Additional file 1 of Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification

Additional file 1: Table S1. Characteristics of the five Cistanche species plastomes. Table S2. Details of plastome or chloroplast genome sequences downloaded from NCBI used in this study. Table S3. Gene content in SSC region of Orobanchaceae species. Table S4. The position of genesin LSC, IR and SSC regions in five Cistanche species. Table S5. The list of lost genes in Orobanchaceae species. Table S6. The list of pseudogenes in Orobanchaceae species. Table S7. The thirteen pairs of primers for the ampilification of DNA barcode markers. Fig. S1. The coverage depth of the four Cistanche plastomes. The raw sequence reads were mapped to the reference plastome sequences. A) C. deserticola; B) C. salsa; C) C. sinensis; D) C. tubulosa. The X-axis shows the plastome positions. The Y-axis shows the depth. The Y-axis shows the coverage depth of the mapped reads. Fig. S2. The dot plots showing the self-2-selfalignment of the four Cistanche plastomes sequences. The plots were generated using Gepard. A) C. deserticola; B) C. salsa; C) C. sinensis; D) C. tubulosa. Fig. S3. A schematic map of the Cistanche deserticola plastome.The first circle shows the species name and specific information regarding the genome (length, GC content, and the number of genes) from the center going outward. The second circle shows the length of the corresponding single short copy (SSC), inverted repeat (IRa and IRb), and large single-copy (LSC) regions from the center going outward. The third circle shows the GC content. The outer circle shows the gene names and their optional codon usage bias in parentheses.The genes are colored based on their functional categories. Genes inside andoutside of the circle are transcribed in clockwise and counterclockwise directions, represented with arrows. Fig. S4. A schematic map of the Cistanche salsa plastome. The first circle shows the species name and specific information regarding the genome (length, GC content, and the number of genes)from the center going outward. The second circle shows the length of the corresponding single short copy (SSC), inverted repeat (IRa and IRb), and large single-copy (LSC) regions from the center going outward. The third circle shows the GC content. The outer circle shows the gene names and their optional codon usage bias in parentheses. The genes are colored based on their functional categories. Genes inside and outside of the circle are transcribed in clockwise and counterclockwise directions, represented with arrows. Fig. S5. Aschematic map of the Cistanche tubulosa plastome. The first circle showsthe species name and specific information regarding the genome (length, GCcontent, and the number of genes) from the center going outward. The second circle shows the length of the corresponding single short copy (SSC), invertedrepeat (IRa and IRb), and large single-copy (LSC) regions from the center going outward. The third circle shows the GC content. The outer circle shows the gene names and their optional codon usage bias in parentheses. The genes are coloredbased on their functional categories. Genes inside and outside of the circle are transcribed in clockwise and counterclockwise directions, represented with arrows. Fig. S6. A schematic map of the Cistanche sinensis plastome.The first circle shows the species name and specific information regarding thegenome (length, GC content, and the number of genes) from the center going outward. The second circle shows the length of the corresponding single shortcopy (SSC), inverted repeat (IRa and IRb), and large single-copy (LSC) regions from the center going outward. The third circle shows the GC content. The outer circle shows the gene names and their optional codon usage bias in parentheses.The genes are colored based on their functional categories. Genes inside andoutside of the circle are transcribed in clockwise and counterclockwise directions, represented with arrows. Fig. S7. Identity plot comparingthe plastid genomes of C. deserticola, C. salsa, C. sinensis,C. tubulosa and C. phelypaea using Rehmannia glutinosa as a reference sequence. The vertical scale indicates the percentage of identity(50% to 100%), using a 50% identity cutoff. The horizontal axis indicates the coordinates in the plastomes. Genome regions are color-coded as protein-coding, rRNA, tRNA, intron, and conserved non-coding sequences (CNS). Fig. S8. Synteny analyses of plastomes for five Cistanche species. Each horizontal black line represents a genome, with conserved regions connected with colored blocks. The plastome sequence of C. deserticola was used as the reference. Fig.S9. Synteny analyses of five Cistanche plastomes compared with Rehmannia glutinosa. Each horizontal black line represents a genome, with conserved regions connected with colored block. The plastome of R. glutinosa was used as the reference. Fig. S10. Extent of the gene rearrangements of 5 Cistanche plastomes. Locally collinear blocks of the sequences are colour-coded and connected by lines. Fig. S11. Maximum likelihood (ML) Phylogenetic tree of 36 Orobanchaceae species. The Cistanche species are highlighted in blue. The bootstrap scores are shown on the corresponding branches. The detail information can be found in Table S2. Fig. S12. Maximum cladecredibility tree obtained from a molecules clock analysis using the BEAST software. The circles having different colors represent the genes positively selected in Orobanchaceae. The background of Cistanche is highlighted in light blue. The detail information can be found in Table S2. Fig.S13. The gel electrophoresis results of the PCR products amplified usingthe primers pairs list in Table S7 using DNA marker. Lane M was the marker of DL 2000. The lanes from left to right corresponded to products amplificated from the first individual of C. deserticola (Cide), C. salsa (Cisa),C. tubulosa(Citu), and C. sinensis (Cisi) by primer Cis-pp01 andCis-pp02, respectively. Fig. S14. The gel electrophoresis results of the PCR products amplified using the primers pairs list in Table S7 using DNAmarker. Lane M was the marker of DL 2000. The lanes from left to right corresponded to products amplificated from the first individual of C.deserticola (Cide), C. salsa (Cisa), C. tubulosa (Citu), andC. sinensis (Cisi) by primer Cis-pp03 to Cis-pp013, respectively. Fig.S15. The alignment of the sequencing chromatogram of the PCR products amplified using DNA marker (Cis-mk03 to Cis-mk13). SNP and Indel regions were highlighted with red squares. Cide: C. deserticola; Cisa: C. salsa;Citu: C. tubulosa; Cisi: C.sinensis.