High-Quality Genome Assembly from Nanopore Sequencing

The high molecular weight genomic DNA of QG10 was extracted from the 15-day-old leaf tissues following a modified CTAB method. Whole genome sequencing was done following the standard instructions of the Ligation Sequencing Kit (Nanopore, Oxford shire, UK). The quantified DNA was randomly sheared, and fragments of ∼20 kb were enriched and purified. Then, a 20-kb library was constructed and sequenced on the Nanopore PromethION platform according to the manufacturer’s protocols (Jiang et al., 2020 (link)).
De novo genome assembly of Nanopore sequence was performed as follow: The raw Nanopore reads were error-corrected and assembled using CANU (v1.7.1) (Koren et al., 2017 (link)), followed by Smartdenovo (https://github.com/ruanjue/smartdenovo) assembly, followed by three rounds of polishing with Racon (Vaser et al., 2017 (link)), followed by three rounds with Pilon v0.3.0 using the Illumina PCR-free paired-end reads (Walker et al., 2014 (link)). Genome completeness was also assessed using the algae dataset of BUSCO v2.0 (Simão et al., 2015 (link)).