A few weeks ago, Jason Kelly explained in his post how Itaya and colleagues (2007) assembled the complete 135 kb rice chloroplast circular genome starting from a collection of 5-6 kb fragments and using sequential in vivo homologous recombination in Bacillus
http://blog-msb.embo.org/blog/2008/01/jcvi10.html
Genome transplantation in bacteria: changing one species to another.
Lartigue C (2007) Science.Highly selective isolation of human DNAs from rodent-human hybrid cells as circular yeast artificial chromosomes by transformation-associated recombination cloning.
Larionov V. (1996) Proceedings of the National Academy of Sciences.Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.
Gibson DG (2008) Science.Bottom-up genome assembly using the Bacillus subtilis genome vector.
Itaya M (2008) Nat Methods.