3
$\begingroup$

The genome size of human is 3.000.000.000 bp and for Arabidopsis it is 255.000.000 bp. I know these numbers because their genomes have been published. Which methods are used by scientists to estimate the genome size before they sequence that genome?

$\endgroup$
  • $\begingroup$ A rough estimate can be given using gel/electrophoresis on different chromosomes. $\endgroup$ – Nandor Poka Jun 18 '15 at 13:25
  • 1
    $\begingroup$ Can U explain more or insert a protocol link, please? $\endgroup$ – MySky Jun 18 '15 at 13:33
  • $\begingroup$ More details and links may help you get better answers. $\endgroup$ – Berne Jun 18 '15 at 13:40
  • 1
    $\begingroup$ This is rather broad as there are many ways to do it. I'd speculate that reassociation kinetics was one of the first methods used. $\endgroup$ – canadianer Jun 18 '15 at 14:15
  • $\begingroup$ this link from NAR is good but I am looking for an up to date review. nar.oxfordjournals.org/content/31/10/e56.full $\endgroup$ – MySky Jun 18 '15 at 14:22
3
$\begingroup$

In the absence of molecular sequencing data the most accurate estimates are based on reassociation kinetics, more commonly known as Cot curves. Here is a classic paper from 1974 that describes the basic approach. While pulsed field electrophoresis can be used to resolve the chromosomes of species with relatively short chromosomes (like baker's yeast), there are really no suitable size markers that you could use to construct a standard curve for size estimation. C. elegans has six chromosomes, but they are all fairly close to each other in length, and the genome size of 100 Mb is the same as a single long human chromosome.

$\endgroup$
3
$\begingroup$

Gel electrophoresis is a basic lab method to get size info about nucleotide fragments, although one might need to chop up larger DNA to be able to apply this method. The wikipedia page covers the topic well, thus I'd suggest reading it. I'll just give a short outline:

  1. Nucleotide fragments are loaded into a gel (agarose or acrylamide).

  2. The gel is put into a static electric field

  3. Nucleotide fragment move to the positive end, because they have negative charge
  4. larger fragments migrate slower than smaller fragments
  5. standardized DNA ladder can be used to get approx size.

UV fluorescent dye is used to stain the fragments.

Another way, is to check closely related species. Among closely related species it is a fair assumption that they have similar genome size. You can also hybridize the unknown DNA to a DNA of such close relative to see how much of them are similar and you can also make estimates based on the size of the hybridized regions.

$\endgroup$
  • $\begingroup$ Thank you. even I think both methods are not sensitive enough $\endgroup$ – MySky Jun 18 '15 at 14:01
  • 1
    $\begingroup$ I find this link: nar.oxfordjournals.org/content/31/10/e56.full But I think there most be some better and easier ways. $\endgroup$ – MySky Jun 18 '15 at 14:03
  • $\begingroup$ Well, I just gave some examples, there are many methods if you look around :) Without knowing how much knowledge do you already have, I've tried to give the simplest examples and explanation. $\endgroup$ – Nandor Poka Jun 18 '15 at 14:05
  • $\begingroup$ General agarose gel electrophoresis for DNA can not tell chromosome length because it is too big to run. It is tough to run DNA having length more than 100kbp, which is too short to estimate the length of chromosomes. Then how can you tell the chromosome length? $\endgroup$ – 243 Jun 18 '15 at 20:14
  • 1
    $\begingroup$ Another way is to digest the DNA and measure the total nucleotide content. I think that's how earlier experiments were done. $\endgroup$ – WYSIWYG Jun 19 '15 at 5:54
-1
$\begingroup$

I guess you could estimate the length various ways. Pulse field electrophoresis could show DNA length, but you need a standard. When you combine Karyogram and FISH, you would could make a map. By genetical approaches, you could estimate distance on the map by centimorgan. Then you could know how many centimorgan chromosomes are. One centimorgan would be 1 million base pairs.

Oh, I forgot the simplest way. For example, take 1 million cells and estimate how many grams of DNA there.

$\endgroup$
  • 1
    $\begingroup$ " One centimorgan would be 1 million base pairs." That is false. Centimorgan is based on recombination frequency and can be very very variable between species (your info is only true for humans at best). It is not an actual distance between genes. $\endgroup$ – Nandor Poka Jun 18 '15 at 13:57
  • $\begingroup$ @canadianer I know, my last comment became obsolete after the edit...still that is a very rough estimate in my opinion. $\endgroup$ – Nandor Poka Jun 18 '15 at 15:01
  • $\begingroup$ I was not able to tell you I edited. About centimorgan, you can not apply human results to others, but you can apply the methods as they do with human chromosome. And DNA amounts would be a very rough estimation , but I do not know how exactly MySky want to estimate. Rough estimations are still estimations. $\endgroup$ – 243 Jun 18 '15 at 16:16

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.