Genome sizes are often discussed with eukaryogenesis, because the anscestral eukaryote should have the smallest genome. Cyanidioschyzon merolae is often cited as the eukaryote having smallest genome. Actually, the genome size of Cyanidioschyzon merolae is larger than budding yeast Saccharomyces cerevisiae, which is the first complete eukaryote of genome sequencing.
Several techniques have been known for determining genome sizes. Classically, we have quantified the DNA-specific staining achieved with the use of the Feulgen reagent under microscope, and this technique is called microphotometry. Recent fluorescence microscopy and DNA-specific fluorescent dyes can achieve higher sensitivity and better quantitativeness, and it is discriminated as microfluorometry. Another technique, called pulsed-field gel electrophoresis (PFGE), can be applied for small organisms such like protozoans and unicellular algae. We can separate the small chromosomes of such organisms in an agarose gel, read off their sizes, and obtain the genome size by accumulating them.
The following is the genome size history of Cyanidioschyzon merolae determined using several techniques. The figures in parentheses was not compensated for base preference of each dye.
|reference||genome size (Mbp)||chromosome numbers||method|
|Suzuki et al. ||(8.0)||N/A||microfluorometry with video-intensified microscopy (VIM) using DAPI|
|Takahashi et al. ||12.2||15||PFGE|
|Takahashi et al. ||14.2||17||PFGE|
|Toda et al.  and Toda ||13.4||N/A||VIM using Feulgen staining|
|16.4(11)||VIM using DAPI|
|15.2(24)||VIM using PI|
|Matsuzaki et al. ||16.5||20||Whole Genome Shotgun|
The reported genome size has doubled for the decade. Needless to say, this has been caused by progress of measuring technique, not by natural evolution of the organism. The major weak point of measurement using PFGE is that it depends on the resolution of chromosomes. It is difficult to distinguish chromosomes of similar size, and we tend to make a lower estimate therefore. On the other hand, the microfluorimetry technique is sensitive to conditions of staining, and using DAPI for better quantitativeness requires knowledge of base composition.
The smallest eukaryotic genome known to date is that of pathogenic microsporidian Encephalitozoon cuniculi and 2.9 Mbp in size . But this genome has been reduced as a result of parasitic adaptation. Then the proposed free-living organism with the smallest genome is marine green alga Ostreococcus tauri. The genome size is estimated to be 10.2 Mbp by PFGE . But the electrophoresis pattern seems to suggest that there are the resolution problems as is the case of C. merolae. In fact, a microfluorometric comparison  shows the genome size of O. tauri is two or three times larger than that of C. merolae. The genome project of O. tauri is also in progress , and will reveal the actual genome size.