Monohaploid Plant Genome Assembly Using PacBio CCS Data

The quality of the extracted DNA was measured with a Genomic DNA ScreenTape System (Agilent) and a Qubit Fluorometer (Thermo Fisher Scientific). A long-read DNA library was prepared with the SMRTbell Express Template Prep Kit 2.0 (PacBio) and sequenced using the PacBio Sequel lle system in CCS mode (PacBio). The resulting raw data were converted to FASTQ format using BAM2fastx 1.3.1 (PacBio). Reads longer than 5 kb were extracted with SeqKit 0.15.0 (Shen et al. 2016 (link)) and used for genome assembly with the Hifiasm 0.15.5-r350 assembler (Cheng et al. 2021 (link)).The -l 0 option was specified to disable the purge haplotigs function since the plant was monohaploid.