Worm numbers
This page is intended to become a collection ground for useful and interesting numbers about C. elegans biology. These numbers include things such as the average volume and mass (calculated estimates) of an adult hermaphrodite, larval stage, or embryo. Some of these numbers are well established facts whereas others are estimations, with a description of the method for calculating or estimating provided.
The Numbers
Here is a summary table of interesting numbers (many are estimates) pertaining to C. elegans:
The Genome
| Size of genome: | 100,272,276 bp |
| %GC Content: | 35% |
| Number of GC base pairs: | 35,537,772 |
| %AT Content: | 65% |
| Number of AT base pairs: | 64,734,504 |
| Mass of a haploid genome: | 103 femtograms (1.03 * 10^-13 grams) |
| Volume of a haploid genome: | 0.1 cubic microns = 0.1 femtoliters = 100 attoliters |
| Total amount of genomic DNA in an adult hermaphrodite: | 360 picograms (3.6 * 10^-10 grams) |
Worm Volumes
| Volume of an embryo: | 30 - 50 picoliters = 30,000 - 50,000 cubic microns = (3*10^-5)-(5*10^-5) cubic millimeters |
| Volume of an L1 larva: | 50 - 200 picoliters = 50,000 - 200,000 cubic microns = (5*10^-5)-(2*10^-4) cubic millimeters |
| Volume of an L2 larva: | 200 - 500 picoliters = 200,000 - 500,000 cubic microns = (2*10^-4)-(5*10^-4) cubic millimeters |
| Volume of an L3 larva: | 500 - 900 picoliters = 500,000 - 900,000 cubic microns = (5*10^-4)-(9*10^-4) cubic millimeters |
| Volume of an L4 larva: | 900 - 2000 picoliters = 900,000 - 2,000,000 cubic microns = (9*10^-4)-(2*10^-3) cubic millimeters |
| Volume of an adult hermaphrodite: | 2 - 6 nanoliters = 2,000,000 - 6,000,000 cubic microns = (2*10^-3)-(6*10^-3) cubic millimeters |
Worm Volume
Based on these images from Worm Atlas (www.wormatlas.org):
... where the scale bar represents 100 microns, we can roughly deduce the volume of the embryo, each larval stage worm, and the adult hermaphrodite of C. elegans.
Volume of a single embryo = ~35 picoliters = ~0.000035 cubic millimeters = ~35,000 cubic microns
Volume of a single L1 larva = ~80 picoliters = ~0.000080 cubic millimeters = ~80,000 cubic microns
Volume of a single L2 larva = ~135 picoliters = ~0.000135 cubic millimeters = ~135,000 cubic microns
Volume of a single L3 larva = ~300 picoliters = ~0.0003 cubic millimeters = ~300,000 cubic microns
Volume of a single L4 larva = ~800 picoliters = ~0.0008 cubic millimeters = ~800,000 cubic microns
Volume of a single Adult hermaphrodite = ~2.2 nanoliters = ~0.0022 cubic millimeters = ~2,200,000 cubic microns
This paper (Lozano E. et al (2006) Curr Biol, [1]) finds wild type (N2) adult hermaphrodite worms growing to upwards of 6 nanoliters (0.006 cubic millimeters) [see Table 2, Figure 1A, and Figure 3 of paper]. Another good reference for larval size is (Knight C. et al (2002) Evol Dev, [2]) as pointed out by David Hall (of Worm Atlas) in the WormBase community forums here [3]. See Figure 4 in particular. This has the following ranges for each larval stage:
L1: 50,000 - 200,000 cubic microns
L2: 200,000 - 400,000 cubic microns
L3: 500,000 - 900,000 cubic microns
L4: 900,000 - 2,000,000 cubic microns
Hence, the calculations above appear to be roughly lower limits on the size of each stage.
Worm Mass
Assuming the worm has a density close to that of water (1 gram per milliliter) these are estimates of mass:
Mass of a single Embryo = ~35 nanograms
Mass of a single L1 larva = ~80 nanograms
Mass of a single L2 larva = ~135 nanograms
Mass of a single L3 larva = ~300 nanograms
Mass of a single L4 larva = ~800 nanograms
Mass of a single Adult hermaphrodite = ~2.2 micrograms
Assuming that the entire mass of the worm is roughly 70% water (as with most cells), this brings the dry weight of these to:
Dry weight of a single Embryo = ~11 nanograms
Dry weight of a single L1 larva = ~24 nanograms
Dry weight of a single L2 larva = ~41 nanograms
Dry weight of a single L3 larva = ~90 nanograms
Dry weight of a single L4 larva = ~240 nanograms
Dry weight of a single Adult hermaphrodite = ~660 nanograms
Estimating that about 15% of total mass (50% dry weight) is protein:
Protein mass of a single Embryo = ~5.3 nanograms
Protein mass of a single L1 larva = ~12 nanograms
Protein mass of a single L2 larva = ~20.3 nanograms
Protein mass of a single L3 larva = ~45 nanograms
Protein mass of a single L4 larva = ~120 nanograms
Protein mass of a single Adult hermaphrodite = ~330 nanograms
Estimating that about 1% of total mass (3% dry weight) is RNA:
RNA mass of a single Embryo = ~350 picograms
RNA mass of a single L1 larva = ~800 picograms
RNA mass of a single L2 larva = ~1.35 nanograms
RNA mass of a single L3 larva = ~3 nanograms
RNA mass of a single L4 larva = ~8 nanograms
RNA mass of a single Adult hermaphrodite = ~22 nanograms
and further estimating that about 3% of total RNA is protein-coding mRNA:
mRNA mass of a single Embryo = ~10.5 picograms
mRNA mass of a single L1 larva = ~24 picograms
mRNA mass of a single L2 larva = ~40.5 picograms
mRNA mass of a single L3 larva = ~90 picograms
mRNA mass of a single L4 larva = ~240 picograms
mRNA mass of a single Adult hermaphrodite = ~660 picograms
Molar mass of NMPs:
AMP = 347.2 grams per mole
CMP = 323.2 grams per mole
GMP = 363.2 grams per mole
UMP = 324.2 grams per mole
in polymer form (i.e. minus one water molecule, 18 grams per mole):
AMP = 329.2 grams per mole
CMP = 305.2 grams per mole
GMP = 345.2 grams per mole
UMP = 306.2 grams per mole
Average mass of polymer-NMP = 321.5 grams per mole
Thus, an estimate of the total number of RNA nucleotides (NMPs) in mRNA polymers is:
Number of polymer NMPs of a single Embryo = ~20 billion
Number of polymer NMPs of a single L1 larva = ~45 billion
Number of polymer NMPs of a single L2 larva = ~76 billion
Number of polymer NMPs of a single L3 larva = ~170 billion
Number of polymer NMPs of a single L4 larva = ~450 billion
Number of polymer NMPs of a single Adult hermaphrodite = ~1,236 billion
... and the number of mRNA molecules (assuming an average length of 1000nt):
Number of mRNAs of a single Embryo = ~20 million
Number of mRNAs NMPs of a single L1 larva = ~45 million
Number of mRNAs NMPs of a single L2 larva = ~76 million
Number of mRNAs NMPs of a single L3 larva = ~170 million
Number of mRNAs NMPs of a single L4 larva = ~450 million
Number of mRNAs NMPs of a single Adult hermaphrodite = ~1,236 million
DNA Numbers
From the WS231 release notes of WormBase, the C. elegans genome has the following number of bases:
A 32,367,418
C 17,780,787
G 17,756,985
T 32,367,086
Total 100,272,276
This means that there are 35,537,772 GC base pairs (35.4% of the genome) and 64,734,504 AT base pairs (64.6% of the genome).
Genome Volume
Knowing that a single complete turn of DNA is approximately 3.4 nanometers in length (34 Ångstroms), 2 nanometers in width (20 Ångstroms), and is about 10 base pairs (bp)(and therefore 1 base pair is .34 nanometers long (3.4 Ångstroms)), we can deduce the volume of a single base pair of DNA to be roughly 1 cubic nanometer (1 nm^3):
Assuming a base pair is like a short cylinder with volume:
Volume = (pi)*(radius)^2*(height)
Volume = (~3.14)*(~1nm)^2*(~.34nm)
Volume of 1 base pair = ~1 cubic nanometer
Therefore:
No. of bp -> Volume
1bp -> 1 cubic nanometer
1kb -> 1000 cubic nanometers = 10^-6 cubic microns
1Mb -> 10^6 cubic nanometers = 10^-3 cubic microns
1Gb -> 10^9 cubic nanometers = 1 cubic micron
So, a single haploid genome of C. elegans (~100Mb) would be approximately 0.1 cubic microns and a diploid genome approximately 0.2 cubic microns.
Packed into spheres, these would each be:
Volume of sphere = (4/3)*(pi)*(radius)^3
Haploid genome radius = ~0.29 microns
Haploid genome diameter = ~0.58 microns
Diploid genome radius = ~0.36 microns
Diploid genome diameter = ~0.72 microns
That is the smallest sphere that the haploid and diploid genomes, respectively, could pack into. We are, of course, ignoring proteins, RNA molecules, and any other small molecules, so the cell nuclei must be significantly larger. For polyploid nuclei, like those of the intestine, the nuclei must be substantially larger. So,
Volume of the adult intestinal (32-ploid) genomes = ~3.2 cubic microns
Radius of the adult intestinal (32-ploid) genomes = ~0.91 microns
Diameter of the adult intestinal (32-ploid) genomes = ~1.82 microns
Genome Mass
Molar mass of dNMPs:
dAMP = 331.2 grams per mole
dCMP = 307.2 grams per mole
dGMP = 347.2 grams per mole
dTMP = 320.2 grams per mole
in polymer form (i.e. minus one water molecule, 18 grams per mole):
dAMP = 313.2 grams per mole
dCMP = 289.2 grams per mole
dGMP = 329.2 grams per mole
dTMP = 302.2 grams per mole
Average mass of polymer-dNMP = 308.5 grams per mole
An AT base pair = 615.4 grams per mole
A CG base pair = 618.4 grams per mole
The C. elegans haploid genome is ~100Mb (100,272,276 bp to be exact) with (as noted above) 35,537,772 GC base pairs and 64,734,504 AT base pairs, hence the total molar mass of the genome is:
[AT base pair molar mass]*[No. of AT base pairs] + [CG base pair molar mass]*[No. of CG base pairs]
(615.4g/mol)(64,734,504bp) + (618.4g/mol)(35,537,772bp) = 39,837,613,761.6 + 21,976,558,204.8
Molar mass of C. elegans genome = 61,814,171,966.4 grams per mole
Mass of C. elegans genome = 61,814,171,966.4 / Avagadro's number (6.022 * 10^23)
Mass of C. elegans genome = 103 * 10^-15 grams = 103 femtograms (fg)
There are 959 somatic nuclei in a single adult hermaphrodite, and so there are roughly 197.6 picograms (assuming each somatic nuclei is diploid) of somatic genomic DNA that can be isolated from a single adult hermaphrodite, not including sperm, oocytes or other germline nuclei. This also does not account for the fact that some of the 959 somatic nuclei are polyploid, such as intestinal nuclei.
A single C. elegans hermaphrodite can give rise to approximately 300 progeny from ~300 oocytes and ~300 sperm, ~150 of each from each gonad arm (see Worm Atlas [4]). As a first order approximation of the number of genomes contributed from the (non-somatic) germline, let's say there are 600 haploid genomes (or 300 diploid genomes) present at any given moment in a mature adult hermaphrodite. These genomes would total to about 61.8 picograms of genomic DNA. Added to the total soma-derived genomic DNA gives us a rough grand total of:
Total amount of genomic DNA from a single C. elegans adult hermaphrodite: ~260 picograms
Again, this is not accounting for polyploidy in special cases; therefore this number is likely an underestimate.
Considering the polyploidy of the intestinal cells (30-34 nuclei each with 32 genomes [5]), (let's assume 32 intestinal nuclei for simplicity) and assuming all other somatic nuclei are diploid, that gives us 937 diploid somatic nuclei and 32 intestinal nuclei at 32-ploid. This gives us an updated estimate of:
Total amount of genomic DNA from a single C. elegans adult hermaphrodite: ~360 picograms
