I recommend that the work of the Blattner Lab in Wisconsin on clean e. coli genomes should feature prominently in this article. They've turned their clean e. coli into a commercial product sold by Scarab Genomics. Is there a version of that sweet graphic that shows the deleted regions on the genome that we're allowed to use?
At some points this article has turned into a wall of text, particularly for the section on estimating the number of essential genes. I think it'd be helpful if a few people took a subheading and cleaned it up (and documented what they did here). For my part, I rewrote the section on "Genome Synthesis".