[1] |
Roger AJ, Muñoz-Gómez SA, Kamikawa R. 2017. The origin and diversification of mitochondria. Current Biology 27(21):R1177−R1192 doi: 10.1016/j.cub.2017.09.015 |
[2] |
Dyall SD, Brown MT, Johnson PJ. 2004. Ancient invasions: from endosymbionts to organelles. Science 304:253−57 doi: 10.1126/science.1094884 |
[3] |
Yu SB, Pekkurnaz G. 2018. Mechanisms orchestrating mitochondrial dynamics for energy homeostasis. Journal of Molecular Biology 430:3922−41 doi: 10.1016/j.jmb.2018.07.027 |
[4] |
van Loo G, Saelens X, van Gurp M, MacFarlane M, Martin SJ, et al. 2002. The role of mitochondrial factors in apoptosis: a Russian roulette with more than one bullet. Cell Death & Differentiation 9:1031−42 doi: 10.1038/sj.cdd.4401088 |
[5] |
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 |
[6] |
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 |
[7] |
Han F, Qu Y, Chen Y, Xu LA, Bi C. 2022. Assembly and comparative analysis of the complete mitochondrial genome of Salix wilsonii using PacBio HiFi sequencing. Frontiers in Plant Science 13:1031769 doi: 10.3389/fpls.2022.1031769 |
[8] |
Wang XD, Xu CY, Zheng YJ, Wu YF, Zhang YT, et al. 2022. Chromosome-level genome assembly and resequencing of camphor tree (Cinnamomum camphora) provides insight into phylogeny and diversification of terpenoid and triglyceride biosynthesis of Cinnamomum. Horticulture Research 9:uhac216 doi: 10.1093/hr/uhac216 |
[9] |
Morley SA, Nielsen BL. 2017. Plant mitochondrial DNA. Frontiers in Bioscience-Landmark (FBL) 22:1023−32 doi: 10.2741/4531 |
[10] |
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 |
[11] |
Møller IM, Rasmusson AG, Van Aken O. 2021. Plant mitochondria – past, present and future. The Plant Journal 108:912−59 doi: 10.1111/tpj.15495 |
[12] |
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−E24 doi: 10.1073/pnas.1504491112 |
[13] |
Putintseva YA, Bondar EI, Simonov EP, Sharov VV, Oreshkova NV, et al. 2020. Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome. BMC Genomics 21:654 doi: 10.1186/s12864-020-07061-4 |
[14] |
Bi C, Qu Y, Hou J, Wu K, Ye N, et al. 2022. Deciphering the Multi-Chromosomal Mitochondrial Genome of Populus simonii. Frontiers in Plant Science 13:914635 doi: 10.3389/fpls.2022.914635 |
[15] |
Logacheva MD, Schelkunov MI, Fesenko AN, Kasianov AS, Penin AA. 2020. Mitochondrial genome of Fagopyrum esculentum and the genetic diversity of extranuclear genomes in buckwheat. Plants 9:618 doi: 10.3390/plants9050618 |
[16] |
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 99:9905−12 doi: 10.1073/pnas.042694899 |
[17] |
Filip E, Skuza L. 2021. Horizontal gene transfer involving chloroplasts. International Journal of Molecular Sciences 22:4484 doi: 10.3390/ijms22094484 |
[18] |
Rodríguez-Moreno L, González VM, Benjak A, Carmen Martí M, Puigdomènech P, et al. 2011. Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin. BMC Genomics 12:424 doi: 10.1186/1471-2164-12-424 |
[19] |
Veltjen E, Testé E, Palmarola Bejerano A, et al. 2022. The evolutionary history of the Caribbean magnolias (Magnoliaceae): Testing species delimitations and biogeographical hypotheses using molecular data. Molecular Phylogenetics and Evolution 167:107359 doi: 10.1016/j.ympev.2021.107359 |
[20] |
Law YW. 1984. A preliminary study on the taxonomy of the family magnoliaceae. Journal of Systematics and Evolution 22(2):89−109 |
[21] |
Taprial S. 2015. A review on phytochemical and pharmacological properties of Michelia champaca Linn. family: Magnoliaceae. International Journal Of Pharmaceutical Sciences And Research 2:430−36 |
[22] |
Shang C, Hu Y, Deng C, Hu K. 2002. Rapid determination of volatile constituents of Michelia alba flowers by gas chromatography-mass spectrometry with solid-phase microextraction. Journal of chromatography. A 942:283−8 doi: 10.1016/S0021-9673(01)01382-6 |
[23] |
Khan MR, Kihara M, Omoloso AD. 2002. Antimicrobial activity of Michelia champaca. Fitoterapia 73:744−48 doi: 10.1016/S0367-326X(02)00248-4 |
[24] |
Cheng KK, Nadri MH, Othman NZ, Rashid SNAA, Lim YC, et al. 2022. Phytochemistry, bioactivities and traditional uses of Michelia × alba. Molecules 27:3450 doi: 10.3390/molecules27113450 |
[25] |
Chericoni S, Testai L, Campeol E, Calderone V, Morelli I, et al. 2004. Vasodilator activity of Michelia figo Spreng (Magnoliaceae) by in vitro functional study. Journal of Ethnopharmacology 91:263−66 doi: 10.1016/j.jep.2003.12.021 |
[26] |
Zhai M. 2020. The complete chloroplast genome sequence of Michelia figo based on landscape design, and a comparative analysis with other Michelia species. Mitochondrial DNA Part B 5:2723−24 doi: 10.1080/23802359.2020.1788446 |
[27] |
Hinsinger DD, Strijk JS. 2017. The chloroplast genome sequence of Michelia alba (Magnoliaceae), an ornamental tree species. Mitochondrial DNA Part B 2:9−10 doi: 10.1080/23802359.2016.1275850 |
[28] |
Li Y, Zhou M, Wang L, Wang J. 2021. The characteristics of the chloroplast genome of the Michelia chartacea (Magnoliaceae). Mitochondrial DNA Part B 6:493−95 doi: 10.1080/23802359.2020.1871432 |
[29] |
Sima Y, Li Y, Yuan X, Wang Y. 2020. The complete chloroplast genome sequence of Michelia chapensis Dandy: an endangered species in China. Mitochondrial DNA Part B 5:1594−95 doi: 10.1080/23802359.2020.1742619 |
[30] |
Arseneau JR, Steeves R, Laflamme M. 2017. Modified low-salt CTAB extraction of high-quality DNA from contaminant-rich tissues. Molecular Ecology Resources 17:686−93 doi: 10.1111/1755-0998.12616 |
[31] |
Shi Q, Tian D, Wang J, Chen A, Miao Y, et al. 2023. Overexpression of miR390b promotes stem elongation and height growth in Populus. Horticulture Research 10:uhac258 doi: 10.1093/hr/uhac258 |
[32] |
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 |
[33] |
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 |
[34] |
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 |
[35] |
Li J, Ni Y, Lu Q, Chen H, Liu C. 2024. PMGA: A plant mitochondrial genome annotator. Plant Communications 00:101191 doi: 10.1016/j.xplc.2024.101191 |
[36] |
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 |
[37] |
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 |
[38] |
Zhang X, Chen H, Ni Y, Wu B, Li J, et al. 2024. Plant mitochondrial genome map (PMGmap): a software tool for the comprehensive visualization of coding, noncoding and genome features of plant mitochondrial genomes. Molecular Ecology Resources 24:e13952 doi: 10.1111/1755-0998.13952 |
[39] |
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 |
[40] |
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 |
[41] |
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, et a l. 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 |
[42] |
Mao J, Wei S, Chen Y, Yang Y, Yin T. 2023. The proposed role of MSL-lncRNAs in causing sex lability of female poplars. Horticulture Research 10:uhad042 doi: 10.1093/hr/uhad042 |
[43] |
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 |
[44] |
Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, et al. 2018. MUMmer4: A fast and versatile genome alignment system. PLOS Computational Biology 14:e1005944 doi: 10.1371/journal.pcbi.1005944 |
[45] |
He W, Yang J, Jing Y, Xu L, Yu K, et al. 2023. NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes. Bioinformatics 39:btad121 doi: 10.1093/bioinformatics/btad121 |
[46] |
Katoh K, Rozewicki J, Yamada KD. 2019. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20:1160−66 doi: 10.1093/bib/bbx108 |
[47] |
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 |
[48] |
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 |
[49] |
Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688−90 doi: 10.1093/bioinformatics/btl446 |
[50] |
Letunic I, Bork P. 2021. Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Research 49:W293−W296 doi: 10.1093/nar/gkab301 |
[51] |
Wu ZQ, Liao XZ, Zhang XN, 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 |
[52] |
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 |
[53] |
Alverson AJ, Wei X, Rice DW, Stern DB, Barry K, et al. 2010. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Molecular Biology and Evolution 27:1436−48 doi: 10.1093/molbev/msq029 |
[54] |
Gualberto JM, Newton KJ. 2017. Plant mitochondrial genomes: dynamics and mechanisms of mutation. Annual Review of Plant Biology 68:225−52 doi: 10.1146/annurev-arplant-043015-112232 |
[55] |
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 |
[56] |
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 |
[57] |
Yu R, Sun C, Zhong Y, Liu Y, Sanchez-Puerta MV, et al. 2022. The minicircular and extremely heteroplasmic mitogenome of the holoparasitic plant Rhopalocnemis phalloides. Current Biology 32:470−479.e5 doi: 10.1016/j.cub.2021.11.053 |
[58] |
Yang H, Ni Y, Zhang X, Li J, Chen H, et al. 2023. The mitochondrial genomes of Panax notoginseng reveal recombination mediated by repeats associated with DNA replication. International Journal of Biological Macromolecules 252:126359 doi: 10.1016/j.ijbiomac.2023.126359 |
[59] |
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 |
[60] |
Sun M, Zhang M, Chen X, Liu Y, Liu B, et al. 2022. Rearrangement and domestication as drivers of Rosaceae mitogenome plasticity. BMC Biology 20:181 doi: 10.1186/s12915-022-01383-3 |
[61] |
Zardoya R. 2020. Recent advances in understanding mitochondrial genome diversity. F1000Research 9:270 doi: 10.12688/f1000research.21490.1 |
[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] |
Mower JP, Sloan DB, Alverson AJ. 2012. Plant mitochondrial genome diversity: The genomics revolution. In Plant Genome Diversity Volume 1: Plant Genomes, their Residents, and their Evolutionary Dynamics, ed. JF Wendel, J Greilhuber, J Dolezel, IJ Leitch: 123-44. Vienna: Springer Vienna. Number of 123-44 pp |
[64] |
Sloan DB, Alverson AJ, Štorchová H, Palmer JD, Taylor DR. 2010. Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia. BMC Evolutionary Biology 10:274 doi: 10.1186/1471-2148-10-274 |
[65] |
Hecht J, Grewe F, Knoop V. 2011. Extreme RNA editing in coding islands and abundant microsatellites in repeat sequences of Selaginella moellendorffii mitochondria: the root of frequent plant mtDNA recombination in early tracheophytes. Genome Biology and Evolution 3:344−58 doi: 10.1093/gbe/evr027 |
[66] |
Regina TMR, Quagliariello C. 2010. Lineage-specific group II intron gains and losses of the mitochondrial rps3 gene in gymnosperms. Plant Physiology and Biochemistry 48:646−54 doi: 10.1016/j.plaphy.2010.05.003 |
[67] |
Timmis JN, Ayliffe MA, Huang CY, Martin W. 2004. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nature Reviews Genetics 5:123−35 doi: 10.1038/nrg1271 |
[68] |
Cheng Y, He X, Priyadarshani SVGN, Wang Y, Ye L, et al. 2021. Assembly and comparative analysis of the complete mitochondrial genome of Suaeda glauca. BMC Genomics 22:167 doi: 10.1186/s12864-021-07490-9 |
[69] |
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 |
[70] |
Zhang T, Fang Y, Wang X, Deng X, Zhang X, et al. 2012. The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: insights into the evolution of plant organellar genomes. PLOS ONE 7:e30531 doi: 10.1371/journal.pone.0030531 |
[71] |
Wang D, Rousseau-Gueutin M, Timmis JN. 2012. Plastid sequences contribute to some plant mitochondrial genes. Molecular Biology and Evolution 29:1707−11 doi: 10.1093/molbev/mss016 |
[72] |
Wang D, Wu YW, Shih AC, Wu CS, Wang YN, et al. 2007. Transfer of Chloroplast Genomic DNA to Mitochondrial Genome Occurred At Least 300 MYA. Molecular Biology and Evolution 24:2040−48 doi: 10.1093/molbev/msm133 |
[73] |
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 |
[74] |
Clifton SW, Minx P, Fauron CMR, Gibson M, Allen JO, et al. 2004. Sequence and Comparative Analysis of the Maize NB Mitochondrial Genome. Plant Physiology 136:3486−503 doi: 10.1104/pp.104.044602 |
[75] |
Nie ZL, Wen J, Azuma H, Qiu YL, Sun H, et al. 2008. Phylogenetic and biogeographic complexity of Magnoliaceae in the Northern Hemisphere inferred from three nuclear data sets. Molecular Phylogenetics and Evolution 48:1027−40 doi: 10.1016/j.ympev.2008.06.004 |
[76] |
Group TAP, 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 |