title: Amycolatopsis BCA-696 mate pair WGS raw reads
design: BCA-696 was inoculated in starch casein broth and incubated for 120 h at 28C. At the end of incubation, the culture was centrifuged at 10,000g for 10 min at 4C and the cells washed twice with STE buffer (sucrose 0.3 M, Tris/ HCl 25 mM and Na2EDTA 25 mM, pH 8.0). The supernatant was discarded but the pellet (1 g) was re suspended in 8.55 ml STE buffer and 950 l lysozyme (20 mg/ml STE buffer) and incubated for 30 min at 30C. This was followed by addition of 500 l of SDS (10%; w/v) and 50 l of protease (20 mg/ml) and the mixture was held at 37C for 1 h. At the end of incubation, 1.8 ml of NaCl (5 M) was added with gentle mixing to avoid shearing the DNA and 1.5 ml of CTAB (10%; w/v) in 0.7 M NaCl (CTAB/NaCl solution) and incubated for 20 min at 65C. Once CTAB was added, all the remaining steps were carried out at room temperature. The lysate was extracted twice with an equal volume of phenol/chloroform/isoamyl alcohol (25:24:1; by vol) and centrifuged at 13,000g for 10 min. Finally, the aqueous phase was extracted with chloroform/isoamyl alcohol (24:1, by vol) and transferred to a tube followed by addition of 600 l of propan-2-ol and DNA spooled out after 10 min. Alternatively, it was recovered by centrifugation at 12,000g for 10 min. The pellet was washed twice with ethanol (70%; v/v), vacuum dried and dissolved in 2 ml of TE buffer (10 mM Tris/HCl and 1 mM EDTA, pH 8.0). RNase A (50 mg/ml) was added with incubation at 37C for 2 h. The sample was again extracted with phenol as described above. DNA was re precipitated from the aqueous phase with addition of 100 l of 3 M sodium acetate (pH 5.3) and 600 l of propan-2-ol. The DNA pellet was washed with ethanol (70%; v/v), dried and dissolved in TE buffer. The purity of the BCA-696 DNA was checked in the agarose gel electrophoresis and quantified using NanoDrop. The genomic DNA was sent to AgriGenome Labs (Kochi, India) for library preparation and next generation sequencing using Illumina HiSeq platform.To ensure a high quality assembly, two libraries were constructed: paired-end and mate-pair library of <2 kb size. The reads were 150 nucleotides long.