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.
January 26, 2008