Many species of cyanobacteria are complex, multicellular organisms [Multicellular Bacteria]. Those species tend to have large genomes.
Recently Degan et al. (2013) sequenced the genomes of six new cyanobacteria species and one of them turns out to have a large genome.1 (see Contradictory Phylogenies for Cyanobacteria for more information on that paper.) The species is Scytonema hofmanni and its genome is 12,073,012 bp in size. It has 12,356 potential protein-coding genes. If all of them are correctly identified then the total, counting non-protein-coding genes, is likely to be 12,500 genes. That's a record for prokaryotes.
Half of these genes are only found in Scytonema and that's very strange.
There are bacteria with larger genomes, notably the soil bacterium Ktedonobacter racemifer with a genome size of 13,661,586 bp.
For comparison, the genome of the yeast, Saccharomyces cerevisiae, is 12,156,677 bp in size and it has 6,200 genes.
Photo Credit: Scytonema hofmanni from cyanobacteria slides.
1. Some of you might be under the impression that I give a shit about Norm Pace and his attempt to banish the word "prokaryote" (Pace, 2009). Don't bother to try and convince me because it requires that I accept the false Three Domain Hypothesis and that ain't gonna happen.
Dagan, T., Roettger, M., Stucken, K., Landan, G., Koch, R., Major, P., Gould, S. B., Goremykin, V.V., Rippka, R., de Marsac, N.T., Gugger, M., Lockhart, P.J., Allen, J.F., Brune, I., Maus, I., Pühler, A. and Martin, W.A. (2013) Genomes of stigonematalean cyanobacteria (Subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome biology and evolution 5:31-44.
Pace, N.R. (2009) Time for a change. Nature 441:289. [doi:10.1038/441289a]