TN-SEQ
The TnSeq libraries were constructed as previously described14. Briefly, DNA was partially digested and ligated with asymmetric adapters. The DNA fragments with the Mariner transposon junction were amplified and Illumina sequencing primer sequences were added by nested PCR16. Amplified fragments were gel purified and fragments between 250-400 base pairs were selected and sequenced with a generic Illumina primer (5ACACTCTTTCCCTACACGACGCTCTTCCGATCT) using an Illumina HiSeq2000 system at the Gnome Qubec Innovation Centre. One hundred base pair reads were generated. The transposon sequence (CGGGGACTT ATCAGCCAACCTGT) was trimmed using cutadapt64. Reads were aligned to the MAP K-10 reference genome using Bowtie2 alignment software65. SAMtools was used to convert Aligned Sequence Alignment/Map (SAM) files into binary BAM files66. Custom scripts in MATLAB were used to analyze and map the reads to genomic TA sites. The number of reads detected, and strand orientation were determined for each TA insertion site. Each insertion site coordinate was mapped to a gene or region as region annotated in RefSeq file