Mower JP, Sloan DB, Alverson AJ. Plant mitochondrial genome diversity: the genomics revolution. Heidelberg: Springer Vienna; 2012.
Google Scholar
Liu Y, Medina R, Goffinet B. 350 my of mitochondrial genome stasis in mosses, an early land plant lineage. Mol Biol Evol. 2014;31(10):2586–91.
Article
PubMed
CAS
Google Scholar
Xue JY, Liu Y, Li L, Wang B, Qiu YL. The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts. Curr Genet. 2009;56(1):53–61.
Article
PubMed
CAS
Google Scholar
Wang B, Xue J, Li L, Yang L, Qiu YL. The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea, reveals extremely conservative mitochondrial genome evolution in liverworts. Curr Genet. 2009;55(6):601–9.
Article
PubMed
CAS
Google Scholar
Sloan DB. One ring to rule them all? Genome sequencing provides new insights into the ‘master circle’ model of plant mitochondrial DNA structure. New Phytol. 2013;200(4):978–85.
Article
PubMed
CAS
Google Scholar
Richardson AO, Rice DW, Young GJ, Alverson AJ, Palmer JD. The “fossilized” mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate. BMC Biol. 2013;11(1):29.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, Palmer JD, Taylor DR. Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biol. 2012;10(1):e1001241.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhu A, Guo W, Jain K, Mower JP. Unprecedented heterogeneity in the synonymous substitution rate within a plant genome. Mol Biol Evol. 2014;31(5):1228–36.
Article
PubMed
CAS
Google Scholar
Guo W, Zhu A, Fan W, Mower JP. Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns. New Phytol. 2017;213(1):391–403.
Article
PubMed
CAS
Google Scholar
Skippington E, Barkman TJ, Rice DW, Palmer JD. Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes. Proc Natl Acad Sci U S A. 2015;112(27):E3515–24.
Article
PubMed
PubMed Central
CAS
Google Scholar
Burger G, Gray MW, Franz Lang B. Mitochondrial genomes: anything goes. Trends in Genet. 2003;19(12):709–16.
Article
CAS
Google Scholar
Lilly JW, Havey MJ. Small, repetitive dnas contribute significantly to the expanded mitochondrial genome of cucumber. Genetics. 2001;159(1):317–28.
PubMed
PubMed Central
CAS
Google Scholar
Alverson AJ, Rice DW, Dickinson S, Barry K, Palmer JD. Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber. Plant Cell. 2011;23(7):2499–513.
Article
PubMed
PubMed Central
CAS
Google Scholar
Alverson AJ, Wei X, Rice DW, Stern DB, Barry K, Palmer JD. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Mol Biol Evol. 2010;27(6):1436–48.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bock R. Witnessing genome evolution: experimental reconstruction of endosymbiotic and horizontal gene transfer. Annu Rev Genet. 2017;51:1–22.
Article
PubMed
CAS
Google Scholar
Rice DW, Alverson AJ, Richardson AO, Young GJ, Sanchezpuerta MV, Munzinger J, Barry K, Boore JL, Zhang L, DePamphilis CW, et al. Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Science. 2013;342(6165):1468–73.
Article
PubMed
CAS
Google Scholar
Chaw SM, Shih AC, Wang D, Wu YW, Liu SM, Chou TY. The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites. Mol Biol Evol. 2008;25(3):603–15.
Article
PubMed
CAS
Google Scholar
Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, Nakazono M, Hirai A, Kadowaki K. The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol Gen Genomics. 2002;268(4):434–45.
Article
CAS
Google Scholar
Darracq A, Varre JS, Touzet P. A scenario of mitochondrial genome evolution in maize based on rearrangement events. BMC Genomics. 2010;11:233.
Article
PubMed
PubMed Central
CAS
Google Scholar
Alverson AJ, Zhuo S, Rice DW, Sloan DB, Palmer JD. The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats. PLoS One. 2011;6(1):e16404.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gualberto JM, Mileshina D, Wallet C, Niazi AK, Weber-Lotfi F, Dietrich A. The plant mitochondrial genome: dynamics and maintenance. Biochimie. 2014;100:107–20.
Article
PubMed
CAS
Google Scholar
André C, Levy A, Walbot V. Small repeated sequences and the structure of plant mitochondrial genomes. Perspectives. 1992;8(4):128–32.
Cheng N, Lo YS, Ansari MI, Ho KC, Jeng ST, Lin NS, Dai H. Correlation between mtDNA complexity and mtDNA replication mode in developing cotyledon mitochondria during mung bean seed germination. New Phytol. 2017;213(2):751–63.
Article
PubMed
CAS
Google Scholar
Davila JI, Arrietamontiel MP, Wamboldt Y, Cao J, Hagmann J, Shedge V, Xu Y, Weigel D, Mackenzie SA. Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis. BMC Biol. 2011;9(1):64.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sloan DB, Muller K, McCauley DE, Taylor DR, Storchova H. Intraspecific variation in mitochondrial genome sequence, structure, and gene content in Silene vulgaris, an angiosperm with pervasive cytoplasmic male sterility. New Phytol. 2012;196(4):1228–39.
Article
PubMed
CAS
Google Scholar
Naito K, Kaga A, Tomooka N, Kawase M. De novo assembly of the complete organelle genome sequences of azuki bean (Vigna angularis) using next-generation sequencers. Breed Sci. 2013;63(2):176–82.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ogihara Y, Yamazaki Y, Murai K, Kanno A, Terachi T, Shiina T, Miyashita N, Nasuda S, Nakamura C, Mori N, et al. Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome. Nucleic Acids Res. 2005;33(19):6235–50.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hecht J, Grewe F, Knoop V. 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 Biol Evol. 2011;3:344–58.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sanchez-Puerta MV, Zubko MK, Palmer JD. Homologous recombination and retention of a single form of most genes shape the highly chimeric mitochondrial genome of a cybrid plant. New Phytol. 2015;206(1):381–96.
Article
PubMed
CAS
Google Scholar
Shearman JR, Sonthirod C, Naktang C, Pootakham W, Yoocha T, Sangsrakru D, Jomchai N, Tragoonrung S, Tangphatsornruang S. The two chromosomes of the mitochondrial genome of a sugarcane cultivar: assembly and recombination analysis using long PacBio reads. Sci Rep. 2016;6:31533.
Article
PubMed
PubMed Central
CAS
Google Scholar
Guo W, Grewe F, Fan W, Young GJ, Knoop V, Palmer JD, Mower JP. Ginkgo and Welwitschia mitogenomes reveal extreme contrasts in gymnosperm mitochondrial evolution. Mol Biol Evol. 2016;33(6):1448–60.
Article
PubMed
CAS
Google Scholar
Sloan DB, Alverson AJ, Storchova H, Palmer JD, Taylor DR. Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia. BMC Evol Biol. 2010;10(1):274.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mower JP, Case AL, Floro ER, Willis JH. Evidence against equimolarity of large repeat arrangements and a predominant master circle structure of the mitochondrial genome from a monkeyflower (Mimulus guttatus) lineage with cryptic CMS. Genome Biol Evol. 2012;4(5):670–86.
Article
PubMed
PubMed Central
CAS
Google Scholar
Won H, Renner SS. Horizontal gene transfer from flowering plants to Gnetum. Proc Natl Acad Sci U S A. 2003;100(19):10824–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Davis CC, Wurdack KJ. Host-to-parasite gene transfer in flowering plants: phylogenetic evidence from malpighiales. Science. 2004;305(5684):676–8.
Article
PubMed
CAS
Google Scholar
Mower JP, Stefanovic S, Young GJ, Palmer JD. Gene transfer from parasitic to host plants. Nature. 2004;432(7014):165–6.
Article
PubMed
CAS
Google Scholar
Skippington E, Barkman TJ, Rice DW, Palmer JD. 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. 2017;17(1):49.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sanchez-Puerta MV, Garcia LE, Wohlfeiler J, Ceriotti LF. Unparalleled replacement of native mitochondrial genes by foreign homologs in a holoparasitic plant. New Phytol. 2017;214(1):376–87.
Article
PubMed
CAS
Google Scholar
Chen F, Liu X, Yu C, Chen Y, Tang H, Zhang L. Water lilies as emerging models for Darwin's abominable mystery. Hort Res. 2017;4:17051.
Article
CAS
Google Scholar
Soltis DE, Bell CD, Kim S, Soltis PS. Origin and early evolution of angiosperms. Ann N Y Acad Sci. 2008;1133:3–25.
Article
PubMed
CAS
Google Scholar
Borsch T, Soltis PS. Nymphaeales – the first globally diverse clade? Taxon. 2008;57(4):1051.
Google Scholar
Löhne C, Yoo MJ, Borsch T, Wiersema J, Wilde V, Bell CD, Barthlott W, Soltis DE, Soltis PS. Biogeography of nymphaeales: extant patterns and historical events. Taxon. 2008;57(4):1123–46.
Google Scholar
Qiu YL, Lee J, Bernasconi-Quadroni F, Soltis DE, Soltis PS, Zanis M, Zimmer EA, Chen Z, Savolainen V, Chase MW. The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature. 1999;402(6760):404–7.
Article
PubMed
CAS
Google Scholar
Barkman TJ, Chenery G, McNeal JR, Lyons-Weiler J, Ellisens WJ, Moore G, Wolfe AD, dePamphilis CW. Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny. Proc Natl Acad Sci U S A. 2000;97(24):13166–71.
Article
PubMed
PubMed Central
CAS
Google Scholar
Xi Z, Liu L, Rest JS, Davis CC. Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies. Syst Biol. 2014;63(6):919–31.
Article
PubMed
Google Scholar
Edwards SV, Xi Z, Janke A, Faircloth BC, McCormack JE, Glenn TC, Zhong B, Wu S, Lemmon EM, Lemmon AR, et al. Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics. Mol Phylogenet Evol. 2016;94:447–62.
Article
PubMed
Google Scholar
Simmons MP. Mutually exclusive phylogenomic inferences at the root of the angiosperms: Amborella is supported as sister and observed variability is biased. Cladistics. 2016;0(2016):1–25.
Google Scholar
Bergthorsson U, Richardson AO, Young GJ, Goertzen LR, Palmer JD. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. Proc Natl Acad Sci U S A. 2004;101(51):17747–52.
Article
PubMed
PubMed Central
CAS
Google Scholar
Goremykin VV, Salamini F, Velasco R, Viola R. Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer. Mol Biol Evol. 2009;26(1):99–110.
Article
PubMed
CAS
Google Scholar
Gui S, Wu Z, Zhang H, Zheng Y, Zhu Z, Liang D, Ding Y. The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features. Sci Rep. 2016;6:30158.
Article
PubMed
PubMed Central
CAS
Google Scholar
Allen JO, Fauron CM, Minx P, Roark L, Oddiraju S, Lin GN, Meyer L, Sun H, Kim K, Wang C, et al. Comparisons among two fertile and three male-sterile mitochondrial genomes of maize. Genetics. 2007;177(2):1173–92.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hanson MR, Bentolila S. Interactions of mitochondrial and nuclear genes that affect male gametophyte development. Plant Cell. 2004;16(Suppl 1):S154–69.
Article
PubMed
PubMed Central
CAS
Google Scholar
Magee AM, Aspinall S, Rice DW, Cusack BP, Semon M, Perry AS, Stefanovic S, Milbourne D, Barth S, Palmer JD, et al. Localized hypermutation and associated gene losses in legume chloroplast genomes. Genome Res. 2010;20(12):1700–10.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li F, Yang A, Lv J, Gong D, Sun Y. The complete mitochondrial genome sequence of Sua-type cytoplasmic male sterility of tobacco (Nicotiana tabacum). Mitochondrial DNA. 2016;27(4):2929–30.
Article
PubMed
CAS
Google Scholar
Fang Y, Wu H, Zhang T, Yang M, Yin Y, Pan L, Yu X, Zhang X, Hu S, Al-Mssallem IS, et al. A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome. PLoS ONE. 2012;7(5):e37164.
Article
PubMed
PubMed Central
CAS
Google Scholar
Farré J-C, Araya A. RNA splicing in higher plant mitochondria: determination of functional elements in group II intron from a chimeric cox II gene in electroporated wheat mitochondria. Plant J. 2002;29(2):203–13.
Article
PubMed
Google Scholar
Huang Y, Niu B, Gao Y, Fu L, Li W. Cd-hit suite. Bioinformatics. 2010;26(5):680–2.
Article
PubMed
PubMed Central
CAS
Google Scholar
Marechal A, Brisson N. Recombination and the maintenance of plant organelle genome stability. New Phytol. 2010;186(2):299–317.
Article
PubMed
CAS
Google Scholar
Woloszynska M. Heteroplasmy and stoichiometric complexity of plant mitochondrial genomes – though this be madness, yet there's method in't. J Exp Bot. 2010;61(3):657–71.
Article
PubMed
CAS
Google Scholar
Tang M, Chen Z, Grover CE, Wang Y, Li S, Liu G, Ma Z, Wendel JF, Hua J. Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes. BMC Genomics. 2015;16(1):770.
Article
PubMed
PubMed Central
CAS
Google Scholar
Chen J, Guan R, Chang S, Du T, Zhang H, Xing H. Substoichiometrically different mitotypes coexist in mitochondrial genomes of Brassica napus L. PLoS One. 2011;6(3):e17662.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sakamoto W, Kondo H, Murata M, Motoyoshi F. Altered mitochondrial gene expression in a maternal distorted leaf mutant of Arabidopsis induced by chloroplast mutator. Plant Cell. 1996;8(8):1377–90.
Article
PubMed
PubMed Central
CAS
Google Scholar
Abdelnoor RV, Yule R, Elo A, Christensen AC, Meyer-Gauen G, Mackenzie SA. Substoichiometric shifting in the plant mitochondrial genome is influenced by a gene homologous to MutS. Proc Natl Acad Sci U S A. 2003;100(10):5968–73.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dietrich A, Wallet C, Janica S, Gualberto JM. Mitochondrial DNA recombination, repair and segregation: recent scientific data and perspectives. J WMS. 2016;2(2):2023.
Google Scholar
Gualberto JM, Newton KJ. Plant mitochondrial genomes: dynamics and mechanisms of mutation. Annu Rev Plant Biol. 2017;68:225–52.
Article
PubMed
CAS
Google Scholar
Odahara M, Kuroiwa H, Kuroiwa T, Sekine Y. Suppression of repeat-mediated gross mitochondrial genome rearrangements by RecA in the moss Physcomitrella patens. Plant Cell. 2009;21(4):1182–94.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kubo T, Nishizawa S, Mikami T. Alterations in organization and transcription of the mitochondrial genome of cytoplasmic male sterile sugar beet (Beta vulgaris L.). Mol Gen Genet. 1999;262(2):283–90.
Article
PubMed
CAS
Google Scholar
Giegé P, Brennicke A. RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proc Natl Acad Sci U S A. 1999;96(26):15324–9.
Article
PubMed
PubMed Central
Google Scholar
Wang D, Wu YW, Shih AC, Wu CS, Wang YN, Chaw SM. Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 MYA. Mol Biol Evol. 2007;24(9):2040–8.
Article
PubMed
CAS
Google Scholar
Li L, Wang B, Liu Y, Qiu YL. The complete mitochondrial genome sequence of the hornwort Megaceros aenigmaticus shows a mixed mode of conservative yet dynamic evolution in early land plant mitochondrial genomes. J Mol Evol. 2009;68(6):665–78.
Article
PubMed
CAS
Google Scholar
Palmer JD, Adams KL, Cho Y, Parkinson CL, Qiu YL, Song K. Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. Proc Natl Acad Sci. 2000;97:6960–6.
Article
PubMed
CAS
Google Scholar
Takemura M, Oda K, Yamato K, Ohta E, Nakamura Y, Nozato N, Akashi K, Ohyama K. Gene clusters for ribosomal proteins in the mitochondrial genome of a liverwort, Marchantia polymorpha. Nucleic Acids Res. 1992;20(12):3199–205.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lowe TM, Chan PP. tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 2016;44(W1):W54–7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hilker R, Sickinger C, Pedersen CN, Stoye J. UniMoG – a unifying framework for genomic distance calculation and sorting based on DCJ. Bioinformatics. 2012;28(19):2509–11.
Article
PubMed
PubMed Central
CAS
Google Scholar