DNA data base?

[sihaya]

I recall from a bioinformatics course I took once that a lot of species have thier complete (or partial) DNA (or RNA) sequences published somewhere on the NCBI website. How easy is it to determine the species or genus of an animal with DNA testing? Is it easier than looking at it under a microscope? Do you think this will ever be a practical way to identify species found in aquariums? (in the future I mean)

I guess, what I'm wondering is... how hard is it to find the DNA sequence of, say, a snail? Because I know a lot of the organisms sequenced right now are bacteria and algae... how hard is getting the sequence to those compared getting one of a snail or coral?

[greenbean36191]

At the moment, even if you had the right equipment to do it, it wouldn't be nearly as easy as using physical characters for most animals (assuming you aren't doing actual taxonomic or phylogenetic work). I have a friend who has been trying to get a good DNA sample from a starfish since last March and AFAIK, she still hasn't been successful. Some animals are easier though. I have another friend that works on your little red Halocaridina shrimp and he's worked up something like 500 of them since this summer (and found that they may not all be the same species). Your ability to ID them that way also assumes that someone else has already done genetic work with them, which isn't true for most animals in the hobby. Some of the species such as Nassarius or Montastrea used more commonly for research are probably easier to find.

[grimmjohn]

<a href=showthread.php?s=&postid=6327881#post6327881 target=_blank>Originally posted</a> by greenbean36191
I have a friend who has been trying to get a good DNA sample from a starfish since last March and AFAIK, she still hasn't been successful.

I feel that, I spent a summer trying to determine the species/subspecies status of the Orangethroat Darter complex using MT-CYTB code, currently it's based on location, breeding coloration, and an iffy head scale count. There are a few code references amazingly already but just various genes/sites of random species/subspecies, we were trying to put it all together and get a nice phylogenetic tree going, but so far it has not been completed. I collected over 100 individuals all over the state and nobody could get anything hardly worth PCRing.

Assuming lots of other people have done all the work before you to get code X from species Y, you would still need to sequence your sample to try to begin to compare them, and unless you have a lab at your disposal it wouldn't be cheap, well, a few minutes of UAMS's sequencer cost us $7-10 a pop I think.

Large labs are able to take a sample, sequence it, and spit out known similarities pretty quickly, but for "aquarium" use it would take a handheld sequencer (impossable right now), and a wireless link to a database of all known speices. A genome database is years (decades) away, but many speceis have at least one site/gene/chromosome sequenced, so that could be an easy source of comparison, but is there enough difference at that location to tell apart species/supspecies? Maybe/maybe not, many sites could tell you the difference between a tang and a angel, but regal from a "red sea regal," probably not, it would take a specific site or a whole genome, so the handheld would have to be very flexable as well and the database much larger as well, tack on a few more years for that () : )

Cheers,

grimmjohn

[sihaya]

What makes getting a DNA sample from an animal difficult? Is it the nature of the tissue?

[grimmjohn]

<a href=showthread.php?s=&postid=6328178#post6328178 target=_blank>Originally posted</a> by sihaya
What makes getting a DNA sample from an animal difficult? Is it the nature of the tissue?

Getting samples are easy, getting lab usable DNA from them can be difficult () : )
Some labs have the tech to get DNA from almost anything you throw at them comparativley easily, but not all labs are well funded/top of the line/state of the art.
In our case we were a small college, and all I had at my disposal to extract DNA was a Qiagen kit (or the carcinogenic way, no thanks, though I ended up playing with enough ethidium bromide to mutate my 2nd cousin's kids anyway :D ) And the Qiagen kits are very picky, you have to find just the right amount of sample to use for each species/case/individual/tissue and use just the right amount of time, so there are a few variables I had to discover myself.
A) The DNA had to be in N2(l) the whole time, when we thawed it to sample it, it immediatly starts to degrade.
B) Proteinase K problems
C) you have to have the right primer for your specific use for the PCR, the primer often has to be special ordered/sequenced/made for you.
D) You can't get enough usable DNA to send to the sequencer without PCR.

It easy for hospitals and parentage labs cuase all the DNA is human and they are set up for it and most things are stadardized. But in the rest of natural science you have to tread lots of nw ground, and without the pimp setups its dificult to just plug and play.

Cheers,

grimmjohn

[sihaya]

What about getting usable DNA from larvae? Is that any easier?

[grimmjohn]

<a href=showthread.php?s=&postid=6328541#post6328541 target=_blank>Originally posted</a> by sihaya
What about getting usable DNA from larvae? Is that any easier?
I think it would depend on what you are trying to do. In many cases you might not want to use larvea cuase you would probably just be grinding the whole thing up including stomach contents containing God knows what and not to mention all sorts of enzymes (which may complicate things) from various organs that would not be present/as prevalent in a tissue sample from say blood or a fin.

Cheers,

grimmjohn

[rshimek]

<a href=showthread.php?s=&postid=6328541#post6328541 target=_blank>Originally posted</a> by sihaya

Hi Sara,

What about getting usable DNA from larvae? Is that any easier?

No, it is generally much harder as the larvae themselves are more delicate and difficult to work with than the adults. And there is no benefit to it, as the larvae and adults have the same genetic material.