Chloroplast Genome Phylogenetic Analysis

A total of 19 chloroplasts sequences (Supplementary Table S4) were used to build the phylogenetic trees. Each of the 67 protein-coding genes shared by all the genomes was compared individually and then linked end to end to form a supergene from each species. The sequences alignment was carried out using the MAFFT v7.309. The best model was determined using the modeltest-ng-0.1.6 software with default parameters; ML analysis was performed using RAxMLNG v0.9.084 based on Linux edition using default parameters. The parameters were GTR + FU + IU + G4m, noname = 1–51,039. Chrysanthemum x morifolium has been situated likewise those out-groups.

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Guo S., Liao X., Chen S., Liao B., Guo Y., Cheng R., Xiao S., Hu H., Chen J., Pei J., Chen Y., Xu J, & Chen S. (2022). A Comparative Analysis of the Chloroplast Genomes of Four Polygonum Medicinal Plants. Frontiers in Genetics, 13, 764534.

Publication 2022

Chloroplasts Chrysanthemum Genomes Protein genes Sequences alignment

Corresponding Organization :

Other organizations : Beijing Emergency Medical Center

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Variable analysis

independent variables

Chloroplast sequences

dependent variables

Phylogenetic trees

control variables

Protein-coding genes shared by all the genomes
MAFFT v7.309 for sequence alignment
Modeltest-ng-0.1.6 software for best model determination
RAxMLNG v0.9.084 based on Linux edition for ML analysis
GTR + FU + IU + G4m, noname = 1–51,039 parameters

positive controls

Chrysanthemum x morifolium as an outgroup

negative controls

Not mentioned

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