2.1. P. vulgaris DNA extraction and mitochondrial genome assembly

The P. vulgaris plants were collected from wild in Hubei province, China, and cultured in Wuhan, China (31°68’ N, 118°45’ E). High quality genomic DNA were isolated from fresh leaves using the standard CTAB method (Arseneau et al., 2017; Cheng et al., 2021). Illumina and Nanopore platforms were used for sequencing. Illumina sequencing and Oxford sequencing were performed by Wuhan Benagen Tech Solutions Company (http://en.benagen.com/). Illumina sequencing data was sequenced using the HiSeq Xten PE150 Illumina, San Diego, CA, USA sequencing platform and Nanopore sequencing was performed by Oxford Nanopore GridION × 5 Oxford Nanopore Technologies, Oxford, UK. GetOrganelle (v1.7.5) (Jin et al., 2020) was used to perform plant mitochondrial genome assembly (default parameters) and a graphical plant mitochondrial genome was obtained. Since the graphical genome generated by GetOrganelle comprised multiple nodes, with redundant fragments existing in the border of two neighbor nodes, Bandage (Wick et al., 2015) was used to visualize the graphical genome and Nanopore data was mapped to help manually check these redundant fragments. BWA (0.7.17) is used to map the third generation sequencing data to the graphical genome, followed by manually identification and removing of the redundant fragments (Li and Durbin, 2009).