| [1] |
Yang J, Dierckxsens N, Bai M, Guo Y. 2023. Multichromosomal mitochondrial genome of Paphiopedilum micranthum: compact and fragmented genome, and rampant intracellular gene transfer. International Journal of Molecular Sciences 24(4):3976 doi: 10.3390/ijms24043976 |
| [2] |
Yang Q. 2018. Study on diversity of Orchidaceae mycorrhizal fungi and its influence on orchid. Thesis. Chinese Academy of Forestry, China. pp. 81–127 |
| [3] |
Sinn BT, Barrett CF. 2020. Ancient mitochondrial gene transfer between fungi and the orchids. Molecular Biology and Evolution 37(1):44−57 doi: 10.1093/molbev/msz198 |
| [4] |
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(1):160−68 doi: 10.1111/jse.12655 |
| [5] |
Shen B, Shen A, Liu L, Tan Y, Li S, et al. 2024. Assembly and comparative analysis of the complete multichromosomal mitochondrial genome of Cymbidium ensifolium, an orchid of high economic and ornamental value. BMC Plant Biology 24(1):255 doi: 10.1186/s12870-024-04962-4 |
| [6] |
Christensen AC. 2013. Plant mitochondrial genome evolution can be explained by DNA repair mechanisms. Genome Biology and Evolution 5(6):1079−86 doi: 10.1093/gbe/evt069 |
| [7] |
Nieuwenhuis M, Groeneveld J, Aanen DK. 2023. Horizontal transfer of tRNA genes to mitochondrial plasmids facilitates gene loss from fungal mitochondrial DNA. Current Genetics 69(1):55−65 doi: 10.1007/s00294-022-01259-7 |
| [8] |
Hou Z, Wang M, Jiang Y, Xue Q, Liu W, et al. 2024. Mitochondrial genome insights into the spatio-temporal distribution and genetic diversity of Dendrobium hancockii Rolfe (Orchidaceae). Frontiers in Plant Science 15:1469267 doi: 10.3389/fpls.2024.1469267 |
| [9] |
Wang M, Hou Z, Li C, Yang J, Niu Z, et al. 2023. Rapid structural evolution of Dendrobium mitogenomes and mito-nuclear phylogeny discordances in Dendrobium (Orchidaceae). Journal of Systematics and Evolution 61(5):790−805 doi: 10.1111/jse.12912 |
| [10] |
Wang L, Liu X, Wang Y, Ming X, Qi J, et al. 2024. Comparative analysis of the mitochondrial genomes of four Dendrobium species (Orchidaceae) reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing. Frontiers in Plant Science 15:1429545 doi: 10.3389/fpls.2024.1429545 |
| [11] |
Tong W, Yu D, Zhu X, Le Z, Chen H, et al. 2024. The whole mitochondrial genome sequence of Dendrobium loddigesii rolfe, an endangered orchid species in China, reveals a complex multi-chromosome structure. Genes 15(7):834 doi: 10.3390/genes15070834 |
| [12] |
Liberatore KL, Dukowic-Schulze S, Miller ME, Chen C, Kianian SF. 2016. The role of mitochondria in plant development and stress tolerance. Free Radical Biology and Medicine 100:238−56 doi: 10.1016/j.freeradbiomed.2016.03.033 |
| [13] |
Omelchenko DO, Makarenko MS, Kasianov AS, Schelkunov MI, Logacheva MD, et al. 2020. Assembly and analysis of the complete mitochondrial genome of Capsella bursa-pastoris. Plants 9(4):469 doi: 10.3390/plants9040469 |
| [14] |
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 |
| [15] |
Dombrovska O, Qiu Y. 2004. Distribution of introns in the mitochondrial gene nad1 in land plants: phylogenetic and molecular evolutionary implications. Molecular Phylogenetics and Evolution 32(1):246−63 doi: 10.1016/j.ympev.2003.12.013 |
| [16] |
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(24):9054−58 doi: 10.1073/pnas.84.24.9054 |
| [17] |
Mower JP, Touzet P, Gummow JS, Delph LF, Palmer JD. 2007. Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evolutionary Biology 7:135 doi: 10.1186/1471-2148-7-135 |
| [18] |
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(11):2773−85 doi: 10.1093/molbev/msy176 |
| [19] |
Zhang Y, Zhang G, Zhang D, Liu X, Xu X, et al. 2021. Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution. Horticulture Research 8:183 doi: 10.1038/s41438-021-00621-z |
| [20] |
Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114−20 doi: 10.1093/bioinformatics/btu170 |
| [21] |
Kolmogorov M, Yuan J, Lin Y, Pevzner PA. 2019. Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology 37(5):540−46 doi: 10.1038/s41587-019-0072-8 |
| [22] |
Wick RR, Schultz MB, Zobel J, Holt KE. 2015. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 31(20):3350−52 doi: 10.1093/bioinformatics/btv383 |
| [23] |
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754−60 doi: 10.1093/bioinformatics/btp324 |
| [24] |
Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Computational Biology 13(6):e1005595 doi: 10.1371/journal.pcbi.1005595 |
| [25] |
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 |
| [26] |
Shan Y, Li J, Duan X, Zhang X, Yu J. 2024. Elucidating the multichromosomal structure within the Brasenia schreberi mitochondrial genome through assembly and analysis. BMC Genomics 25(1):422 doi: 10.1186/s12864-024-10331-0 |
| [27] |
Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25(5):955−64 doi: 10.1093/nar/25.5.955 |
| [28] |
Chen Y, Ye W, Zhang Y, Xu Y. 2015. High speed BLASTN: an accelerated MegaBLAST search tool. Nucleic Acids Research 43(16):7762−68 doi: 10.1093/nar/gkv784 |
| [29] |
Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, et al. 2002. Apollo: a sequence annotation editor. Genome Biology 3(12):research0082.1 doi: 10.1186/gb-2002-3-12-research0082 |
| [30] |
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(1):348−55 doi: 10.1111/1755-0998.13096 |
| [31] |
Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology Evolution 33(7):1870−74 doi: 10.1093/molbev/msw054 |
| [32] |
Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research 27(2):573−80 doi: 10.1093/nar/27.2.573 |
| [33] |
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(22):4633−42 doi: 10.1093/nar/29.22.4633 |
| [34] |
Beier S, Thiel T, Münch T, Scholz U, Mascher M. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics 33(16):2583−85 doi: 10.1093/bioinformatics/btx198 |
| [35] |
Zhang H, Meltzer P, Davis S. 2013. RCircos: an R package for Circos 2D track plots. BMC Bioinformatics 14(1):244 doi: 10.1186/1471-2105-14-244 |
| [36] |
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 |
| [37] |
Shi L, Chen H, Jiang M, Wang L, Wu X, et al. 2019. CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Research 47(W1):W65−W73 doi: 10.1093/nar/gkz345 |
| [38] |
Liu S, Ni Y, Li J, Zhang X, Yang H, et al. 2023. CPGView: a package for visualizing detailed chloroplast genome structures. Molecular Ecology Resources 23(3):694−704 doi: 10.1111/1755-0998.13729 |
| [39] |
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 |
| [40] |
Valencia-D J, Neubig KM, Clark DP. 2023. The origin and fate of fungal mitochondrial horizontal gene transferred sequences in orchids (Orchidaceae). Botanical Journal of the Linnean Society 203(2):162−79 doi: 10.1093/botlinnean/boad019 |
| [41] |
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(7):e49 doi: 10.1093/nar/gkr1293 |
| [42] |
Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30(4):772−80 doi: 10.1093/molbev/mst010 |
| [43] |
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(1):268−74 doi: 10.1093/molbev/msu300 |
| [44] |
Letunic I, Bork P. 2019. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Research 47(W1):W256−W259 doi: 10.1093/nar/gkz239 |
| [45] |
Zimmer M, Lückemann G, Lang BF, Wolf K. 1984. The mitochondrial genome of the fission yeast Schizosaccharomyces pombe: 3. Gene mapping in strain EF1 (CBS 356) and analysis of hybrids between the strains EF1 and ade7–50h. Molecular and General Genetics MGG 196:473−81 doi: 10.1007/BF00436195 |
| [46] |
Cummings DJ, McNally KL, Domenico JM, Matsuura ET. 1990. The complete DNA sequence of the mitochondrial genome of Podospora anserina. Current Genetics 17:375−402 doi: 10.1007/BF00334517 |
| [47] |
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(1):e1001241 doi: 10.1371/journal.pbio.1001241 |
| [48] |
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(27):E3515−E3524 doi: 10.1073/pnas.1504491112 |
| [49] |
Yuan Y, Jin X, Liu J, Zhao X, Zhou J, et al. 2018. The Gastrodia elata genome provides insights into plant adaptation to heterotrophy. Nature Communications 9(1):1615 doi: 10.1038/s41467-018-03423-5 |
| [50] |
Zhao Z, Li Y, Zhai J, Liu Z, Li M. 2024. Organelle genomes of Epipogium roseum provide insight into the evolution of mycoheterotrophic orchids. International Journal of Molecular Sciences 25(3):1578 doi: 10.3390/ijms25031578 |
| [51] |
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 |
| [52] |
Mower JP, Bonen L. 2009. Ribosomal protein L10 is encoded in the mitochondrial genome of many land plants and green algae. BMC Evolutionary Biology 9:265 doi: 10.1186/1471-2148-9-265 |
| [53] |
Zhang K, Wang Y, Zhang X, Han Z, Shan X. 2022. Deciphering the mitochondrial genome of Hemerocallis citrina (Asphodelaceae) using a combined assembly and comparative genomic strategy. Frontiers in Plant Science 13:1051221 doi: 10.3389/fpls.2022.1051221 |
| [54] |
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. 2009. The B73 maize genome: complexity, diversity, and dynamics. Science 326(5956):1112−15 doi: 10.1126/science.1178534 |
| [55] |
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 |
| [56] |
Yang Z, Ni Y, Lin Z, Yang L, Chen G, et al. 2022. De novo assembly of the complete mitochondrial genome of sweet potato (Ipomoea batatas [L.] Lam) revealed the existence of homologous conformations generated by the repeat-mediated recombination. BMC Plant Biology 22(1):285 doi: 10.1186/s12870-022-03665-y |
| [57] |
Liu D, Guo H, Zhu J, Qu K, Chen Y, et al. 2022. Complex physical structure of complete mitochondrial genome of Quercus acutissima (Fagaceae): a significant energy plant. Genes 13(8):1321 doi: 10.3390/genes13081321 |
| [58] |
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(4):e0231020 doi: 10.1371/journal.pone.0231020 |
| [59] |
Jiang M, Ni Y, Li J, Liu C. 2023. Characterisation of the complete mitochondrial genome of Taraxacum mongolicum revealed five repeat-mediated recombinations. Plant Cell Reports 42(4):775−89 doi: 10.1007/s00299-023-02994-y |
| [60] |
Wang D, Wu YW, Shih ACC, 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(9):2040−48 doi: 10.1093/molbev/msm133 |
| [61] |
Wang M, Yu W, Yang J, Hou Z, Li C, et al. 2023. Mitochondrial genome comparison and phylogenetic analysis of Dendrobium (Orchidaceae) based on whole mitogenomes. BMC Plant Biology 23(1):586 doi: 10.1186/s12870-023-04618-9 |
| [62] |
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(6165):1468−73 doi: 10.1126/science.1246275 |
| [63] |
Tang W, Luo C. 2018. Molecular and functional diversity of rna editing in plant mitochondria. Molecular Biotechnology 60(12):935−45 doi: 10.1007/s12033-018-0126-z |
| [64] |
Rieder LE, Savva YA, Reyna MA, Chang YJ, Dorsky JS, et al. 2015. Dynamic response of RNA editing to temperature in Drosophila. BMC Biology 13:1 doi: 10.1186/s12915-014-0111-3 |
| [65] |
Rodrigues NF, da Fonseca GC, Kulcheski FR, Margis R. 2017. Salt stress affects mRNA editing in soybean chloroplasts. Genetics and Molecular Biology 40:200−08 doi: 10.1590/1678-4685-GMB-2016-0055 |
| [66] |
Riemondy KA, Gillen AE, White EA, Bogren LK, Hesselberth JR, et al. 2018. Dynamic temperature-sensitive A-to-I RNA editing in the brain of a heterothermic mammal during hibernation. RNA 24(11):1481−95 doi: 10.1261/rna.066522.118 |
| [67] |
Zhang D, Zhao X, Li Y, Ke S, Yin W, et al. 2022. Advances and prospects of orchid research and industrialization. Horticulture Research 9:uhac220 doi: 10.1093/hr/uhac220 |
| [68] |
Liu Q, Yuan H, Xu J, Cui D, Xiong G, et al. 2023. The mitochondrial genome of the diploid oat Avena longiglumis. BMC Plant Biology 23(1):218 doi: 10.1186/s12870-023-04217-8 |