Whole Genome Analysis and Elucidation of Docosahexaenoic Acid (DHA) Biosynthetic Pathway in Aurantiochytrium sp. SW1
The whole-genome sequencing platforms used in this study were Pacific Biosciences Sequel sequencing platform (Pacific Biosciences, Menlo Park, CA, USA) coupled with Illumina Hiseq2500 (Illumina Inc., San Diego, CA, USA). Briefly, the genomic DNA sample was prepared for constructing a 10-kb Single-Molecule Real-Time (SMRT) bell library using a 10-kb template barcoded library preparation workflow. Then, the constructed 10-kb SMRT bell library was processed to SMRT sequencing on a PacBio Sequel sequencing platform using the SMRT v3.0 cell. After adaptor removal and low-quality reads filtered out, clean PacBio reads were generated and used for de novo genome assembly. On the other hand, Illumina libraries were prepared using TruSeq DNA sample prep kits (Illumina Inc., San Diego, CA, USA) as recommended by the included instructions. Subsequently, the libraries were sequenced with an Illumina HiSeq2000 instrument with paired-end (PE) mode. After removal of adaptor and low-quality reads being filtered out, the Illumina clean data was gained and used to proofread the PacBio assembly sequence. PacBio read sequences were later subjected to de novo genome assembly using continuous long reads (CLR) following the Hierarchical Genome Assembly Process (HGAP4)