Multiplexed Paired-end Library Construction

Multiplexed paired-end libraries were constructed from 5 μg of genomic DNA purified using the Purgene kit (Qiagen). The genomic DNA was sheared by sonication and end-repaired using the End-it DNA End-repair kit (Epicentre Technologies). Common adaptors from the Multiplexing Sample Preparation Oligo Kit (Illumina) were then ligated to the genomic DNA fragments, and the fragments were then subjected to 18 cycles of amplification using the Library Amplification Readymix (KAPA Biosystems). The amplified products were fractionated on an agarose gel to select 600 bp fragments, which were subsequently sequenced on an Illumina HiSeq 2000 using the Illumina GAII sequencing procedure for paired-end short read sequencing. Reads from each read pair were mapped separately by bowtie version 2.2.1 [108 (link)] to a reference sequence that contained revision 64 of the S. cerevisiae S288c genome [109 (link)], hisG from Samonella enterica, and the kanMX4 marker (S3 Table). Reads are available from National Center for Biotechnology Information Sequence Read Archive under accession number: SRP107803.