DNA was extracted from the leaves of JI128 plants using the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany). Short-read DNA sequencing libraries were prepared according to the manufacturer’s instructions, and sequenced on DNA sequencers, NextSeq 500 (Illumina) and DNBSEQ-G400 (MGI Tech, Shenzhen, China). The genome size of line JI128 was estimated by k-mer distribution analysis using the Jellyfish software (Marcais and Kingsford 2011 (link)).
High-molecular-weight DNA was extracted from JI128 DNA using the Genomic-tip kit (Qiagen), and a long-read sequence library was constructed using the Rapid Sequencing Kit (version SQK-RAD004) (Oxford Nanopore Technologies, Oxford, UK). The library was sequenced with the MinION using flow cell version FLO-MIN107 R9 (Oxford Nanopore Technologies). Base calling from the FAST5 files was performed using Guppy v2.3.5 (Oxford Nanopore Technologies). Long reads were assembled with wtdbg2 v2.2 (Ruan and Li 2020 (link)), and potential sequencing errors in the contigs were corrected only once using Pilon (Walker et al. 2014 (link)). The resulting genome assembly was designated as PSA_r1.0. Assembly completeness was evaluated with the embryophyta_odb10 data using Benchmarking Universal Single-Copy Orthologs (BUSCO) v3.0.2 (Simao et al. 2015 (link)).
High-molecular-weight DNA was extracted from JI128 DNA using the Genomic-tip kit (Qiagen), and a long-read sequence library was constructed using the Rapid Sequencing Kit (version SQK-RAD004) (Oxford Nanopore Technologies, Oxford, UK). The library was sequenced with the MinION using flow cell version FLO-MIN107 R9 (Oxford Nanopore Technologies). Base calling from the FAST5 files was performed using Guppy v2.3.5 (Oxford Nanopore Technologies). Long reads were assembled with wtdbg2 v2.2 (Ruan and Li 2020 (link)), and potential sequencing errors in the contigs were corrected only once using Pilon (Walker et al. 2014 (link)). The resulting genome assembly was designated as PSA_r1.0. Assembly completeness was evaluated with the embryophyta_odb10 data using Benchmarking Universal Single-Copy Orthologs (BUSCO) v3.0.2 (Simao et al. 2015 (link)).
Free full text: Click here
