Assembling and annotation of the chloroplast genomes
The raw paired-end reads were filtered and de novo assembled using the GetOrganelle toolkit (Jin et al. 2020). The filtered reads were assembled using the SPAdes version 3.9 using k-mer 21, 33, 45, 65 and 85 (Bankevich et al. 2012). To retain pure chloroplast contigs, the final “fastg” files were filtered using the “slim” script of GetOrganelle toolkit. The filtered De Brujin graph was viewed and the final sequence exported using Bandage (Wick et al. 2015). The chloroplast genome was automatically annotated using CpGAVAS (Liu et al. 2012), then adjusted using Geneious version 9.0 (Kearse et al. 2012).