[1]

Wolfe KH, Li WH, Sharp PM. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences of the United States of America 84:9054−58

doi: 10.1073/pnas.84.24.9054
[2]

Gualberto JM, Mileshina D, Wallet C, Niazi AK, Weber-Lotfi F, et al. 2014. The plant mitochondrial genome: Dynamics and maintenance. Biochimie 100:107−20

doi: 10.1016/j.biochi.2013.09.016
[3]

Yurina NP, Odintsova MS. 2016. Mitochondrial genome structure of photosynthetic eukaryotes. Biochemistry 81:101−13

doi: 10.1134/s0006297916020048
[4]

Palmer JD, Herbon LA. 1988. Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. Journal of Molecular Evolution 28:87−97

doi: 10.1007/BF02143500
[5]

Sloan DB, Wu Z, Sharbrough J. 2018. Correction of persistent errors in Arabidopsis reference mitochondrial genomes. The Plant Cell 30:525−27

doi: 10.1105/tpc.18.00024
[6]

Wang L, Liu X, Xu Y, Zhang Z, Wei Y, et al. 2024. Assembly and comparative analysis of the first complete mitochondrial genome of a traditional Chinese medicine Angelica biserrata (Shan et Yuan) Yuan et Shan. International Journal of Biological Macromolecules 257:128571

doi: 10.1016/j.ijbiomac.2023.128571
[7]

Zhang K, Qu G, Zhang Y, Liu J. 2024. Assembly and comparative analysis of the first complete mitochondrial genome of Astragalus membranaceus (Fisch.) Bunge: an invaluable traditional Chinese medicine. BMC Plant Biology 24:1055

doi: 10.1186/s12870-024-05780-4
[8]

Chen X, Wu Z, Yang Y, Tao Q, Na N, et al. 2025. The complete mitochondrial genome and phylogenetic analysis of Lotus corniculatus (Fabaceae, Papilionoideae). Frontiers in Plant Science 16:1555595

doi: 10.3389/fpls.2025.1555595
[9]

Editorial Committee of Flora of China, Chinese Academy of Sciences. 2010. Flora of China, Vol. 10: Fabaceae. Volume 10. Beijing: Science Press

[10]

Shi FY, Qiu MN, Li GZ, Zhang G, Wu CC, et al. 2019. Research progress on the resource status, chemical composition, toxicity, exploitation and utilization of Sophora alopecuroides. Heilongjiang Animal Science and Veterinary Medicine 13:34−38 (in Chinese)

doi: 10.13881/j.cnki.hljxmsy.2018.08.0282
[11]

Li JG, Yang XY, Huang W. 2016. Total alkaloids of Sophora alopecuroides inhibit growth and induce apoptosis in human cervical tumor HeLa Cells in vitro. Pharmacognosy Magazine 12:S253−S256

doi: 10.4103/0973-1296.182157
[12]

Guo C, Yang L, Luo J, Zhang C, Xia Y, et al. 2016. Sophoraflavanone G from Sophora alopecuroides inhibits lipopolysaccharide-induced inflammation in RAW264.7 cells by targeting PI3K/Akt, JAK/STAT and Nrf2/HO-1 pathways. International Immunopharmacology 38:349−56

doi: 10.1016/j.intimp.2016.06.021
[13]

Wan CX, Luo JG, Ren XP, Kong LY. 2015. Interconverting flavonostilbenes with antibacterial activity from Sophora alopecuroides. Phytochemistry 116:290−97

doi: 10.1016/j.phytochem.2015.02.022
[14]

Duan N, Deng Y, Liu Y, Zhang Y, Zhang LG, et al. 2019. The complete chloroplast genome of Sophora alopecuroides (Fabaceae). Mitochondrial DNA Part B 4:1336−37

doi: 10.1080/23802359.2019.1596760
[15]

Zhu Y, Wang Y, Ma Z, Wang D, Yan F, et al. 2024. Genome-wide identification of CHYR gene family in Sophora alopecuroides and functional analysis of SaCHYR4 in response to abiotic stress. International Journal of Molecular Sciences 25:6173

doi: 10.3390/ijms25116173
[16]

Abdel-Latif A, Osman G. 2017. Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize. Plant Methods 13:1

doi: 10.1186/s13007-016-0152-4
[17]

Bi C, Shen F, Han F, Qu Y, Hou J, et al. 2024. PMAT: an efficient plant mitogenome assembly toolkit using low-coverage HiFi sequencing data. Horticulture Research 11:uhae023

doi: 10.1093/hr/uhae023
[18]

Wick RR, Schultz MB, Zobel J, Holt KE. 2015. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 31:3350−52

doi: 10.1093/bioinformatics/btv383
[19]

Jin JJ, Yu WB, Yang JB, Song Y, DePamphilis CW, et al. 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology 21:241

doi: 10.1186/s13059-020-02154-5
[20]

Lowe TM, Eddy SR. 1997. tRNAscan-SE a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25:955−64

doi: 10.1093/nar/25.5.955
[21]

Chen Y, Ye W, Zhang Y, Xu Y. 2015. High speed BLASTN: an accelerated MegaBLAST search tool. Nucleic Acids Research 43:7762−68

doi: 10.1093/nar/gkv784
[22]

Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647−49

doi: 10.1093/bioinformatics/bts199
[23]

Zhang D, Gao F, Jakovlić I, Zou H, Zhang J, et al. 2020. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Molecular Ecology Resources 20:348−55

doi: 10.1111/1755-0998.13096
[24]

Tamura K, Stecher G, Kumar S. 2021. MEGA11: molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution 38:3022−27

doi: 10.1093/molbev/msab120
[25]

Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, et al. 2006. KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics, Proteomics & Bioinformatics 4:259−63

doi: 10.1016/S1672-0229(07)60007-2
[26]

Moberly JG, Bernards MT, Waynant KV. 2018. Key features and updates for Origin 2018. Journal of Cheminformatics 10:5

doi: 10.1186/s13321-018-0259-x
[27]

Wright F. 1990. The ‘effective number of codons’ used in a gene. Gene 87:23−29

doi: 10.1016/0378-1119(90)90491-9
[28]

Sueoka N. 1988. Directional mutation pressure and neutral molecular evolution. Proceedings of the National Academy of Sciences of the United States of America 85:2653−57

doi: 10.1073/pnas.85.8.2653
[29]

Beier S, Thiel T, Münch T, Scholz U, Mascher M. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics 33:2583−85

doi: 10.1093/bioinformatics/btx198
[30]

Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, et al. 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research 29:4633−42

doi: 10.1093/nar/29.22.4633
[31]

Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research 27:573−80

doi: 10.1093/nar/27.2.573
[32]

Edera AA, Small I, Milone DH, Sanchez-Puerta MV. 2021. Deepred-Mt: Deep representation learning for predicting C-to-U RNA editing in plant mitochondria. Computers in Biology and Medicine 136:104682

doi: 10.1016/j.compbiomed.2021.104682
[33]

Lenz H, Hein A, Knoop V. 2018. Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0. BMC Bioinformatics 19:255

doi: 10.1186/s12859-018-2244-9
[34]

Chen C, Wu Y, Li J, Wang X, Zeng Z, et al. 2023. TBtools-II: a “one for all, all for one” bioinformatics platform for biological big-data mining. Molecular Plant 16:1733−42

doi: 10.1016/j.molp.2023.09.010
[35]

Wang Y, Tang H, Debarry JD, Tan X, Li J, et al. 2012. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research 40:e49

doi: 10.1093/nar/gkr1293
[36]

Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30:772−80

doi: 10.1093/molbev/mst010
[37]

Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972−73

doi: 10.1093/bioinformatics/btp348
[38]

Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, et al. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic Era. Molecular Biology and Evolution 37:1530−34

doi: 10.1093/molbev/msaa015
[39]

Cole LW, Guo W, Mower JP, Palmer JD. 2018. High and variable rates of repeat-mediated mitochondrial genome rearrangement in a genus of plants. Molecular Biology and Evolution 35:2773−85

doi: 10.1093/molbev/msy176
[40]

Xu WQ. 2020. The Mitochondrial Genome of Cistanche Genus in China. Thesis. Chinese Academy of Medical Sciences & Peking Union Medical College. doi: 10.27648/d.cnki.gzxhu.2020.000890

[41]

Smith DR, Keeling PJ. 2015. Mitochondrial and plastid genome architecture: reoccurring themes, but significant differences at the extremes. Proceedings of the National Academy of Sciences of the United States of America 112:10177−84

doi: 10.1073/pnas.1422049112
[42]

Hao Z, Zhang Z, Jiang J, Pan L, Zhang J, et al. 2024. Complete mitochondrial genome of Melia azedarach L., reveals two conformations generated by the repeat sequence mediated recombination. BMC Plant Biology 24:645

doi: 10.1186/s12870-024-05319-7
[43]

Xu D, Wang T, Huang J, Wang Q, Wang Z, et al. 2025. Comparative analysis of mitochondrial genomes of Stemona tuberosa lour. reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing. BMC Plant Biology 25:23

doi: 10.1186/s12870-024-06034-z
[44]

Yang JX, Dierckxsens N, Bai MZ, Guo YY. 2023. Multichromosomal mitochondrial genome of Paphiopedilum micranthum: compact and fragmented genome, and rampant intracellular gene transfer. International Journal of Molecular Sciences 24:3976

doi: 10.3390/ijms24043976
[45]

Sun T, Bentolila S, Hanson MR. 2016. The unexpected diversity of plant organelle RNA editosomes. Trends in Plant Science 21:962−73

doi: 10.1016/j.tplants.2016.07.005
[46]

Zhu L, Xian FJ, Zhang QN, Hu J. 2022. Research progress of RNA editing. Biotechnology Bulletin 38:1−14

doi: 10.13560/j.cnki.biotech.bull.1985.2021-1326
[47]

Planchard N, Bertin P, Quadrado M, Dargel-Graffin C, Hatin I, et al. 2018. The translational landscape of Arabidopsis mitochondria. Nucleic Acids Research 46:6218−28

doi: 10.1093/nar/gky489
[48]

Picardi E, Horner DS, Chiara M, Schiavon R, Valle G, et al. 2010. Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing. Nucleic Acids Research 38:4755−67

doi: 10.1093/nar/gkq202
[49]

Li J, Li J, Ma Y, Kou L, Wei J, et al. 2022. The complete mitochondrial genome of okra (Abelmoschus esculentus): using nanopore long reads to investigate gene transfer from chloroplast genomes and rearrangements of mitochondrial DNA molecules. BMC Genomics 23:481

doi: 10.1186/s12864-022-08706-2
[50]

Unseld M, Marienfeld JR, Brandt P, Brennicke A. 1997. The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nature Genetics 15:57−61

doi: 10.1038/ng0197-57