[1]

Schühly W, Skarbina J, Kunert O, Nandi OI, Bauer R. 2009. Chemical characterization of Magnolia biondii (Flos Magnoliae, Xin Yi). Natural Product Communications 4:231−34

[2]

Wu H, Liu T, Zhang Z, Wang W, Zhu W, et al. 2018. Leaves of Magnolia liliflora Desr. as a high-potential by-product: lignans composition, antioxidant, anti-inflammatory, anti-phytopathogenic fungal and phytotoxic activities. Industrial Crops And Products 125:416−24

doi: 10.1016/j.indcrop.2018.09.023
[3]

Liang Z. 2011. Chemical analysis of Magnolia liliflora essential oil and its pharmacological function in nursing pregnant women suffering from decubitus ulcer. Journal of Medicinal Plants Research 5:2283−88

[4]

Bajpai VK, Rahman A, Dung NT, Huh MK, Kang SC. 2008. In vitro inhibition of food spoilage and foodborne pathogenic bacteria by essential oil and leaf extracts of Magnolia liliflora Desr. Journal of Food Science 73:M314−M320

doi: 10.1111/j.1750-3841.2008.00841.x
[5]

Shen Z, Ding X, Cheng J, Wu F, Yin H, et al. 2022. Phylogenetic studies of magnoliids: advances and perspectives. Frontiers in Plant Science 13:1100302

doi: 10.3389/fpls.2022.1100302
[6]

The Angiosperm Phylogeny Group, Chase MW, Christenhusz MJM, Fay MF, Byng JW, et al. 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Botanical Journal of the Linnean Society 181:1−20

doi: 10.1111/boj.12385
[7]

Shen Y, Chen K, Gu C, Zheng S, Ma L. 2018. Comparative and phylogenetic analyses of 26 Magnoliaceae species based on complete chloroplast genome sequences. Canadian Journal of Forest Resarch 48:1456−69

doi: 10.1139/cjfr-2018-0296
[8]

Wang Z, Kang M, Li J, Zhang Z, Wang Y, et al. 2022. Genomic evidence for homoploid hybrid speciation between ancestors of two different genera. Nature Communication 13:1987

doi: 10.1038/s41467-022-29643-4
[9]

Sun N, Han F, Wang S, Shen F, Liu W, et al. 2024. Comprehensive analysis of the Lycopodium japonicum mitogenome reveals abundant tRNA genes and cis-spliced introns in Lycopodiaceae species. Frontiers in Plant Science 15:1446015

doi: 10.3389/fpls.2024.1446015
[10]

Ma Q, Wang Y, Li S, Wen J, Zhu L, et al. 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 Biology 22:29

doi: 10.1186/s12870-021-03416-5
[11]

Ye N, Wang X, Li J, Bi C, Xu Y, et al. 2017. Assembly and comparative analysis of complete mitochondrial genome sequence of an economic plant Salix suchowensis. PeerJ 5:e3148

doi: 10.7717/peerj.3148
[12]

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 29:754−69

doi: 10.1016/j.tplants.2023.12.014
[13]

Oda K, Kohchi T, Ohyama K. 1992. Mitochondrial DNA of Marchantia polymorpha as a single circular form with no incorporation of foreign DNA. Bioscience, Biotechnology, and Biochemistry 56:132−35

doi: 10.1271/bbb.56.132
[14]

Smith DR, Keeling PJ. 2013. Gene conversion shapes linear mitochondrial genome architecture. Genome Biology and Evolution 5:905−12

doi: 10.1093/gbe/evt059
[15]

Xiang Q, Tang J, Yu J, Smith DR, Zhu Y, et al. 2022. The evolution of extremely diverged plastomes in Selaginellaceae (lycophyte) is driven by repeat patterns and the underlying DNA maintenance machinery. The Plant Journal 111:768−84

doi: 10.1111/tpj.15851
[16]

Skippington E, Barkman TJ, Rice DW, Palmer JD. 2015. Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes. Proceedings of the National Academy of Sciences of the United States of America 112:E3515−E3524

doi: 10.1073/pnas.1504491112
[17]

Huang K, Xu W, Hu H, Jiang X, Sun L, et al. 2024. The mitochondrial genome of Cathaya argyrophylla reaches 18.99 Mb: analysis of super-large mitochondrial genomes in pinaceae. arXiv 00:2410.07006

doi: 10.48550/arXiv.2410.07006
[18]

Guo W, Grewe F, Fan W, Young GJ, Knoop V, et al. 2016. Ginkgo and Welwitschia mitogenomes reveal extreme contrasts in gymnosperm mitochondrial evolution. Molecular Biology and Evolution 33:1448−60

doi: 10.1093/molbev/msw024
[19]

Zardoya R. 2020. Recent advances in understanding mitochondrial genome diversity. F1000Research 9:270

doi: 10.12688/f1000research.21490.1
[20]

Shearman JR, Sonthirod C, Naktang C, Pootakham W, Yoocha T, et al. 2016. The two chromosomes of the mitochondrial genome of a sugarcane cultivar: assembly and recombination analysis using long PacBio reads. Scientific Reports 6:31533

doi: 10.1038/srep31533
[21]

Dong S, Zhao C, Chen F, Liu Y, Zhang S, et al. 2018. The complete mitochondrial genome of the early flowering plant Nymphaea colorata is highly repetitive with low recombination. BMC Genomics 19:614

doi: 10.1186/s12864-018-4991-4
[22]

Wang Y, Cui G, He K, Xu K, Liu W, et al. 2024. Assembly and comparative analysis of the complete mitochondrial genome of Ilex rotunda Thunb. Forests 15:1117

doi: 10.3390/f15071117
[23]

Kraft F, Kurth I. 2020. Long-read sequencing to understand genome biology and cell function. International Journal Of Biochemistry & Cell Biology 126:105799

doi: 10.1016/j.biocel.2020.105799
[24]

Lu N, Qiao Y, An P, Luo J, Bi C, et al. 2023. Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data. Briefings in Bioinformatics 24:bbad275

doi: 10.1093/bib/bbad275
[25]

Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, et al. 2019. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nature Biotechnology 37:1155−62

doi: 10.1038/s41587-019-0217-9
[26]

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
[27]

Zhou C, Brown M, Blaxter M, The Darwin Tree of Life Project Consortium, McCarthy SA, et al. 2024. Oatk: a de novo assembly tool for complex plant organelle genomes. bioRxiv Preprint

doi: 10.1101/2024.10.23.619857
[28]

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
[29]

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 49:9077−96

doi: 10.1093/nar/gkab688
[30]

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
[31]

Greiner S, Lehwark P, Bock R. 2019. OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research 47:W59−W64

doi: 10.1093/nar/gkz238
[32]

Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for bigger datasets. Molecular Biology and Evolution 33:1870−74

doi: 10.1093/molbev/msw054
[33]

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
[34]

Jia Y, Bai J, Liu M, Jiang Z, Wu Y, et al. 2019. Transcriptome analysis of the endangered Notopterygium incisum: cold-tolerance gene discovery and identification of EST-SSR and SNP markers. Plant Diversity 41:1−6

doi: 10.1016/j.pld.2019.01.001
[35]

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
[36]

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
[37]

Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, et al. 2020. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant 13:1194−202

doi: 10.1016/j.molp.2020.06.009
[38]

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(1):481

doi: 10.1186/s12864-022-08706-2
[39]

Liu Y, Lu N, Bi C, Han T, Guo Z, et al. 2021. FEM: mining biological meaning from cell level in single-cell RNA sequencing data. PeerJ 9:e12570

doi: 10.7717/peerj.12570
[40]

Yan J, Zhang Q, Yin P. 2018. RNA editing machinery in plant organelles. Science China Life Sciences 61:162−69

doi: 10.1007/s11427-017-9170-3
[41]

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
[42]

Robinson JT, Thorvaldsdottir H, Turner D, Mesirov JP. 2023. igv. js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). Bioinformatics 39:btac830

doi: 10.1093/bioinformatics/btac830
[43]

Hao Z, Lv D, Ge Y, Shi J, Weijers D, et al. 2020. RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms. PeerJ Computer Science 6:e251

doi: 10.7717/peerj-cs.251
[44]

Löytynoja A. 2021. Phylogeny-aware alignment with PRANK and PAGAN. Methods in Molecular Biology 2231:17−37

doi: 10.1007/978-1-0716-1036-7_2
[45]

Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32:268−74

doi: 10.1093/molbev/msu300
[46]

Letunic I, Bork P. 2019. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Research 47:W256−W259

doi: 10.1093/nar/gkz239
[47]

Sun L, Jiang Z, Wan X, Zou X, Yao X, et al. 2020. The complete chloroplast genome of Magnolia polytepala: comparative analyses offer implication for genetics and phylogeny of Yulania. Gene 736:144410

doi: 10.1016/j.gene.2020.144410
[48]

Hu H, Dong B, Fan X, Wang M, Wang T, et al. 2023. Mutational bias and natural selection driving the synonymous codon usage of single-exon genes in rice (Oryza sativa L.). Rice 16:11

doi: 10.1186/s12284-023-00627-2
[49]

Labella AL, Opulente DA, Steenwyk JL, Hittinger CT, Rokas A. 2019. Variation and selection on codon usage bias across an entire subphylum. PLoS Genetics 15:e1008304

doi: 10.1371/journal.pgen.1008304
[50]

Almutairi MM. 2021. Analysis of chromosomes and nucleotides in rice to predict gene expression through codon usage pattern. Saudi Journal of Biological Sciences 28:4569−74

doi: 10.1016/j.sjbs.2021.04.059
[51]

Mohasses FC, Solouki M, Ghareyazie B, Fahmideh L, Mohsenpour M. 2020. Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study. PLoS One 15:e0237334

doi: 10.1371/journal.pone.0237334
[52]

Wang X, Chen H, Yang D, Liu C. 2018. Diversity of mitochondrial plastid DNAs (MTPTs) in seed plants. Mitochondrial DNA Part A 29:635−42

doi: 10.1080/24701394.2017.1334772
[53]

Gui S, Wu Z, Zhang H, Zheng Y, Zhu Z, et al. 2016. The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features. Scientific Reports 6:30158

doi: 10.1038/srep30158
[54]

Sloan DB, Wu Z. 2014. History of plastid DNA insertions reveals weak deletion and AT mutation biases in angiosperm mitochondrial genomes. Genome Biology and Evolution 6:3210−21

doi: 10.1093/gbe/evu253
[55]

Lukeš J, Kaur B, Speijer D. 2021. RNA editing in mitochondria and plastids: weird and widespread. Trends in Genetics 37:99−102

doi: 10.1016/j.tig.2020.10.004
[56]

Dong S, Chen L, Liu Y, Wang Y, Zhang S, et al. 2020. The draft mitochondrial genome of Magnolia biondii and mitochondrial phylogenomics of angiosperms. PLoS One 15:e0231020

doi: 10.1371/journal.pone.0231020
[57]

Wang J, Zou Y, Mower JP, Reeve W, Wu Z. 2024. Rethinking the mutation hypotheses of plant organellar DNA. Genomics Communications 1(1):e003

doi: 10.48130/gcomm-0024-0003
[58]

Bi C, Xu Y, Ye Q, Yin T, Ye N. 2016. Genome-wide identification and characterization of WRKY gene family in Salix suchowensis. PeerJ 4:e2437

doi: 10.7717/peerj.2437
[59]

Wynn EL, Christensen AC. 2019. Repeats of unusual size in plant mitochondrial genomes: identification, incidence and evolution. G3 Genes|Genomes|Genetics 9:549−59

doi: 10.1534/g3.118.200948
[60]

Xiong Y, Lei X, Bai S, Xiong Y, Liu W, et al. 2021. Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L. BMC Plant Biology 21:3

doi: 10.1186/s12870-020-02770-0
[61]

Bi C, Paterson AH, Wang X, Xu Y, Wu D, et al. 2016. Analysis of the complete mitochondrial genome sequence of the diploid cotton Gossypium raimondii by comparative genomics approaches. BioMed Research International 2019:5040598

doi: 10.1155/2016/5040598
[62]

Richardson AO, Rice DW, Young GJ, Alverson AJ, Palmer JD. 2013. The "fossilized" mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate. BMC Biology 11:29

doi: 10.1186/1741-7007-11-29
[63]

Rice DW, Alverson AJ, Richardson AO, Young GJ, Sanchez-Puerta MV, et al. 2013. Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Science 342:1468−73

doi: 10.1126/science.1246275
[64]

Wang Y, Sun N, Shi W, Ma Q, Sun L, et al. 2023. Assembly and comparative analysis of the complete mitochondrial genome of Ilex macrocarpa. Forests 14:2372

doi: 10.3390/f14122372
[65]

Chen X, Zhang L, Huang Y, Zhao F. 2020. Mitochondrial genome of Salix cardiophylla and its implications for infrageneric division of the genus of Salix. Mitochondrial DNA Part B 5:3485−86

doi: 10.1080/23802359.2020.1827065
[66]

Liu M, Liu F, Chen N, Melton JT, Luo M. 2020. Mitochondrial genomes and phylogenomic analysis of Ulva lactuca Linnaeus (Ulvophyceae, Chlorophyta). Mitochondrial DNA Part B 5:1638−39

doi: 10.1080/23802359.2020.1745712
[67]

Li F, Yang A, Lv J, Gong D, Sun Y. 2016. The complete mitochondrial genome sequence of Sua-type cytoplasmic male sterility of tobacco (Nicotiana tabacum). Mitochondrial DNA Part A 27:2929−30

doi: 10.3109/19401736.2015.1060445
[68]

Bi C, Sun N, Han F, Xu K, Yang Y, et al. 2024. The first mitogenome of Lauraceae (Cinnamomum chekiangense). Plant Diversity 46:144−48

doi: 10.1016/j.pld.2023.11.001
[69]

Wu Z, Liao X, Zhang X, Tembrock LR, Broz A. 2022. Genomic architectural variation of plant mitochondria—a review of multichromosomal structuring. Journal of Systematics and Evolution 60:160−68

doi: 10.1111/jse.12655
[70]

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
[71]

Alverson AJ, Rice DW, Dickinson S, Barry K, Palmer JD. 2011. Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber. The Plant Cell 23:2499−513

doi: 10.1105/tpc.111.087189
[72]

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 37:1615−20

doi: 10.1093/molbev/msaa029
[73]

Mower JP. 2020. Variation in protein gene and intron content among land plant mitogenomes. Mitochondrion 53:203−13

doi: 10.1016/j.mito.2020.06.002
[74]

Yu R, Sun C, Liu Y, Zhou R. 2021. Shifts from cis -to trans-splicing of five mitochondrial introns in Tolypanthus maclurei. PeerJ 9:e12260

doi: 10.7717/peerj.12260
[75]

Sloan DB, Warren JM, Williams AM, Wu Z, Abdel-Ghany SE, et al. 2018. Cytonuclear integration and co-evolution. Nature Reviews Genetics 19:635−48

doi: 10.1038/s41576-018-0035-9
[76]

He P, Huang S, Xiao G, Zhang Y, Yu J. 2016. Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis. BMC Plant Biology 16:257

doi: 10.1186/s12870-016-0944-8
[77]

Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, et al. 2002. The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants. Molecular Genetics and Genomics 268:434−45

doi: 10.1007/s00438-002-0767-1
[78]

Yu J, Chen Q, Ren J, Yang Y, Wang J, et al. 2015. Analysis of the multi-copied genes and the impact of the redundant protein coding sequences on gene annotation in prokaryotic genomes. Journal of Theoretical Biology 376:8−14

doi: 10.1016/j.jtbi.2015.04.002
[79]

De Abreu VAC, Alves RM, Silva SR, Ferro JA, Domingues DS, et al. 2023. Comparative analyses of Theobroma cacao and T. grandiflorum mitogenomes reveal conserved gene content embedded within complex and plastic structures. Gene 849:146904

doi: 10.1016/j.gene.2022.146904
[80]

Guo X, Fang D, Sahu SK, Yang S, Guang X, et al. 2021. Chloranthus genome provides insights into the early diversification of angiosperms. Nature Communications 12:6930

doi: 10.1038/s41467-021-26922-4
[81]

Hu H, Sun P, Yang Y, Ma J, Liu J. 2023. Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets. Journal of Integrative Plant Biology 65:1479−89

doi: 10.1111/jipb.13455