Adams KL, Palmer JD (2003) Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol 29:380–395. https://doi.org/10.1016/s1055-7903(03)00194-5
Article CAS PubMed Google Scholar
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. Proc Natl Acad Sci USA 99:9905–9912. https://doi.org/10.1073/pnas.042694899
Article CAS PubMed PubMed Central Google Scholar
Chaisson MJ, Tesler G (2012) Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. Bmc Bioinformatics 13. https://doi.org/10.1186/1471-2105-13-238
Chase M, Cameron K, Freudenstein J, Pridgeon A, Salazar G, van den Berg C, Schuiteman A (2015) An updated classification of Orchidaceae. Bot J Linn Soc 177:151–174. https://doi.org/10.1111/boj.12234
Cheng N, Lo YS, Ansari MI, Ho KC, Jeng ST, Lin NS, Dai H (2017) Correlation between mtDNA complexity and mtDNA replication mode in developing cotyledon mitochondria during mung bean seed germination. New Phytol 213:751–763. https://doi.org/10.1111/nph.14158
Article CAS PubMed Google Scholar
Cox A, Abdelnour G, Bennett M, Leitch I (1998) Genome size and karyotype evolution in the slipper orchids (Cypripedioideae: Orchidaceae). Am J Bot 85:681
Article CAS PubMed Google Scholar
Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO et al (2021) Twelve years of SAMtools and BCFtools. Gigascience 10. https://doi.org/10.1093/gigascience/giab008
Dong S, Zhao C, Zhang S, Zhang L, Wu H, Liu H, Zhu R, Jia Y, Goffinet B, Liu Y (2019) Mitochondrial genomes of the early land plant lineage liverworts (Marchantiophyta): conserved genome structure, and ongoing low frequency recombination. BMC Genomics 20:953. https://doi.org/10.1186/s12864-019-6365-y
Article CAS PubMed PubMed Central Google Scholar
Drijber RA, McPherson MR (2021) 12 - Mycorrhizal symbioses. In: Fuhrmann JJ, Zuberer DA (eds) Gentry TJ. Elsevier, Principles and Applications of Soil Microbiology (Third Edition), pp 303–325
Edler D, Klein J, Antonelli A, Silvestro D (2021) raxmlGUI 2.0: a graphical interface and toolkit for phylogenetic analyses using RAxML. Methods Ecol Evol 12:373–377. https://doi.org/10.1111/2041-210x.13512
Gualberto JM, Newton KJ (2017) Plant mitochondrial genomes: dynamics and mechanisms of mutation. In: Merchant SS (ed) Ann Rev Plant Biol 68:225–252
Guisinger MM, Kuehl JV, Boore JL, Jansen RK (2011) Extreme Reconfiguration of Plastid Genomes in the Angiosperm Family Geraniaceae: Rearrangements, Repeats, and Codon Usage. Mol Biol Evol 28:583–600. https://doi.org/10.1093/molbev/msq229
Article CAS PubMed Google Scholar
Guo XL, Hu XD, Li JW, Shao BY, Wang YJ, Wang L et al (2023) The Sapria himalayana genome provides new insights into the lifestyle of endoparasitic plants. BMC Biology 21. https://doi.org/10.1186/s12915-023-01620-3
Jin JJ, Yu WB, Yang JB, Song Y, dePamphilis CW, Yi TS, Li DZ (2020) GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol 21(1):241. https://doi.org/10.1186/s13059-020-02154-5
Article PubMed PubMed Central Google Scholar
Ke S-J et al (2023) Apostasiamitochondrial genome analysis and monocot mitochondria phylogenomics. Int J Mol Sci 24. https://doi.org/10.3390/ijms24097837
Kim YK, Jo S, Cheon SH, Joo MJ, Hong JR, Kwak M, Kim KJ (2020) Plastome evolution and phylogeny of orchidaceae, with 24 new sequences. Front Plant Sci 11:22. https://doi.org/10.3389/fpls.2020.00022
Article CAS PubMed PubMed Central Google Scholar
Kim Y-K, Jo S, Cheon S-H, Hong J-R, Kim K-J (2023) Ancient horizontal gene transfers from plastome to mitogenome of a nonphotosynthetic Orchid, Gastrodia pubilabiata (Epidendroideae, Orchidaceae). Int J Mol Sci 24. https://doi.org/10.3390/ijms241411448
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736. https://doi.org/10.1101/gr.215087.116
Kozik A, Rowan BA, Lavelle D, Berke L, Schranz ME, Michelmore RW, Christensen AC (2019) The alternative reality of plant mitochondrial DNA: one ring does not rule them all. PLoS Genet 15:e1008373. https://doi.org/10.1371/journal.pgen.1008373
Article CAS PubMed PubMed Central Google Scholar
Kubo N, Arimura S-I (2010) Discovery of the rpl10 gene in diverse plant mitochondrial genomes and its probable replacement by the nuclear gene for chloroplast RPL10 in two lineages of angiosperms. DNA Res 17:1–9. https://doi.org/10.1093/dnares/dsp024
Article CAS PubMed Google Scholar
Lane N, Martin W (2010) The energetics of genome complexity. Nature 467: 929–934. Nature 467:929–934. https://doi.org/10.1038/nature09486
Article CAS PubMed Google Scholar
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357-U354. https://doi.org/10.1038/nmeth.1923
Article CAS PubMed PubMed Central Google Scholar
Li YX, Li ZH, Schuiteman A, Chase MW, Li JW, Huang WC, Hidayat A, Wu SS, Jin XH (2019) Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes. Mol Phylogenet Evol 139:06540. https://doi.org/10.1016/j.ympev.2019.106540
Li X, Zhe M, Huang Y, Fan W, Yang J, Zhu A (2023) The evolution of mitochondrial genomes between two Cymbidium sister species: dozens of circular chromosomes and the maintenance and deterioration of genome synteny. Genes 14. https://doi.org/10.3390/genes14040864
Liao M, Zhang JY, Feng Y, Ren ZX, Deng HN, Xu B (2024) Phylogenomic insights into the historical biogeography, character-state evolution, and species diversification rates of Cypripedioideae (Orchidaceae). Mol Phylogenet Evol 199. https://doi.org/10.1016/j.ympev.2024.108138
Lin YX, Li P, Zhang YC, Akhter D, Pan R, Fu Z, Huang M, Li X, Feng YL (2022) Unprecedented organelle genomic variations in morning glories reveal independent evolutionary scenarios of parasitic plants and the diversification of plant mitochondrial complexes. BMC Biol 20. https://doi.org/10.1186/s12915-022-01250-1
Lowe TM, Chan PP (2016) tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44:W54-57. https://doi.org/10.1093/nar/gkw413
Article CAS PubMed PubMed Central Google Scholar
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R (2020) IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 37:2461–2461. https://doi.org/10.1093/molbev/msaa131
Mower JP (2020) Variation in protein gene and intron content among land plant mitogenomes. Mitochondrion 53:203–213. https://doi.org/10.1016/j.mito.2020.06.002
Article CAS PubMed Google Scholar
Mower J, Sloan D, Alverson A (2012) Plant mitochondrial genome diversity: the genomics revolution. In. Mower J, Sloan D, Andrew J. Alverson A (eds) Plant genome diversity. Springer 1:123–144
Myszczyński K, Ślipiko M, Sawicki J (2019) Potential of Transcript Editing Across Mitogenomes of Early Land Plants Shows Novel and Familiar Trends. Int J Mol Sci. https://doi.org/10.3390/ijms20122963
Article PubMed PubMed Central Google Scholar
Palmer JD, Shields CR (1984) Tripartite structure of the Brassica campestris mitochondrial genome. Nature 307:437–440. https://doi.org/10.1038/307437a0
Petersen G, Shyama Prasad Rao R, Anderson B, Zervas A, Seberg O, Rasmusson AG, Max Møller I (2022) Genes from oxidative phosphorylation complexes II-V and two dual-function subunits of complex I are transcribed in Viscum album despite absence of the entire mitochondrial holo-complex I. Mitochondrion 62:1–12. https://doi.org/10.1016/j.mito.2021.10.006
Article CAS PubMed Google Scholar
Pridgeon AM, Cribb PJ, Chase MW, Rasmussen F (1999). Genera orchidacearum: Volume 1: Apostasioideae and cypripedioideae: Oxford University Press
Rice DW, Alverson AJ, Richardson AO, Young GJ, Sanchez-Puerta MV, Munzinger J et al (2013) Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Sci 342:1468–1473. https://doi.org/10.1126/science.1246275
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 Biol 11:29. https://doi.org/10.1186/1741-7007-11-29
Article CAS PubMed PubMed Central Google Scholar
Sanchez-Puerta MV, Garcia LE, Wohlfeiler J, Ceriotti LF (2017) Unparalleled replacement of native mitochondrial genes by foreign homologs in a holoparasitic plant. New Phytol 214:376–387. https://doi.org/10.1111/nph.14361
Article CAS PubMed Google Scholar
Shen B, Shen A, Liu L, Tan Y, Li S, Tan Z, Shen B 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 Biol 24. https://doi.org/10.1186/s12870-024-04962-4
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. Proc Natl Acad Sci USA 112:E3515–E3524. https://doi.org/10.1073/pnas.1504491112
Article CAS PubMed PubMed Central Google Scholar
Skippington E, Barkman TJ, Rice DW, Palmer JD (2017) Comparative mitogenomics indicates respiratory competence in parasitic Viscum despite loss of complex I and extreme sequence divergence, and reveals horizontal gene transfer and remarkable variation in genome size. Bmc Plant Biol 17. https://doi.org/10.1186/s12870-017-0992-8
Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, Palmer JD, Taylor DR (2012) Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biol 10:e1001241. https://doi.org/10.1371/journal.pbio.1001241
Article CAS PubMed PubMed Central Google Scholar
Sloan DB, Warren JM, Williams AM, Wu Z, Abdel-Ghany SE, Chicco AJ, Havird JC (2018) Cytonuclear integration and co-evolution. Nat Rev Genet 19:635–648. https://doi.org/10.1038/s41576-018-0035-9
Comments (0)