3.4 Amount of DNA (c-value) and Number of Chromosomes (n-value)

The amount of DNA within a cell changes during the following events: fertilization, DNA synthesis and mitosis (Figure 3.4.1). We use “c” (or C) to represent the DNA content in a cell, and “n” (or N) to represent the number of complete sets of chromosomes. In a haploid gamete (i.e. sperm or egg), the amount of DNA is 1c, and the number of chromosomes is 1n. Upon fertilization, both the DNA content and the number of chromosomes in the diploid zygote doubles to 2c and 2n, respectively. Following DNA replication, the DNA content doubles again to 4c, but each pair of sister chromatids are still attached by the centromere, and so is still counted as a single chromosome (a replicated chromosome), so the number of chromosomes remains unchanged at 2n. If the cell undergoes mitosis, each daughter cell will return to 2c and 2n, because it will receive half of the DNA, and one of each pair of sister chromatids.

 

Simple graphic showing changes in DNA and chromosome content during the cell cycle and mitosis.
Figure 3.4.1 Changes in DNA and Chromosome Content During the Cell Cycle and Mitosis. For simplicity, nuclear membranes are not shown, and all chromosomes are represented in a similar stage of condensation.
Pictorial representation of mitosis and changes in chromosome number at the various stages - a pink cell with blue and green chromosomes
Figure 3.4.2 Chromosomes and Mitosis.

The c-Value of the Nuclear Genome

The complete set of DNA within the nucleus of any organism is called its nuclear genome and is measured as the c-value in units of either the number of base pairs or picograms of DNA. There is a general correlation between the nuclear DNA content of a genome (i.e. the C-value) and the physical size or complexity of an organism. Compare the size of E. coli and humans, for example, in the Table 3.4.1 There are, however, many exceptions to this generalization, such as the human genome contains only 3.2 x 109 DNA bases, while the wheat genome contains 17 x 109 DNA bases — almost 6 times as much. The Marbled Lungfish (Protopterus aethiopicus – Figure 3.4.3) contains ~133 x 109 DNA bases, (~45 times as much as a human) and a fresh water amoeboid, Polychaos dubium, has as much as 670 x 109 bases (200x a human).

Photo of a grey Marbled Lungfish in its natural habitat
Figure 3.4.3 Marbled Lungfish (Protopterus aethiopicus) Has a Genome of ~133 x 109 Base Pairs, Which is ~45X That of a Human. It is an example of the C-value paradox.
Table 3.4.1 Measures of genome size in selected organisms.  The DNA content (1C) is shown in millions of base pairs (Mb). For eukaryotes, the chromosome number is the chromosomes counted in a gamete (1N) from each organism. The average gene density is the mean number of non-coding bases (in bp) between genes in the genome.
Organism DNA Content (Mb, 1C) Estimated Gene Number Average Gene Density Chromosome Number (1N)
Homo sapiens 3,200 25,000 100,000 23
Mus musculus 2,600 25,000 100,000 20
Drosophila melanogaster 140 13,000 9,000 4
Arabidopsis thaliana 130 25,000 4,000 5
Caenorhabditis elegans 100 19,000 5,000 6
Saccharomyces cerevisiae 12 6,000 2,000 16
Escherichia coli 5 3,200 1,400 1

The c-Value Paradox

This apparent paradox (called the C-value paradox) can be explained by the fact that not all nuclear DNA encodes genes — much of the DNA in larger genomes is non-gene coding. In fact, in many organisms, genes are separated from each other by long stretches of DNA that do not code for genes or any other genetic information. Much of this “non-gene” DNA consists of transposable elements of various types, which are an interesting class of self-replicating DNA elements. Other non-gene DNA includes short, highly repetitive sequences of various types. Together, this non-functional DNA is often referred to as “Junk DNA”.

The “Onion Test”

This “test” deals with any proposed explanation for the function(s) of non-coding (junk) DNA. For any proposed function for the excess of DNA in eukaryote genomes (c-value paradox), can it “explain why an onion needs about five times more non-coding DNA for this function than a human?” The onion, Allium cepa, has a haploid genome size of ~17 pg, while humans have only ~3.5 pg. Why? Also, onion species range from 7 to 31.5 pg, so why is there this range of genome size in organisms of similar complexity?

The term “onion test” was first coined in April 2007 by T. Ryan Gregory, the Canadian evolutionary biologist and genome biologist. For an interesting alternative view of the onion test, see Jonathan McLatchie’s (2011) article, “Why the “Onion Test” Fails as an Argument for “Junk DNA”” on the Evolution News website.

Metaphase chromosomes stained purple, spread out on a slide
Figure 3.4.4 Human Metaphase Chromosome Spreads. To make these figures, white blood cells in metaphase were dropped onto a slide. The cells burst open and the chromosomes can then be stained with giemsa (a purple colour). This image shows chromosomes from three cells that hit the slide close to one another. They can be distinguished by the size difference among the chromosome sets, which is due to the differences in condensation during the stages of mitosis (prophase).

To calculate how much DNA is seen in the nuclei in Figure 3.4.4, consider that a human gamete has about 3000 million base pairs. We can shorten this statement to  1c = 3000 Mb  where c is the cvalue, the DNA content in a gamete. When an egg and sperm join the resulting zygote is  2c = 6000 Mb. Before the zygote can divide and become two cells it must undergo DNA replication. This doubles the DNA content to  4c = 12 000 Mb. When the zygote divides, each daughter cell inherits half the DNA and is therefore back to  2c = 6000 Mb. Then each cell will become 4c again (replication) before dividing themselves to become 2c each. From this point forward, every cell in the embryo will be  2c = 6000 Mb before its S phase and  4c = 12 000 Mb  afterwards. The same is true for the cells of fetuses, children, and adults. Because the cells used to prepare this chromosome spread were adult cells in metaphase each is  4c = 12 000 Mb. Note, there are some rare exceptions, such as some stages of meiocytes that make germ cells and other rare situations like the polyploidy of terminally differentiated liver cells.

In summary:

Table 3.4.2 c-Values in Human Cells
Human Cell DNA Content
gamete (egg or sperm) 1c = 3000 Mb
regular cell before S phase 2c = 6000 Mb
regular cell after S phase 4c = 12 000 Mb

The Number of Chromosomes (n-Value)

Human gametes contain 23 chromosomes. We can summarize this statement as  1n = 23 where n is the n‑value, the number of chromosomes in a gamete. When a 1n = 23 sperm fertilizes a 1n = 23  egg, the zygote will be 2n = 46. But, unlike DNA content (c), the number of chromosomes (n) does not change with DNA replication. A replicated chromosome is still just one chromosome. Thus, the zygote stays  2n = 46 after S phase. When the zygote divides into two cells, both contain 46 chromosomes and are still 2n = 46. Every cell in the embryo, fetus, child, and adult is also  2n = 46 (with the exceptions noted above).

In summary:

Table 3.4.3 n-Values in Human Cells
Human Cell Chromosome Number
gamete (egg or sperm) 1n = 23
regular cell before S phase 2n = 46
regular cell after S phase 2n = 46

Note that in a normal cell, the chromosome number is 2n before and after chromosome replication. The n-value does not change while the c-value does.

Media Attributions

 References

McLatchie, J. (2011, November 2). Why the “Onion Test” Fails as an Argument for “Junk DNA”. Evolution News. https://evolutionnews.org/2011/11/why_the_onion_test_fails_as_an/

Deyholos, M., & Canham, L. (2017). Figure: 4. Changes in DNA and chromosome content … [diagram]. In Locke, J., Harrington, M., Canham, L. and Min Ku Kang (Eds.), Open Genetics Lectures, Fall 2017 (Chapter 14, p. 3). Dataverse/ BCcampus. http://solr.bccampus.ca:8001/bcc/file/7a7b00f9-fb56-4c49-81a9-cfa3ad80e6d8/1/OpenGeneticsLectures_Fall2017.pdf

Smith, A. (2017). Figure 1. Human metaphase chromosome spreads [micrograph image]. In Locke, J., Harrington, M., Canham, L. and Min Ku Kang (Eds.), Open Genetics Lectures, Fall 2017 (Chapter 15, p. 1). Dataverse/ BCcampus. http://solr.bccampus.ca:8001/bcc/file/7a7b00f9-fb56-4c49-81a9-cfa3ad80e6d8/1/OpenGeneticsLectures_Fall2017.pdf

 

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Open Genetics by Natasha Ramroop Singh, Thompson Rivers University is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, except where otherwise noted.

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