Sequencing projects generally adopt a shotgun approach, sequencing fragments at random and piecing them together to form an increasingly complete whole. This leads to rapid accumulation of sequence but provides no direct help for the ultimate task of assessing the function of genes. Susan Golden has adopted a different approach with Synechococcus PCC 7942, focusing on specific segments of the genome at a time and determining function as the sequence is also determined. The strain is perhaps the premier organism for understanding the molecular basis of circadian rhythm.
The idea centers on the ability of Mu phage to hop randomly in vitro into DNA. DNA sequence is determined from the site of insertion outwards but in parallel, the mutant DNA is used to transform Synechoccus, producing a mutant whose circadian phenotype is related to the Mu-disrupted gene. Progress is considerably slower than with shotgun sequencing, but the genes identified by sequence are matched to phenotypes. At present, somewhere between 10% and 20% of the total genome has been sequenced in this way, and roughly 240 kb of chromosomal sequence has been deposited fully annotated in GenBank, plus two endogenous plasmids pANL and pANS.
Progress on the sequencing end will soon pick up, as Joint Genomes Institute has agreed to perform rapid sequencing of the genome.
You can follow progress in both sequence and functional annotation and also get a visual tutorial on the protocols used by going to the Synechococcus PCC 7942 web page.