Whole genome sequencing of tea plant (Camellia assamica)
Mate Pair sequencing library was prepared with Illumina - compatible Nextera Mate Pair Sample Preparation Kit (Illumina Inc., Austin, TX,U.S.A.) at Genotypic Technology Pvt. Ltd., Bangalore, India. About 4 ug of genomic DNA was simultaneously fragmented and tagged with mate pair adapters in a transpos on based tagmentation step. Tagmented DNA was then purified using AMPure XP magnetic beads (Beckman Coulter, U.S.A.) followed by strand displacement to fill gaps in the tagmented DNA. Strand displaced DNA was further purified with AMPure XP beads before size-selecting 8-11kb fragments on Low melting agarose gel. Size selected fragments were circularized in an overnight blunt-end in tramolecular ligation stepwhich will result in circular DNA with the insert flanked mate pair adapter junction. Circularized  DNA  was  sheared using  Covaris  S220 sonicator  (Covaris,  Woburn, Massachusetts, USA) to generate fragment size distribution from 300 bp to 1000 bp.Sheared DNA was purified to collect the Mate pair junction positive fragments using Dynabeads M-280 Streptavidin  magnetic  beads (Thermo  Fisher  Scientific,  Waltham,  MA,  U.S.A.).Purified fragments were end-repaired, adenylated and ligated to Illumina multiplex barcode adaptorsas per Nextera Mate Pair Sample Preparation Kit protocol. Adapter-ligated DNA was then amplified for 15cycles of PCR using Illumina-compatible primers. Final PCR product (sequencing library) was purified with AMPure XP beads,followed by library quality control check. Illumina-compatible sequencing library was quantified by Qubit fluorometer (Thermo Fisher Scientific, MA, USA) and its fragment size distribution was analyzed on Agilent TapeStation.