Plastid Genome Sequencing and Annotation

Total DNA of fresh young leaves was extracted using a plant DNA extraction kit (TIANGEN Biotech, Beijing, China). Based on the quality, integrity, and concentration of the extracted DNA, the Illumina HiSeq PE150 double-end sequencing strategy was used to build the library. Then FastQC was used to evaluate raw read quality and then raw reads were filtered by removing low-quality reads at the cutoff of Q20 using Trimmomatic (Bolger et al., 2014 (link)) to obtain clean reads. GetOrganelle¹ was used to assemble the plastid genome sequence by selecting 15 million reads from the dataset of clean reads. Both our newly acquired plastid genomes and the downloaded plastid genomes from NCBI website were annotated using the online annotation tool GeSeq (Tillich et al., 2017 (link)). All the annotations were manually curated. In addition, we used HMMER (Wheeler and Eddy, 2013 (link)) and ARAGORN Version 1.2.38 (Laslett and Canback, 2004 (link)) to ensure the prediction accuracy of the encoded protein and RNA genes, respectively. Finally, the resulting plastid genome maps were drawn with Chloroplot (Zheng et al., 2020 (link)).