Additional file 3 of Comparative chloroplast genome analyses of Amomum: insights into evolutionary history and species identification
Creators: name: Gong, Lu
name: Ding, Xiaoxia
name: Guan, Wan
name: Zhang, Danchun
name: Zhang, Jing
name: Bai, Junqi
name: Xu, Wen
name: Huang, Juan
name: Qiu, Xiaohui
name: Zheng, Xiasheng
name: Zhang, Danyan
name: Li, Shijie
name: Huang, Zhihai
name: Su, He
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 3: Fig. S1. Analysis of simple sequence repeats (SSRs) in the cp genomes of three Amomum species. Fig. S2. Frequency of identified SSR motifs in different repeat class types. Fig. S3. Repeat sequences of three Amomum species. F, P, R, and C indicate the repeat types F (forward), P (palindrome), R (reverse), and C (complement), respectively. Fig. S4. ML tree based on ccsA sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S5. ML tree based on trnC-GCA_petN sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S6. ML tree based on ndhB_rps7 sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S7. ML tree based on psaI_ycf4 sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S8. ML tree based on rpl20 sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S9. ML tree based on rpl33 sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S10. ML tree based on rps3 sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S11. ML tree based on rpoA sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S12. ML tree based on rps4 sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S13. ML tree based on ndhD_1 sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S14. ML tree based on ndhD_2 sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S15. ML tree based on ITS sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S16. ML tree based on ITS2 sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S17. ML tree based on psbA-trnH sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S18. ML tree based on matK sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S19. ML tree based on rbcL sequences of Amomum species. This Bootstrap consensus tree was constructed by K2P model with 1000 bootstrap replicates. Numbers under the nodes indicate bootstrap probabilities. The cut off value for the condensed tree was 50%. Fig. S20. 3D-structure for the represented positively-selected genes with 1 substitution. Fig. S21. Phylogenetic tree constructed by NJ based on complete chloroplast genome. Numbers under the nodes indicate bootstrap probabilities. Our sequenced samples are marked in red. Species from different genuses are marked in different color on the nodes.