[thedoc (OP)]

Matt  asked the Naked Scientists:
   
I was just listening to the naked genetics podcast (mice on drugs). They mention genetic differences between mice and trying to compensate for variations in the population when analysing data. I was also thinking about how rotten the weather was this winter and how beneficial it has been that our observational weather records date back so far.

Untangling that mess from my head into a hopefully coherent question or two:

Given the cheapish £600 to sequence a full genome;
1).   should all scientists now be routinely sequencing their animal subject's genomes?
2).   would that miss the point due to lack of epigenetic information?
3).   would it be more cost effective just to store a hair or something cryogenically and let future scientists sequence if they needed to know something useful about the experiments? (would epigenetic information survive the freeze?)

I hope I'm not wasting your time with such ramblings. Still loving the show, thanks for all the hard work you & the team do to bring us science stuff we'd never hear about otherwise!

It's been FAR too long since I asked you scientist types a question. better put that right.

Thanks,

Matt.

What do you think?

[CliffordK]

I think it is a good question.

At this moment, scientists are still at the experimental stage of cloning.  I think as we are making "seed banks", it would be reasonable to make tissue banks.  Perhaps fertilized eggs, especially for endangered mammals.

Currently, I think the official count of Northern White Rhinos is 7.   Unfortunately, if the species survives, the inbreeding will be significant, and it may experience rapid genetic drift.

There is a quagga restoration project trying to breed quagga-like zebras.  The original will never return, but the selective breeding should create at least a superficially similar animal.  Gene manipulation might be able to restore the species, if one had enough historical DNA and chromosomes to differentiate quaggas from other zebras. 

The Pyrenean ibex was unsuccessfully cloned post-extinction. 

It is quite possible that understanding the animals around us better will help us understand ourselves, and potentially assist our own species. 

[evan_au]

would it be more cost effective just to store a hair or something?

The price of genome sequencing is dropping at a phenomenal rate, so storing a sample for 10 years before trying to sequence it will make the price far lower (assuming sequencing technology continues to improve at the current rate).

Some methods of  genetic sequencing chop up the genome into little pieces, which are then sequenced. A supercomputer then joins the pieces together into a whole genome.

The hardest part of sequencing is obtaining the first genome for a species. Once you have this master copy, it is much easier to sequence individuals of this species, because the supercomputer just needs to fit each short sequence into the existing template (the price quoted assumes a human genome with an existing template). But this may become easier with some new techniques that are able to sequence much longer segments of DNA - and perhaps a whole chromosome.

Whatever technology comes along, it is best to capture the best-quality genome you can obtain. This would more likely come from a sample of live tissue like skin or white blood cells, rather than from dead tissue like a hair. Rapid cryogenic freezing would preserve the sample's DNA before it started to break down.

would epigenetic information survive the freeze?

Epigenetic markers would survive the freeze as well as the DNA to which it is attached. Traditional DNA sequencing are unable to read this epigenetic information, but some newer machines can read some of this information.

Even if you could read the epigenetic markers, you would read instructions on how to make a skin cell or white blood cell. However, some of the techniques demonstrated for induced pluripotent stem cells show that it is possible to strip away the epigenetic markers for skin cells, and return the cell to something like an embryonic stem cell.