Additional file 1 of Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae
Creators: name: Wanichthanarak, Kwanjeera
name: Nookaew, Intawat
name: Pasookhush, Phongthana
name: Wongsurawat, Thidathip
name: Jenjaroenpun, Piroon
name: Leeratsuwan, Namkhang
name: Wattanachaisaereekul, Songsak
name: Visessanguan, Wonnop
name: Sirivatanauksorn, Yongyut
name: Nuntasaen, Narong
name: Kuhakarn, Chutima
name: Reutrakul, Vichai
name: Ajawatanawong, Pravech
name: Khoomrung, Sakda
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. The number of spanning reads over the IR boundaries. (A) Boundary A locates between LSC and IRb. (B) Boundary B locates between IRb and SSC. (C) Boundary C locates between SSC and IRa. (D) Boundary D locates between IRa and LSC. The number of ONT reads spanning over the four IR boundaries at different distances (nt) from the boundaries are illustrated as bar charts. Large single-copy (LSC); inverted repeats (IRs) and small single-copy (SSC). Figure S2. Comparative gene arrangement in IR regions of Rhamnaceae, C. sativa and F. religios. Each box represents a gene. The rps19 and ycf1 genes (bold and underline) are located at the borders of IR regions. A missing gene that was re-annotated is highlighted in red. A gene in LSC is represented by an orange box. A gene in IR is in a blue box and a gene in both LSC and IR regions is in a white box. The C. sativa NC_027223 and F. religiosa NC_033979 are the outgroup of phylogenetic analysis. Reversed inverted repeat (revIR). Figure S3. Domain analysis of Ycf1 protein sequences. The full-length colored bar represents the presence of an entire Ycf1 domain. A shorter colored bar within the grey bar indicates the matching part of the domain. A truncated domain is shown by a jagged edge. The number indicates the amino acid length. Ycf1 copy in IRb (ycf1_IRb) and ycf1 gene in IRa (ycf1_IRa). Figure S4. A shift in the origin of H. acerba MN794429 chloroplast genome and correction. Suggested origin is presented in red color. Figure S5. Multiple alignment of the ycf15 gene sequences and matching domain fragments. This figure shows the alignment of the deposited ycf15 DNA sequences from six Rhamnaceae organisms and the ycf15 sequence of V. harmandiana. The predicted Ycf15 domain of each ycf15 is illustrated on the right column. A missing T-base from the ycf15 sequence of V. harmandiana is pointed out by an arrow. The full-length colored bar represents the presence of an entire Ycf15 domain. A truncated omain is shown by a jagged edge. The number indicates the amino acid length. Only the ycf15 copy in IRb is shown, as its copy in IRa is identical. Figure S6. Re-annotation of the ycf15 gene in Barbeya oleoides NC_040984 and the outgroup. The alignment of the ycf15 gene sequences of Barbeya oleoides, C. sativa and F. religiosa to the ycf15 gene sequence of N. tabacum Z00044 is illustrated. The TA-gap is pointed out by a black arrow. The predicted Ycf15 domain of each ycf15 is illustrated on the right column. The full-length colored bar represents the presence of an entire Ycf15 domain. A truncated domain is shown by a jagged edge. The number indicates the amino acid length. Only the ycf15 copy in IRb is shown, as its copy in IRa is identical. Figure S7. Re-annotation of the ycf15 gene in Rhamnaceae. (A) The alignment of the reference gene sequence to the first exon and (B) to the second exon of the ycf15 gene in Rhamnaceae organisms. The figure shows the multiple sequence alignment using N. tabacum Z00044 as a reference to re-annotate the ycf15 gene of the organisms in this study. TA-gaps in the ycf15 sequences of the Rhamnaceae are pointed out by a black arrow. The predicted Ycf15 domain of each ycf15 is illustrated on the right column. The full-length colored bar represents the presence of an entire Ycf15 domain. A truncated domain is shown by a jagged edge. The number indicates the amino acid length. Only the ycf15 copy in IRb is shown, as its copy in IRa is identical Figure S8. Re-annotation of infA gene in V. leiocarpa. (A) The alignment of infA DNA sequences between V. harmandiana and V. leiocarpa. A-gap is pointed out by an arrow. (B) Comparing amino acid sequences of the infA between V. harmandiana and V. leiocarpa. A dashed line (−) indicates a stop codon. Figure S9. Comparisons of the atpF and clpP gene structures. (A) Comparing the atpF gene structure of Z. jujuba species. (B) Comparing the clpP gene structure of H. acerba species. A blue box represents a coding region and the red wavy line represents an intergenic region. The base position of the atpF in Z. jujuba NC_030299 and the clpP in H. acerba MN794429 is used as a reference for each gene. Figure S10. Phylogenetic trees of Rhamnaceae reconstructed from the orthologous proteins (A) using ML method, (B) using MP method, (C) using BI method and (D) the tree reconstructed from the orthologous genes using RAxML method. Different colors correspond to tribes labelled in square brackets. The outgroup branch is not colored. Two major groups of Rhamnaceae: ziziphoid and rhamnoid are presented on the rightmost text. A number in each tree indicates the ML bootstrap value, the MP bootstrap value, the posterior probability of BI, the ML bootstrap value, respectively. Figure S11. Characteristics and comparisons of Rhamnaceae chloroplast genome features. (A) Comparison of the SSR types. (B) Distribution of SSRs in LSC, SSC and IR regions. (C) Comparison of the long repeat types. (D) Distribution of long repeats in LSC, SSC and IR regions. The total number of SSRs and long repeat sequences in each species is in the parenthesis. Figure S12. The original image of gel in Fig. 1C before cropping and inverting color.