Bos taurus Bull Genome Sequencing
Libraries were constructed according to protocols provided by Applied Biosystems (SOLID 4 System Library Preparation Guide). For long mate-paired (2 x 50 bp) library 40ug of genomic DNA was fragmented to 1.0–6.0kb using HydroShear (Digilab Genomic Solutions Inc). The fragmented DNA was then end repaired and LMP CAP adaptor was ligated to the ends (SOLID TM Long Mate-Paired Library Construction Kit, Applied Biosystems). DNA fragments were further size selected to 1.2-6.0 kb by 1.0% agarose TAE gel and biotinylated internal adaptor was used to circularize the fragments.   Plasmid-Safe DNase was used to eliminate non-circularized DNA fragments and circularized DNA was subjected to nick translation with E. coli DNA polymerase I. Fragments containing the target genomic DNA and adaptors were cleaved from the circularized DNA by single-strand specific S1 nuclease. P1 and P2 adaptors were ligated to the fragments and 9 cycles of PCR amplification was used to create the library. Finally, E-Gel SizeSelect 2% Agarose gels (Invitrogen) were used to select fragments for long mate paired sequencing library.