10.6084/M9.FIGSHARE.21532593
Lu Gong
Lu
Gong
Guangzhou University of Chinese Medicine
Xiaoxia Ding
Xiaoxia
Ding
Guangzhou University of Chinese Medicine
Wan Guan
Wan
Guan
Zhejiang Taizhou Hospital
Danchun Zhang
Danchun
Zhang
Guangzhou University of Chinese Medicine
Jing Zhang
Jing
Zhang
Guangzhou University of Chinese Medicine
Junqi Bai
Junqi
Bai
Guangzhou University of Chinese Medicine
Wen Xu
Wen
Xu
Guangzhou University of Chinese Medicine
Juan Huang
Juan
Huang
Guangzhou University of Chinese Medicine
Xiaohui Qiu
Xiaohui
Qiu
Guangzhou University of Chinese Medicine
Xiasheng Zheng
Xiasheng
Zheng
Guangzhou University of Chinese Medicine
Danyan Zhang
Danyan
Zhang
Guangzhou University of Chinese Medicine
Shijie Li
Shijie
Li
Guangzhou University of Chinese Medicine
Zhihai Huang
Zhihai
Huang
Guangzhou University of Chinese Medicine
He Su
He
Su
Guangzhou University of Chinese Medicine
Additional file 3 of Comparative chloroplast genome analyses of Amomum: insights into evolutionary history and species identification
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.
Genetics
figshare
2022
2022-11-10
2023-06-19
Journal contribution
1051489 Bytes
10.1186/s12870-022-03898-x
CC BY + CC0