Resequencing of Penaeus vannamei: female muscle
The DNA of each pool were fragmented into about 500 bp DNA fragments using Covaris S2/E210. Sheared DNA was end-repaired and A single nucleotide (A) overhang was added subsequently to the repaired fragments using Klenow Fragment (3 5 exo) (NEB) and dATP at 37C, and then barcodes and Illumina sequencing adapters were ligated to the A-tailed fragments using T4 DNA ligase. Polymerase chain reaction (PCR) was performed using diluted shearing-ligation DNA samples, dNTP, Q5 High-Fidelity DNA Polymerase and PCR primers. PCR products were then purified using Agencourt AMPure XP beads (Beckman Coulter, High Wycombe, UK) and pooled. Pooled samples were separated by 2% agarose gel electrophoresis. 500 base pairs (with barcodes and adaptors) fragments were excised and purified using a QIAquick gel extraction kit (Qiagen, Hilden, Germany). Gel-purified products were then diluted for pair-end sequencing (each end 125bp) on an Illumina HiSeq 2500 system using standard protocol (Illumina, Inc; San Diego, CA, USA).