Supergene for supercolour
Welcome to the update page of “Supergene for supercolour” !!
In order to identify the supergene for colour polymorphism in the snail Cepaea nemoralis we first need to sequence its genome. Several sequencing techniques are available nowadays, for example Illumina short-read sequencing. The costs of sequencing a complete genome, however, are still quite high. Especially because, to achieve good results, one needs to sequence at high coverage. At least 30x coverage (i.e. each letter of the genome must be sequenced 30 times) is recommended to reduce the amount of errors.
Hence, before starting on such an expensive endeavour, we would like to know how many letters there are in the genome of our snail. This is because we want to sequence it at exactly 30x coverage, not more (or it would become too expensive) and not less (or there will be too many errors). That’s why we need to determine the genome size.
It is, of course, possible that someone else has already done this before. We check the website Animal Genome Size Database which contains information on 6222 animal species. Genome size is indicated as C-value, or the amount of DNA in picograms (1pg = 10-12 gram) in the nucleus of a haploid cell (haploid = contains one set of chromosomes). Unfortunately, there is no data on Cepaea nemoralis in this database. But we can find information on four other species of Helicidae, the snail family Cepaea belongs to. All four of these species have quite large genomes, between 2.84 and 4.00 pg. This is similar to human genome which is 3.50 pg!
Well, we need to measure the size of Cepaea genome ourselves. The most widely used technique for this purpose is “flow cytometry”. It works by comparing the amount of DNA in your organism of interest with that in a control animal with known genome size. In our case we can use the zebrafish as it’s C-value is known to be 1,7 pg. We travel to Didam (NL) where we visit “Plant Cytometry Services”. This company will measure the DNA amounts in our snail samples.
The tissues of snails and zebrafish are crushed together to release the cell nuclei. Then propidium iodide is added to the mixture. This chemical binds to nuclear DNA. The mixture is then passed through a very fine filter. Now we have a solution with nuclei of the snail and the zebrafish to be analysed by the flow cytometer. The nuclei pass through a very thin tube where they are radiated with the UV-light. Propidium iodide emits fluorescent signal which is measured by the instrument. The amount of fluorescent signal depends on the amount of DNA in the nuclei.
Fluorescence is shown in a graph such as this one. There are two peaks – one for the zebrafish (left) and one for the snail (right). The software calculates the ratio between the two peaks, in this case it’s 2.11 (snail) : 1.00 (zebrafish). The analysis is repeated three times and the average ratio is 2.06 : 1.00. Now we can calculate the amount of DNA is the snail: 2.06 x 1.7 (zebrafish C-value) = 3.50 pg. The genome of Cepaea nemoralis is just as large as the human genome!
Now we can also calculate the number of bases (letters A, G, T, C) as 1 pg is equal to 978 million bases. The snail has approximately 3.50 x 978 = 3432 million letters in its genome!
The challenge now is to find the supergene for supercolour among all these letters! (to be continued…)
Colour polymorphic snail reveals the evolution of supergene architecture
The three researchers from Naturalis Biodiversity Centre (Leiden, The Netherlands) have been awarded a grant
from the Netherlands Organisation for Scientific Research (NWO) for the project “Evolution of supergenes and the
genetic basis of snail colour polymorphism”. Dr. Suzanne Saenko, Dr. Dick Groenenberg, and Prof. Menno
Schilthuizen will study the the supergene that controls shell colour polymorphism in a classical
model for ecological genetics and climate-induced evolutionary change, the land snail Cepaea nemoralis.
A supergene is a cluster of several genes, each of which affects a different morphological or behavioural trait.
Because of tight physical linkage within supergenes multiple phenotypic characters are inherited as a single locus.
Supergenes are thought to be crucial for the maintenance of highly discrete adaptive phenotypes which can
eventually lead to reproductive isolation and speciation. Multiple complex polymorphisms are presumably
controlled by supergenes, but the molecular evidence for this phenomenon is still scarce and the emergence of
such genetic architecture is surprisingly poorly understood. To help fill this scientific gap, the researchers will
sequence and assemble the genome of C. nemoralis, identify the individual components of its supergene through
linkage mapping, and investigate their role in shell coloration through studies of gene expression and function.
Information about the progress will be posted on our website regularly.