phiX174 virus - one of the world's smallest self-replicating programs :-)
http://www.ncbi.nlm.nih.gov/nuccore/NC_001422.1
Enterobacteria phage phiX174 sensu lato, complete genome
5386 bp ss-DNA
http://www.ncbi.nlm.nih.gov/nuccore/NC_001422.1
Enterobacteria phage phiX174 sensu lato, complete genome
5386 bp ss-DNA
In college I actually got to take part in refactoring that virus' genome into a decompressed version with no gene overlaps. And it worked! The decompressed version is still a functioning phage, and since there are no longer gene overlaps, future genetic engineers will have a much easier time modifying the phage as they see fit.
http://www.sciencedirect.com/science/article/pii/S0042682212...
[The naive] decompression added 909 nucleotides to the wild-type genome. We next addressed practical constraints arising from the length of DNA that can be physically packaged within a øX174 capsid without impacts to reproductive fitness. Previous work has shown that the length of a øX174 genome, when packaged in vitro, must be kept within a few percent of the 5386 nucleotide wild-type length in order to avoid any significant fitness decrease ( Aoyama and Hayashi, 1985). Similar results were shown in vivo ( Russell and Muller, 1984). To reduce the decompressed genome length we removed the first 916 nucleotides of gene F, encoding the coat protein ( Air et al., 1978). We chose gene F because a plasmid containing a restriction fragment encoding wild-type gene F was able to complement two conditional gene F mutations ( Avoort et al., 1983). Additionally, the gene F coding sequence is greater than the total of the combined increases needed to implement the øX174.1 genome design. The truncated gene F version of the decompressed genome was named øX174.1f. To complement øX174.1f when transformed into host cells we designed a medium copy vector expressing gene F under control of a rhamnose-inducible promoter ( Fig. S1).
I have no doubt that viruses of the computer kind also have made use of such techniques; and overlapping for obfuscation, not size-optimisation, is also a commonly seen trick in malware.
Get your genome compiler here: http://genomecompiler.com