design: DNA from Schizosaccharomyces japonicus genome was obtained, fragmented, size-selected, library-prepped, and sequenced according to standard Roche-454 Titanium protocols: the General Library prep(Apr 2009)- the Double SPRI method was used, the library was titrated using the Lib-L SV emPCR Method Manual (Jan 2010), and full emPCR'd using the Lib-L LV emPCR Method (Jan 2010), and Sequenced using the GS FLX Sequencing method manual (Apr 2009). Standard 454 Titanium adaptors that were used. The only variation from the method manuals is in the Library prep as we use the Covaris S2 for DNA shearing not a Nebulizer as outlined. (The covaris settings were for 500bp peaks)