Library construction, quality control (QC), and sequencing
Approximately 0.2 μg of DNA per sample was used as input material for
the DNA library preparations. In brief, the genomic DNA samples were
fragmented by sonication to a size of 350 bp, then polished, A-tailed,
and ligated with the full-length adapter for Illumina sequencing,
followed by polymerase chain reaction (PCR) amplification. The resulting
PCR products were purified using the AMPure XP system (Beverly, USA).
Subsequently, library quality was assessed using the Agilent 5400 system
(Agilent, USA) and quantified by quantitative PCR (QPCR) (1.5 nM). The
qualified libraries, each with an effective concentration over 2 nM,
were pooled and sequenced on the Illumina HiSeq 2500/MiSeq platform
using the PE150 strategy by Novogene Bioinformatics Technology Co., Ltd.
(Beijing, China). The original fluorescence image files obtained were
transformed to short reads (raw reads) by base calling and BclToFastq,
and recorded in FASTQ format (Cock et al., 2010 ).