from my tank, it will help us isolate if it is a condition in my tank that causes the DNA degradation you observed or if the issue is potentially the duration of recorded captivity. Link to comment Share on other sites More sharing options...
Gig 'em @ NDstructible Posted September 18, 2017 Share Posted September 18, 2017 Is DNA impacted by longer term captivity? Trying to wrap my head around that one.Ty you can also give me a frag of your blue Mille and I can grow it for a few months in the same conditions as the "Indonesian green" and then send that to the lab. That could isolate environmental conditions being an influencing factor. Link to comment Share on other sites More sharing options...
jolt Posted September 18, 2017 Share Posted September 18, 2017 I'm curious how a decade of fragging and moving through so many different hobbyist aquariums along the journey does affect DNA. It seems like that takes natural selection out of the process of adaptation, since it is completely asexual? Link to comment Share on other sites More sharing options...
FarmerTy Posted September 18, 2017 Share Posted September 18, 2017 Is DNA impacted by longer term captivity? Trying to wrap my head around that one. Ty you can also give me a frag of your blue Mille and I can grow it for a few months in the same conditions as the "Indonesian green" and then send that to the lab. That could isolate environmental conditions being an influencing factor.I think that's the next step if both of my frags turn out to have DNA degradation. Its also a good way to trick me into giving you frags out of my tank. [emoji12] In the name of science... I swear! Link to comment Share on other sites More sharing options...
FarmerTy Posted September 18, 2017 Share Posted September 18, 2017 I'm curious how a decade of fragging and moving through so many different hobbyist aquariums along the journey does affect DNA. It seems like that takes natural selection out of the process of adaptation, since it is completely asexual?I'm very curious about this myself. I have several acros that have been in captivity for over a decade (not just me but through fragmentation and distribution from other reefers) so it would be an interesting experiment. Link to comment Share on other sites More sharing options...
Gig 'em @ NDstructible Posted September 18, 2017 Share Posted September 18, 2017 I think that's the next step if both of my frags turn out to have DNA degradation. Its also a good way to trick me into giving you frags out of my tank. [emoji12] In the name of science... I swear!Dang it! You caught on to my scheme [emoji31] It's an interesting question about DNA degradation in a tank over time. I guess the question is what would cause the palmers blue results to come out poorly? Could it have been too small of a sample? Poor laboratory preparation? I personally don't know about DNA degradation as a result of living longer within captivity, unless the environmental itself is causing physical damage to the makeup of the DNA. Corals are constantly growing and replenishing tissue as they build new skeleton. Single coral colonies in the wild can live to be hundreds and thousands of years old, so age may not be a factor. It does raise many new questions though. Like do blue corals yield poor DNA results compared to brown or green corals? Does the lack or abundance of zooxanthellae impact the DNA results? Truly fascinating issue to say the least!! Link to comment Share on other sites More sharing options...
mFrame Posted September 18, 2017 Share Posted September 18, 2017 Could it be natural light versus artificial light causing DNA degradation? I'm thinking UV or other damage to the DNA from higher intensities of certain wavelengths in the tank. Link to comment Share on other sites More sharing options...
Timfish Posted September 18, 2017 Share Posted September 18, 2017 For my two cents: Has past research ruled out the possibility of senescence? If not that would be something to look at, reproduction of a coral colony by "fragging" does not stop an aging process . Does the initial extraction by Dr. Matz's lab include DNA from the holobiont? Are we seeing changes due to shifts in the corals associated microbes? Link to comment Share on other sites More sharing options...
Mikhail Matz Posted September 18, 2017 Author Share Posted September 18, 2017 Actually, Acropora is one of few coral genera that do show senescence. Very good idea, Timfish Link to comment Share on other sites More sharing options...
Mikhail Matz Posted September 18, 2017 Author Share Posted September 18, 2017 The first thing to show is that the effect is statistically reproducible - i.e., we have fragmented DNA in long-timer clones and intact DNA in newly "domesticated" clones. This will require not just one more, but many more fragments (at least 20 if we are talking 10 old and 10 new, but ideally more), with decent enough knowledge of when they were brought into culture (there could be more than two grades, for example "old", ""medium", "new"). The senescence angle suggested by Timfish is really interesting and might lead to a very cool paper if we are able to gather good evidence. I will need to secure a small grant to fund this, which is always iffy but should be doable, but finding experimental fragments will be the major contingency - do you folks think it is realistic to find >20 coral clones with approximately known time since brought to aquarium culture?.. Misha Link to comment Share on other sites More sharing options...
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