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In this study, we have assembled and annotated for the first time the entire mitochondrial genome (mitogenome) of T. mongolicus. The mitochondrial genome of T. mongolicus is composed in a monocyclic structure, with an overall size of 450,543 base pairs (bp) and a GC composition of 45.63%. It contains 32 unique protein-encoding genes. The repetitive sequences of the T. mongolicus mitogenome include 165 forward repetitive sequences and 200 palindromic repetitive sequences, in addition to 88 simple sequence repeats, of which tetramers accounted for the highest proportion (40.91%). An analysis of the mitogenome codons revealed that synonymous codons generally end with A\/U. With the exception of nad4L, which uses ACG\/ATG as an initiation codon, all other genes begin with the ATG start codon. Codon analysis of the mitogenome also showed that leucine (909) are the most abundant amino acid, while tryptophan (134) are the least prevalent. In total, 374 RNA editing sites were detected. Moreover, 180 homologous segments totaling 105,901 bp were found when the mitochondrial and chloroplast genomes of T. mongolicus were compared. Phylogenetic analysis further indicated that T. mongolicus is most closely related to Prunella vulgaris in the Lamiaceae family. Our findings offer important genetic insights for further research on this Lamiaceae species. To the best of our knowledge, this study is the first description of the entire mitogenome of T. mongolicus.<\/jats:p>","DOI":"10.3390\/biom15030343","type":"journal-article","created":{"date-parts":[[2025,2,27]],"date-time":"2025-02-27T05:13:58Z","timestamp":1740633238000},"page":"343","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["The Complete Mitochondrial Genome of Thymus mongolicus and Its Phylogenetic Relationship with Lamiaceae Species"],"prefix":"10.3390","volume":"15","author":[{"given":"Na","family":"Na","sequence":"first","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010011, China"},{"name":"Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010018, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4121-4529","authenticated-orcid":false,"given":"Zinian","family":"Wu","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010011, China"},{"name":"Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010018, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiyong","family":"Wang","sequence":"additional","affiliation":[{"name":"Inner Mongolia General Station of Seed and Seedling of Forestry and Grassland, Hohhot 010021, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-9086-9097","authenticated-orcid":false,"given":"Yanting","family":"Yang","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010011, China"},{"name":"Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010018, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chunyu","family":"Tian","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010011, China"},{"name":"Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010018, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8078-3292","authenticated-orcid":false,"given":"Lin","family":"Zhu","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010011, China"},{"name":"Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010018, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taiyou","family":"Ou","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010011, China"},{"name":"Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010018, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaofei","family":"Chen","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010011, China"},{"name":"Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010018, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongyan","family":"Xia","sequence":"additional","affiliation":[{"name":"Inner Mongolia General Station of Seed and Seedling of Forestry and Grassland, Hohhot 010021, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiyong","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010011, China"},{"name":"Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010018, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,2,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2597","DOI":"10.1080\/23802359.2020.1778573","article-title":"The complete chloroplast genome sequence of thymus mongolicus (labiatae), a special spice plant","volume":"5","author":"Huaizhu","year":"2020","journal-title":"Mitochondrial DNA Part B"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Zhou, D., Liu, Y., Yao, J., Yin, Z., Wang, X., Xu, L., Que, Y., Mo, P., and Liu, X. (2022). Characterization and phylogenetic analyses of the complete mitochondrial genome of sugarcane (saccharum spp. Hybrids) line A1. Diversity, 14.","DOI":"10.3390\/d14050333"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Stahl-Biskup, E., and Venskutonis, R.P. (2012). Thyme. Handbook of Herbs and Spices, Elsevier. Available online: https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/B978085709039350027X.","DOI":"10.1533\/9780857095671.499"},{"key":"ref_4","first-page":"30","article-title":"Intraspecific variability of wild thyme (thymus serpyllum L.) occurring in poland","volume":"12","author":"Kosakowska","year":"2019","journal-title":"J. Appl. Res. Med. Aromat. Plants"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1007\/s10068-015-0095-y","article-title":"Protective effect of carvacrol from thymus quinquecostatus celak against tert-butyl hydroperoxide-induced oxidative damage in chang cells","volume":"24","author":"Kim","year":"2015","journal-title":"Food Sci. Biotechnol."},{"key":"ref_6","first-page":"77","article-title":"Application research progress of thymus mongolicus","volume":"29","author":"Qiu","year":"2018","journal-title":"J. Longdong Univ."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Xiang, Y., An, S., Cheng, M., Liu, L., and Xie, Y. (2018). Changes of soil microbiological properties during grass litter decomposition in loess hilly region, China. IJERPH, 15.","DOI":"10.3390\/ijerph15091797"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Shen, J., Li, X., Li, M., Cheng, H., Huang, X., and Jin, S. (2022). Characterization, comparative phylogenetic, and gene transfer analyses of organelle genomes of rhododendron \u00d7 pulchrum. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.969765"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Wang, Y., Chen, S., Chen, J., Chen, C., Lin, X., Peng, H., Zhao, Q., and Wang, X. (2023). Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of photinia serratifolia. Sci. Rep., 13.","DOI":"10.1038\/s41598-022-24327-x"},{"key":"ref_10","first-page":"8584","article-title":"Creation of A Male Sterility Line and Identification ofIts Candidate Mitochondrial Male Sterile Gene in Celery","volume":"22","author":"Tan","year":"2022","journal-title":"J. Plant Genet. Resour."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Day, D.A., Millar, A.H., and Whelan, J. (2004). Plant Mitochondria: From Genome to Function, Springer Netherlands. Available online: https:\/\/link.springer.com\/10.1007\/978-1-4020-2400-9.","DOI":"10.1007\/978-1-4020-2400-9"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/j.biochi.2013.09.016","article-title":"The plant mitochondrial genome: Dynamics and maintenance","volume":"100","author":"Gualberto","year":"2014","journal-title":"Biochimie"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Putintseva, Y.A., Bondar, E.I., Simonov, E.P., Sharov, V.V., Oreshkova, N.V., Kuzmin, D.A., Konstantinov, Y.M., Shmakov, V.N., Belkov, V.I., and Sadovsky, M.G. (2020). Siberian larch (larix sibirica ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome. BMC Genom., 21.","DOI":"10.1186\/s12864-020-07061-4"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"jkaa025","DOI":"10.1093\/g3journal\/jkaa025","article-title":"A high-quality genome assembly and annotation of the gray mangrove, avicennia marina","volume":"11","author":"Friis","year":"2021","journal-title":"G3"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Xiong, Y., Yu, Q., Xiong, Y., Zhao, J., Lei, X., Liu, L., Liu, W., Peng, Y., Zhang, J., and Li, D. (2022). The complete mitogenome of elymus sibiricus and insights into its evolutionary pattern based on simple repeat sequences of seed plant mitogenomes. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.802321"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Chen, J., Ma, H., Fan, H., Lin, F., Chai, T., and Wang, H. (2023). De novo assembly and comparative analysis of the mitochondrial genome of reynoutria japonica. Front. Genet., 14.","DOI":"10.3389\/fgene.2023.1289811"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"270","DOI":"10.12688\/f1000research.21490.1","article-title":"Recent advances in understanding mitochondrial genome diversity","volume":"9","author":"Zardoya","year":"2020","journal-title":"F1000Res"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Sheng, W., Deng, J., Wang, C., and Kuang, Q. (2023). The garden asparagus (asparagus officinalis L.) mitochondrial genome revealed rich sequence variation throughout whole sequencing data. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1140043"},{"key":"ref_19","first-page":"277","article-title":"Analysis of the complete mitochondrial genome sequence of the resurrection plant haberlea rhodopensis","volume":"68","author":"Baev","year":"2021","journal-title":"Acta Biochim. Pol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/1746-4811-7-38","article-title":"An efficient procedure for plant organellar genome assembly, based on whole genome data from the 454 GS FLX sequencing platform","volume":"7","author":"Zhang","year":"2011","journal-title":"Plant Methods"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Zhong, F., Ke, W., Li, Y., Chen, X., Zhou, T., Xu, B., Qi, L., Yan, Z., and Ma, Y. (2023). Comprehensive analysis of the complete mitochondrial genomes of three coptis species (C. chinensis, C. deltoidea and C. omeiensis): The important medicinal plants in China. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1166420"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Yu, R., Chen, X., Long, L., Jost, M., Zhao, R., Liu, L., Mower, J.P., de Pamphilis, C.W., Wanke, S., and Jiao, Y. (2023). De novo assembly and comparative analyses of mitochondrial genomes in piperales. Genome Biol. Evol., 15.","DOI":"10.1093\/gbe\/evad041"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1007\/s00294-009-0273-7","article-title":"The complete mitochondrial genome sequence of the liverwort pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts","volume":"55","author":"Wang","year":"2009","journal-title":"Curr. Genet."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Dong, S., Zhao, C., Chen, F., Liu, Y., Zhang, S., Wu, H., Zhang, L., and Liu, Y. (2018). The complete mitochondrial genome of the early flowering plant nymphaea colorata is highly repetitive with low recombination. BMC Genom., 19.","DOI":"10.1186\/s12864-018-4991-4"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Cheng, Q., Wang, P., Li, T., Liu, J., Zhang, Y., Wang, Y., Sun, L., and Shen, H. (2021). Complete mitochondrial genome sequence and identification of a candidate gene responsible for cytoplasmic male sterility in celery (apium graveolens L.). IJMS, 22.","DOI":"10.3390\/ijms22168584"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Ren, W., Wang, L., Feng, G., Tao, C., Liu, Y., and Yang, J. (2023). High-quality assembly and comparative analysis of Actinidia latifolia and A. valvata mitogenomes. Genes, 14.","DOI":"10.3390\/genes14040863"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1007\/BF02772108","article-title":"Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components","volume":"15","author":"Porebski","year":"1997","journal-title":"Plant Mol. Biol. Rep."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2, Pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: Scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation","volume":"27","author":"Koren","year":"2017","journal-title":"Genome Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Wick, R.R., Judd, L.M., Gorrie, C.L., and Holt, K.E. (2017). Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol., 13.","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3350","DOI":"10.1093\/bioinformatics\/btv383","article-title":"Bandage: Interactive visualization of de novo genome assemblies","volume":"31","author":"Wick","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"W6","DOI":"10.1093\/nar\/gkx391","article-title":"GeSeq\u2013versatile and accurate annotation of organelle genomes","volume":"45","author":"Tillich","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"101191","DOI":"10.1016\/j.xplc.2024.101191","article-title":"PMGA: A plant mitochondrial genome annotator","volume":"9","author":"Li","year":"2024","journal-title":"Plant Commun."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.955","article-title":"tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence","volume":"25","author":"Lowe","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"W59","DOI":"10.1093\/nar\/gkz238","article-title":"OrganellarGenomeDRAW (OGDRAW) version 1.3.1, Expanded toolkit for the graphical visualization of organellar genomes","volume":"47","author":"Greiner","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1007\/s00122-002-1031-0","article-title":"Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (hordeum vulgare L.)","volume":"106","author":"Thiel","year":"2003","journal-title":"Theor. Appl. Genet."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2583","DOI":"10.1093\/bioinformatics\/btx198","article-title":"MISA-web: A web server for microsatellite prediction","volume":"33","author":"Beier","year":"2017","journal-title":"Bioinformatics"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem repeats finder: A program to analyze DNA sequences","volume":"27","author":"Benson","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"4633","DOI":"10.1093\/nar\/29.22.4633","article-title":"REPuter: The manifold applications of repeat analysis on a genomic scale","volume":"29","author":"Kurtz","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1007\/s00239-021-10027-z","article-title":"Codon usage bias: An endless tale","volume":"89","author":"Iriarte","year":"2021","journal-title":"J. Mol. Evol."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Edera, A.A., Small, I., Milone, D.H., and Sanchez-Puerta, M.V. (2021). Deepred-mt: Deep representation learning for predicting C-to-U RNA editing in plant mitochondria. Comput. Biol. Med., 136.","DOI":"10.1016\/j.compbiomed.2021.104682"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Jin, J.-J., Yu, W.-B., Yang, J.-B., Song, Y., Claude, W., de Pamphilis, C.W., Yi, T.-S., and Li, D.-Z. (2020). GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol., 21.","DOI":"10.1186\/s13059-020-02154-5"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"W65","DOI":"10.1093\/nar\/gkz345","article-title":"CPGAVAS2, an integrated plastome sequence annotator and analyzer","volume":"47","author":"Shi","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"7762","DOI":"10.1093\/nar\/gkv784","article-title":"High speed BLASTN: An accelerated MegaBLAST search tool","volume":"43","author":"Chen","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1016\/j.molp.2020.06.009","article-title":"TBtools: An integrative toolkit developed for interactive analyses of big biological data","volume":"13","author":"Chen","year":"2020","journal-title":"Mol. Plant"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7, Improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1093\/sysbio\/sys029","article-title":"MrBayes 3.2, Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space","volume":"61","author":"Ronquist","year":"2012","journal-title":"Syst. Biol."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Hao, W., Liu, G., Wang, W., Shen, W., Zhao, Y., Sun, J., Yang, Q., Zhang, Y., Fan, W., and Pei, S. (2021). RNA editing and its roles in plant organelles. Front. Genet., 12.","DOI":"10.3389\/fgene.2021.757109"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1007\/s00425-021-03684-3","article-title":"Assembly of the complete mitochondrial genome of an endemic plant, Scutellaria tsinyunensis, revealed the existence of two conformations generated by a repeat-mediated recombination","volume":"254","author":"Li","year":"2021","journal-title":"Planta"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1111\/nph.14135","article-title":"Complete mitochondrial genomes from the ferns ophioglossum californicum and psilotum nudum are highly repetitive with the largest organellar introns","volume":"213","author":"Guo","year":"2017","journal-title":"New Phytol."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Cheng, Y., He, X., Priyadarshani, S.V.G.N., Wang, Y., Ye, L., Shi, C., Ye, K., Zhou, Q., Luo, Z., and Deng, F. (2021). Assembly and comparative analysis of the complete mitochondrial genome of suaeda glauca. BMC Genom., 22.","DOI":"10.1186\/s12864-021-07490-9"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"114210","DOI":"10.1016\/j.indcrop.2021.114210","article-title":"Comprehensive analysis of complete mitochondrial genome of sapindus mukorossi gaertn.: An important industrial oil tree species in China","volume":"174","author":"Wang","year":"2021","journal-title":"Ind. Crop. Prod."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Niu, Y., Zhang, T., Chen, M., Chen, G., Liu, Z., Yu, R., Han, X., Chen, K., Huang, A., and Chen, C. (2023). Analysis of the complete mitochondrial genome of the bitter gourd (momordica charantia). Plants, 12.","DOI":"10.3390\/plants12081686"},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Wang, J., Liu, X., Zhang, M., and Liu, R. (2024). The mitochondrial genome of lavandula angustifolia mill. (lamiaceae) sheds light on its genome structure and gene transfer between organelles. BMC Genom., 25.","DOI":"10.1186\/s12864-024-10841-x"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1146\/annurev.genet.42.110807.091442","article-title":"Selection on Codon Bias","volume":"42","author":"Hershberg","year":"2008","journal-title":"Annu. Rev. Genet."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"9382","DOI":"10.1093\/nar\/gkt740","article-title":"Selection on codon bias in yeast: A transcriptional hypothesis","volume":"41","author":"Trotta","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"1909","DOI":"10.1007\/s00018-020-03685-7","article-title":"The effects of codon bias and optimality on mRNA and protein regulation","volume":"78","author":"Hia","year":"2021","journal-title":"Cell Mol. Life Sci."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Guo, Y., Li, Z., Jin, S., Chen, S., Li, F., and Wu, H. (2023). Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Two Species of Calla Lilies (Zantedeschia, Araceae). IJMS, 24.","DOI":"10.3390\/ijms24119566"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Ke, S.J., Liu, D.K., Tu, X.D., He, X., Zhang, M.M., Zhu, M.J., Zhang, D.Y., Zhang, C.L., Lan, S.R., and Liu, Z.J. (2023). Apostasia mitochondrial genome analysis and monocot mitochondria phylogenomics. IJMS, 24.","DOI":"10.3390\/ijms24097837"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1111\/nph.14158","article-title":"Correlation between mtDNA complexity and mtDNA replication mode in developing cotyledon mitochondria during mung bean seed germination","volume":"213","author":"Cheng","year":"2017","journal-title":"New Phytol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"2499","DOI":"10.1105\/tpc.111.087189","article-title":"Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber","volume":"23","author":"Alverson","year":"2011","journal-title":"Plant Cell"},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Zhou, P., Zhang, Q., Li, F., Huang, J., and Zhang, M. (2023). Assembly and comparative analysis of the complete mitochondrial genome of ilex metabaptista (aquifoliaceae), a Chinese endemic species with a narrow distribution. BMC Plant Biol., 23.","DOI":"10.1186\/s12870-023-04377-7"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"e115","DOI":"10.1093\/nar\/gkr517","article-title":"Transfection of plant mitochondria and in organello gene integration","volume":"39","author":"Mileshina","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Rudenko, V., and Korotkov, E. (2024). Study of dispersed repeats in the cyanidioschyzon merolae genome. IJMS, 25.","DOI":"10.3390\/ijms25084441"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1007\/s10142-021-00815-7","article-title":"An empirical analysis of mtSSRs: Could microsatellite distribution patterns explain the evolution of mitogenomes in plants?","volume":"22","author":"Busanello","year":"2022","journal-title":"Funct. Integr. Genom."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Fang, B., Li, J., Zhao, Q., Liang, Y., and Yu, J. (2021). Assembly of the complete mitochondrial genome of Chinese plum (prunus salicina): Characterization of genome recombination and RNA editing sites. Genes, 12.","DOI":"10.3390\/genes12121970"},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Guang, X.-M., Xia, J.-Q., Lin, J.-Q., Yu, J., Wan, Q.-H., and Fang, S.-G. (2019). IDSSR: An efficient pipeline for identifying polymorphic microsatellites from a single genome sequence. IJMS, 20.","DOI":"10.3390\/ijms20143497"},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Sun, Z., Wu, Y., Fan, P., Guo, D., Zhang, S., and Song, C. (2023). Assembly and analysis of the mitochondrial genome of prunella vulgaris. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1237822"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1111\/nph.18323","article-title":"The ecology of palm genomes: Repeat-associated genome size expansion is constrained by aridity","volume":"236","author":"Schley","year":"2022","journal-title":"New Phytol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"1040","DOI":"10.1111\/tpj.14578","article-title":"Plant organellar RNA editing: What 30 years of research has revealed","volume":"101","author":"Small","year":"2020","journal-title":"Plant J."},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Ma, Q., Wang, Y., Li, S., Wen, J., Zhu, L., Yan, K., Du, Y., Ren, J., Li, S., and Chen, Z. (2022). Assembly and comparative analysis of the first complete mitochondrial genome of acer truncatum bunge: A woody oil-tree species producing nervonic acid. BMC Plant Biol., 22.","DOI":"10.1186\/s12870-021-03416-5"},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Bi, C., Lu, N., Xu, Y., He, C., and Lu, Z. (2020). Characterization and analysis of the mitochondrial genome of common bean (phaseolus vulgaris) by comparative genomic approaches. IJMS, 21.","DOI":"10.3390\/ijms21113778"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1016\/j.molp.2015.12.004","article-title":"Ion channels in plant bioenergetic organelles, chloroplasts and mitochondria: From molecular identification to function","volume":"9","author":"Carraretto","year":"2016","journal-title":"Mol. Plant"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.bbrc.2008.08.116","article-title":"Gene duplication and transfer events in plant mitochondria genome","volume":"376","author":"Xiong","year":"2008","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"912","DOI":"10.1111\/tpj.15495","article-title":"Plant mitochondria\u2014Past, present and future","volume":"108","author":"Rasmusson","year":"2021","journal-title":"Plant J."},{"key":"ref_79","first-page":"2629","article-title":"Anatomical characteristics of laminae and petioles of 11 species of Salvia and their taxonomic significance","volume":"39","author":"Wang","year":"2014","journal-title":"Zhongguo Zhong Yao Za Zhi"}],"container-title":["Biomolecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2218-273X\/15\/3\/343\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T16:43:28Z","timestamp":1760028208000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2218-273X\/15\/3\/343"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,27]]},"references-count":79,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2025,3]]}},"alternative-id":["biom15030343"],"URL":"https:\/\/doi.org\/10.3390\/biom15030343","relation":{},"ISSN":["2218-273X"],"issn-type":[{"value":"2218-273X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,27]]}}}