[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 84:9054−9058

doi: 10.1073/pnas.84.24.9054
[2]

Drouin G, Daoud H, Xia J. 2008. Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants. Molecular Phylogenetics and Evolution 49:827−831

doi: 10.1016/j.ympev.2008.09.009
[3]

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 112:10177−10184

doi: 10.3410/f.725409765.793515683
[4]

Wang J, Kan S, Liao X, Zhou J, Tembrock LR, et al. 2024. Plant organellar genomes: much done, much more to do. Trends in Plant Science 29:754−769

doi: 10.1016/j.tplants.2023.12.014
[5]

Mower JP, Vickrey TL. 2018. Structural diversity among plastid genomes of land plants. In Advances in Botanical Research, eds. Chaw SM, Jansen RK. vol. 85. New York: Academic Press. pp. 263−292 doi: 10.1016/bs.abr.2017.11.013
[6]

Dobrogojski J, Adamiec M, Luciński R. 2020. The chloroplast genome: a review. Acta Physiologiae Plantarum 42:98

doi: 10.1007/s11738-020-03089-x
[7]

Maréchal A, Brisson N. 2010. Recombination and the maintenance of plant organelle genome stability. New Phytologist 186:299−317

doi: 10.1111/j.1469-8137.2010.03195.x
[8]

Gray BN, Ahner BA, Hanson MR. 2009. Extensive homologous recombination between introduced and native regulatory plastid DNA elements in transplastomic plants. Transgenic Research 18:559−572

doi: 10.1007/s11248-009-9246-3
[9]

Guo W, Grewe F, Cobo-Clark A, Fan W, Duan Z, et al. 2014. Predominant and substoichiometric isomers of the plastid genome coexist within Juniperus plants and have shifted multiple times during cupressophyte evolution. Genome Biology and Evolution 6:580−590

doi: 10.1093/gbe/evu046
[10]

Mower JP. 2020. Variation in protein gene and intron content among land plant mitogenomes. Mitochondrion 53:203−213

doi: 10.1016/j.mito.2020.06.002
[11]

Wynn EL, Christensen AC. 2019. Repeats of unusual size in plant mitochondrial genomes: identification, incidence and evolution. G3 Genes| Genomes| Genetics 9:549−559

doi: 10.1534/g3.118.200948
[12]

Mower JP, Jain K, Hepburn NJ. 2012. The role of horizontal transfer in shaping the plant mitochondrial genome. In Advances in Botanical Research. vol. 63. Academic Press. pp. 41−69 doi: 10.1016/B978-0-12-394279-1.00003-X
[13]

Cauz-Santos LA. 2025. Beyond conservation: the landscape of chloroplast genome rearrangements in angiosperms. New Phytologist 247:2571−2580

doi: 10.1111/nph.70364
[14]

Fan W, Liu F, Jia Q, Du H, Chen W, et al. 2022. Fragaria mitogenomes evolve rapidly in structure but slowly in sequence and incur frequent multinucleotide mutations mediated by microinversions. New Phytologist 236:745−759

doi: 10.1111/nph.18334
[15]

Song Y, Pan SJ, Chen B, Xiao ZT, Huang KR, et al. 2025. Structural variations and phylogenetic implications of mitochondrial genomes in oaks. Industrial Crops and Products 235:121817

doi: 10.1016/j.indcrop.2025.121817
[16]

Wang N, Li C, Kuang L, Wu X, Xie K, et al. 2022. Pan-mitogenomics reveals the genetic basis of cytonuclear conflicts in citrus hybridization, domestication, and diversification. Proceedings of the National Academy of Sciences of the United States of America 119:e2206076119

doi: 10.1073/pnas.2206076119
[17]

Kong J, Wang J, Nie L, Tembrock LR, Zou C, et al. 2025. Evolutionary dynamics of mitochondrial genomes and intracellular transfers among diploid and allopolyploid cotton species. BMC Biology 23:9

doi: 10.1186/s12915-025-02115-z
[18]

Lin Y, Li P, Zhang Y, Akhter D, Pan R, et al. 2022. Unprecedented organelle genomic variations in morning glories reveal independent evolutionary scenarios of parasitic plants and the diversification of plant mitochondrial complexes. BMC Biology 20:49

doi: 10.1186/s12915-022-01250-1
[19]

Feng Y, Xiang X, Akhter D, Pan R, Fu Z, et al. 2021. Mitochondrial phylogenomics of Fagales provides insights into plant mitogenome mosaic evolution. Frontiers in Plant Science 12:762195

doi: 10.3389/fpls.2021.762195
[20]

Feng Y, Wicke S. 2025. Systemic organellar genome reconfiguration along the parasitic continuum in the broomrape family (Orobanchaceae). Plant and Cell Physiology 00:pcaf131

doi: 10.1093/pcp/pcaf131
[21]

Su X, Dong Z, Yu H, Yi S, Gao S, et al. 2025. Pan-mitogenome in Dipterocarpoideae: mitochondrial plastid DNAs and repeats shape the dynamic evolution of mitogenomes. BMC Plant Biology 25:1440

doi: 10.1186/s12870-025-07506-6
[22]

Yu R, Chen X, Long L, Jost M, Zhao R, et al. 2023. De novo assembly and comparative analyses of mitochondrial genomes in Piperales. Genome Biology and Evolution 15:evad041

doi: 10.1093/gbe/evad041
[23]

Liu F, Fan W, Yang JB, Xiang CL, Mower JP, et al. 2020. Episodic and guanine-cytosine-biased bursts of intragenomic and interspecific synonymous divergence in Ajugoideae (Lamiaceae) mitogenomes. New Phytologist 228:1107−1114

doi: 10.1111/nph.16753
[24]

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
[25]

Albach DC, Meudt HM, Oxelman B. 2005. Piecing together the "new" Plantaginaceae. American Journal of Botany 92:297−315

doi: 10.3732/ajb.92.2.297
[26]

Bräuchler C, Meimberg H, Heubl G. 2004. Molecular phylogeny of the genera Digitalis L. and Isoplexis (Lindley) Loudon (Veronicaceae) based on ITS- and trnL-F sequences. Plant Systematics and Evolution 248:111−128

doi: 10.1007/s00606-004-0145-z
[27]

Sales E, Müller-Uri F, Nebauer SG, Segura J, Kreis W, et al. 2011. Digitalis. In Wild Crop Relatives: Genomic and Breeding Resources: Plantation and Ornamental Crops, ed. Kole C. Berlin, Heidelberg: Springer. pp. 73−112 doi: https://doi.org/10.1007/978-3-642-21201-7_5
[28]

Kreis W. 2017. The foxgloves (Digitalis) revisited. Planta Medica 83:962−976

doi: 10.1055/s-0043-111240
[29]

Herl V, Albach DC, Müller-Uri F, Bräuchler C, Heubl G, et al. 2008. Using progesterone 5β-reductase, a gene encoding a key enzyme in the cardenolide biosynthesis, to infer the phylogeny of the genus Digitalis. Plant Systematics and Evolution 271:65−78

doi: 10.1007/s00606-007-0616-0
[30]

Hunter ES, Fo S, Literman R, Uva RH, Wolny JL, et al. 2025. From WGS to gels: development and testing of PCR primers targeting toxic Digitalis in support of food safety. Applications in Plant Science 13:e70013

doi: 10.1002/aps3.70013
[31]

Hunter ES, Literman R, Handy SM. 2021. Utilizing big data to identify tiny toxic components: Digitalis. Foods 10:1794

doi: 10.3390/foods10081794
[32]

Zhang N, Ramachandran P, Wen J, Duke JA, Metzman H, et al. 2017. Development of a reference standard library of chloroplast genome sequences, GenomeTrakrCP. Planta Medica 83:1420−1430

doi: 10.1055/s-0043-113449
[33]

Zhao F, Liu B, Liu S, Min DZ, Zhang T, et al. 2023. Disentangling a 40-year-old taxonomic puzzle: the phylogenetic position of Mimulicalyx (Lamiales). Botanical Journal of the Linnean Society 201:135−153

doi: 10.1093/botlinnean/boac033
[34]

Mower JP, Hanley L, Wolff K, Pabón-Mora N, González F. 2021. Complete mitogenomes of two Aragoa species and phylogeny of Plantagineae (Plantaginaceae, Lamiales) using mitochondrial genes and the nuclear ribosomal RNA repeat. Plants 10:2673

doi: 10.3390/plants10122673
[35]

Huang X, Wang J, Aluru S, Yang SP, Hillier L. 2003. PCAP: a whole-genome assembly program. Genome Research 13:2164−2170

doi: 10.1101/gr.1390403
[36]

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19:455−477

doi: 10.1089/cmb.2012.0021
[37]

Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18:821−829

doi: 10.1101/gr.074492.107
[38]

Sigmon BA, Adams RP, Mower JP. 2017. Complete chloroplast genome sequencing of vetiver grass (Chrysopogon zizanioides) identifies markers that distinguish the non-fertile 'Sunshine' cultivar from other accessions. Industrial Crops and Products 108:629−635

doi: 10.1016/j.indcrop.2017.07.029
[39]

Mower JP, Ma PF, Grewe F, Taylor A, Michael TP, et al. 2019. Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat. New Phytologist 222:1061−1075

doi: 10.1111/nph.15650
[40]

Chan PP, Lin BY, Mak AJ, Lowe TM. 2021. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Research 49:9077−9096

doi: 10.1093/nar/gkab688
[41]

Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, et al. 2017. GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Research 45:W6−W11

doi: 10.1093/nar/gkx391
[42]

Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30:772−780

doi: 10.1093/molbev/mst010
[43]

Vaidya G, Lohman DJ, Meier R. 2011. SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics 27:171−180

doi: 10.1111/j.1096-0031.2010.00329.x
[44]

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 37:1530−1534

doi: 10.1093/molbev/msaa015
[45]

Krzywinski M, Schein J, Birol İ, Connors J, Gascoyne R, et al. 2009. Circos: an information aesthetic for comparative genomics. Genome Research 19:1639−1645

doi: 10.1101/gr.092759.109
[46]

Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17:540−552

doi: 10.1093/oxfordjournals.molbev.a026334
[47]

Lavergne S, Pouchon C, Roquet C, Alberti A, Boleda M, et al. 2025. Towards a comprehensive barcoding and phylogenomic reference for the European arctic–alpine flora. Botany Letters 172:495−507

doi: 10.1080/23818107.2025.2549565
[48]

Warren JM, Sloan DB. 2020. Interchangeable parts: The evolutionarily dynamic tRNA population in plant mitochondria. Mitochondrion 52:144−56

doi: 10.1016/j.mito.2020.03.007
[49]

Qiu YL, Palmer JD. 2004. Many independent origins of trans splicing of a plant mitochondrial group II intron. Journal of Molecular Evolution 59:80−89

doi: 10.1007/s00239-004-2606-y
[50]

Guo W, Zhu A, Fan W, Adams RP, Mower JP. 2020. Extensive shifts from cis- to trans-splicing of gymnosperm mitochondrial introns. Molecular Biology and Evolution 37:1615−1620

doi: 10.1093/molbev/msaa029
[51]

Mower JP, Guo W, Partha R, Fan W, Levsen N, et al. 2021. Plastomes from tribe Plantagineae (Plantaginaceae) reveal infrageneric structural synapormorphies and localized hypermutation for Plantago and functional loss of ndh genes from Littorella. Molecular Phylogenetics and Evolution 162:107217

doi: 10.1016/j.ympev.2021.107217
[52]

Xie P, Tang L, Luo Y, Liu C, Yan H. 2023. Plastid phylogenomic insights into the inter-tribal relationships of Plantaginaceae. Biology 12:263

doi: 10.3390/biology12020263
[53]

Ha YH, Kim SC, Kim TH, Gil HY. 2025. The complete chloroplast genome sequence of Pseudolysimachion kiusianum var. diamantiacum (Plantaginaceae). Journal of Asia-Pacific Biodiversity 18:499−503

doi: 10.1016/j.japb.2024.10.008
[54]

Wang J, Kan S, Kong J, Nie L, Fan W, et al. 2024. Accumulation of large lineage-specific repeats coincides with sequence acceleration and structural rearrangement in Plantago plastomes. Genome Biology and Evolution 16:evae177

doi: 10.1093/gbe/evae177
[55]

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 35:2773−2785

doi: 10.1093/molbev/msy176
[56]

Alverson AJ, Rice DW, Dickinson S, Barry K, Palmer JD. 2011. Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber. Plant Cell 23:2499−2513

doi: 10.1105/tpc.111.087189
[57]

Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, et al. 2012. Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biology 10:e1001241

doi: 10.1371/journal.pbio.1001241
[58]

Yu R, Zhi X, Ceriotti LF, Skippington E, Rice DW, et al. 2025. A record-setting mitogenome in the holoparasitic plant Balanophora yakushimensis accompanied by exceptional loss of organellar DNA repair and recombination genes. BMC Biology 23:344

doi: 10.1186/s12915-025-02449-8
[59]

Adams KL, Qiu YL, Stoutemyer M, Palmer JD. 2002. Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proceedings of the National Academy of Sciences of the United States of America 99:9905−9912

doi: 10.3410/f.1008814.111157
[60]

Allen JO, Fauron CM, Minx P, Roark L, Oddiraju S, et al. 2007. Comparisons among two fertile and three male-sterile mitochondrial genomes of maize. Genetics 177:1173−1192

doi: 10.1534/genetics.107.073312
[61]

Darracq A, Varré JS, Maréchal-Drouard L, Courseaux A, Castric V, et al. 2011. Structural and content diversity of mitochondrial genome in beet: a comparative genomic analysis. Genome Biology and Evolution 3:723−736

doi: 10.1093/gbe/evr042
[62]

Fischer A, Dotzek J, Walther D, Greiner S. 2022. Graph-based models of the Oenothera mitochondrial genome capture the enormous complexity of higher plant mitochondrial DNA organization. NAR Genomics and Bioinformatics 4:lqac027

doi: 10.1093/nargab/lqac027
[63]

Tu XD, Xin YX, Fu HH, Zhou CY, Liu QL, et al. 2024. The complete mitochondrial genome of Castanopsis carlesii and Castanea henryi reveals the rearrangement and size differences of mitochondrial DNA molecules. BMC Plant Biology 24:988

doi: 10.1186/s12870-024-05618-z
[64]

Kozik A, Rowan BA, Lavelle D, Berke L, Schranz ME, et al. 2019. The alternative reality of plant mitochondrial DNA: one ring does not rule them all. PLoS Genetics 15:e1008373

doi: 10.1371/journal.pgen.1008373