Genomic DNA was extracted using a Rapid Bacterial Genomic DNA Isolation Kit (Sangon Biotech, Shanghai, China) according to the manufacturer’s instructions. The concentration and purity of the extracted DNA were determined using a DNA Qubit 2.0 (Invitrogen, Carlsbad, CA, USA). The extracted genomic DNA was used to construct next-generation libraries with an insert size of 500 bp using a NEBNext® Ultra™ DNA Library Prep Kit for Illumina® and PacBio RS II libraries with an insert size of 10 kb.
Genome sequencing was conducted by Sangon Biotech Co., Ltd. (Shanghai, China) using the next-generation Illumina MiSeq (Illumina, San Diego, CA, USA) and the third-generation PacBio RS II sequencing platform (Pacific Biosciences, Menlo Park, CA, USA), respectively. The raw sequences obtained from the third-generation PacBio RS II sequencing platform were assembled using Canu (Koren et al., 2016 (link)). Gapcloser and GapFiller were used to close the gaps with next-generation sequence reads where possible after assembly (Boetzer & Pirovano, 2012 (link)) and the sequence variants were detected and assembled by PrInSeS-G to obtain high-quality, whole-genome sequences (Massouras et al., 2010 (link)).
Genome sequencing was conducted by Sangon Biotech Co., Ltd. (Shanghai, China) using the next-generation Illumina MiSeq (Illumina, San Diego, CA, USA) and the third-generation PacBio RS II sequencing platform (Pacific Biosciences, Menlo Park, CA, USA), respectively. The raw sequences obtained from the third-generation PacBio RS II sequencing platform were assembled using Canu (Koren et al., 2016 (link)). Gapcloser and GapFiller were used to close the gaps with next-generation sequence reads where possible after assembly (Boetzer & Pirovano, 2012 (link)) and the sequence variants were detected and assembled by PrInSeS-G to obtain high-quality, whole-genome sequences (Massouras et al., 2010 (link)).
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