Burton RS, Pereira RJ, Barreto FS. Cytonuclear genomic interactions and hybrid breakdown. Annu Rev Ecol Evol Syst. 2013;44(1):281–302.
Article
Google Scholar
Budar F, Roux F. The role of organelle genomes in plant adaptation. Plant Signal Behav. 2014;6(5):635–9.
Article
CAS
Google Scholar
Roux F, Mary-Huard T, Barillot E, Wenes E, Botran L, Durand S, Villoutreix R, Martin-Magniette ML, Camilleri C, Budar F. Cytonuclear interactions affect adaptive traits of the annual plant Arabidopsis thaliana in the field. Proc Natl Acad Sci U S A. 2016;113(13):3687–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Greiner S, Bock R. Tuning a menage a trois: co-evolution and co-adaptation of nuclear and organellar genomes in plants. BioEssays. 2013;35(4):354–65.
Article
CAS
PubMed
Google Scholar
Greiner S, Sobanski J, Bock R. Why are most organelle genomes transmitted maternally? BioEssays. 2015;37(1):80–94.
Article
CAS
PubMed
Google Scholar
Sato M, Sato K. Maternal inheritance of mitochondrial DNA by diverse mechanisms to eliminate paternal mitochondrial DNA. Biochim Biophys Acta. 2013;1833(8):1979–84.
Article
CAS
PubMed
Google Scholar
Barr CM, Neiman M, Taylor DR. Inheritance and recombination of mitochondrial genomes in plants, fungi and animals. New Phytol. 2005;168(1):39–50.
Article
CAS
PubMed
Google Scholar
McCauley DE. Paternal leakage, heteroplasmy, and the evolution of plant mitochondrial genomes. New Phytol. 2013;200(4):966–77.
Article
PubMed
Google Scholar
Wicke S, Schneeweiss GM, De Pamphilis CW, Muller KF, Quandt D. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol Biol. 2011;76(3–5):273–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ward B, Anderson R, Bendich A. The mitochondrial genome is large and variable in a family of plants (cucurbitaceae). Cell. 1981;25:793–803.
Article
CAS
PubMed
Google Scholar
Elansary HO, Müller K, Olson MS, Štorchová H. Transcription profiles of mitochondrial genes correlate with mitochondrial DNA haplotypes in a natural population of Silene vulgaris. BMC Plant Biol. 2010;10(1):11.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wang S, Li D, Yao X, Song Q, Wang Z, Zhang Q, Zhong C, Liu Y, Huang H. Evolution and diversification of kiwifruit mitogenomes through extensive whole-genome rearrangement and mosaic loss of intergenic sequences in a highly variable region. Genome Biol Evol. 2019;11(4):1192–206.
Article
CAS
PubMed
PubMed Central
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
CAS
PubMed
Google Scholar
Gao LZ, Innan H. Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. indica and ssp. japonica, demonstrated by multilocus microsatellites. Genetics. 2008;179(2):965–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang X, Kurata N, Wei X, Wang ZX, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, et al. A map of rice genome variation reveals the origin of cultivated rice. Nature. 2012;490(7421):497–501.
Article
CAS
PubMed
PubMed Central
Google Scholar
Londo JP, Chiang YC, Hung KH, Chiang TY, Schaal BA. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci U S A. 2006;103(25):9578–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Civáň P, Craig H, Cox CJ, Brown TA. Three geographically separate domestications of Asian rice. Nat Plants. 2015;1(11):15164.
Article
PubMed
PubMed Central
Google Scholar
Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes RR, Zhang F, et al. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature. 2018;557(7703):43–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xie H, Wang J, Qian M, Li N, Zhu Y, Li S. Mitotype-specific sequences related to cytoplasmic male sterility in Oryza species. Mol Breed. 2013;33(4):803–11.
Article
Google Scholar
Tesler G. GRIMM: genome rearrangements web server. Bioinformatics. 2002;18(3):492–3.
Article
CAS
PubMed
Google Scholar
Cole LW, Guo W, Mower JP, Palmer JD. High and variable rates of repeat-mediated mitochondrial genome rearrangement in a genus of plants. Mol Biol Evol. 2018;35(11):2773–85.
CAS
PubMed
Google Scholar
Arrieta-Montiel MP, Shedge V, Davila J, Christensen AC, Mackenzie SA. Diversity of the Arabidopsis mitochondrial genome occurs via nuclear-controlled recombination activity. Genetics. 2009;183(4):1261–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tadi SK, Sebastian R, Dahal S, Babu RK, Choudhary B, Raghavan SC. Microhomology-mediated end joining is the principal mediator of double-strand break repair during mitochondrial DNA lesions. Mol Biol Cell. 2016;27(2):223–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hastings PJ, Ira G, Lupski JR. A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet. 2009;5(1):e1000327.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chateigner-Boutin AL, Small I. Organellar RNA editing. Wiley Interdiscip Rev RNA. 2011;2(4):493–506.
Article
CAS
PubMed
Google Scholar
Luan J, Liu T, Luo W, Liu W, Peng M, Li W, Dai X, Liang M, Chen L. Mitochondrial DNA genetic polymorphism in thirteen rice cytoplasmic male sterile lines. Plant Cell Rep. 2013;32(4):545–54.
Article
CAS
PubMed
Google Scholar
Song Z, Lu B, Wang B, Chen J. Fitness estimation through performance comparison of F1 hybrids with their parental species Oryza rufipogon and O. sativa. Ann Bot. 2004;93:311–6.
Article
PubMed
PubMed Central
Google Scholar
Fan F, Li N, Chen Y, Liu X, Sun H, Wang J, He G, Zhu Y, Li S. Development of elite BPH-resistant wide-spectrum restorer lines for three and two line hybrid rice. Front Plant Sci. 2017;8:986.
Article
PubMed
PubMed Central
Google Scholar
Li ZK, Sanchez A, Angeles E, Singh S, Domingo J, Huang N, Khush GS. Are the dominant and recessive plant disease resistance genes similar? A case study of rice R genes and Xanthomonas oryzae pv. oryzae races. Genetics. 2001;159(2):757–65.
CAS
PubMed
PubMed Central
Google Scholar
Tanksley SD, McCouch SR. Seed banks and molecular maps: unlocking genetic potential from the wild. Science. 1997;277(5329):1063–6.
Article
CAS
PubMed
Google Scholar
Li SQ, Yang DC, Zhu YG. Characterization and use of male sterility in hybrid rice breeding. J Integr Plant Biol. 2007;49(6):791–804.
Article
CAS
Google Scholar
Meyer VG. A study of reciprocal hybrids between upland cotton (Gossypium hirsutum L.) and experimental lines with cytoplasms from seven other species. Crop Sci. 1973;13(4):439–44.
Article
Google Scholar
Hu Q, Hansen N, Laursen J, Dixelius C, Andersen B. Intergeneric hybrids between Brassica napus and Orychophragmus violaceus containing traits of agronomic importance for oilseed rape breeding. Theor Appl Genet. 2002;105(6–7):834–40.
Article
CAS
PubMed
Google Scholar
Price HJ, Hodnett GL, Burson BL, Dillon SL, Rooney WL. A Sorghum bicolor × S. macrospermum hybrid recovered by embryo rescue and culture. Aust J Botany. 2005;53(6):579.
Article
Google Scholar
Sloan DB, Warren JM, Williams AM, Wu Z, Abdel-Ghany SE, Chicco AJ, Havird JC. Cytonuclear integration and co-evolution. Nat Rev Genet. 2018;19(10):635–48.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gualberto JM, Newton KJ. Plant mitochondrial genomes: dynamics and mechanisms of mutation. Annu Rev Plant Biol. 2017;68:225–52.
Article
CAS
PubMed
Google Scholar
Arrieta-Montiel MP. Mackenzie SA. Plant mitochondrial genomes and recombination. Advances in Plant Biology. 2011:65–82.
Stern D, Palmer J. Extensive and widespread homologies between mitochondrial DNA and chloroplast DNA in plants. Proc Natl Acad Sci U S A. 1984;81(7):1946–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Palmer JD, Shields CR. Tripartite structure of the Brassica campestris mitochondrial genome. Nature. 1984;307:437–40.
Article
CAS
Google Scholar
Lonsdale DM, Hodge TP, Fauron CMR. The physical map and organisation of the mitochondrial genome from the fertile cytoplasm of maize. Nucleic Acids Res. 1984;12:9249–61.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weng ML, Blazier JC, Govindu M, Jansen RK. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates. Mol Biol Evol. 2014;31(3):645–59.
Article
CAS
PubMed
Google Scholar
Seol JH, Shim EY, Lee SE. Microhomology-mediated end joining: good, bad and ugly. Mutat Res. 2018;809:81–7.
Article
CAS
PubMed
Google Scholar
Schumer M, Rosenthal GG, Andolfatto P. How common is homoploid hybrid speciation? Evolution. 2014;68(6):1553–60.
Article
PubMed
Google Scholar
Budar F, Touzet P, Pelletier G. Cytoplasmic male sterility. Annual Plant Reviews Online. 2018:147–80.
Kamiński P, Podwyszyńska M, Starzycki M, Starzycka-Korbas E. Interspecific hybridisation of cytoplasmic male-sterile rapeseed with Ogura cytoplasm and Brassica rapa var. pekinensis as a method to obtain male-sterile Chinese cabbage inbred lines. Euphytica. 2015;208(3):519–34.
Article
CAS
Google Scholar
Chen G, Ye X, Zeng F, Wang J, Yuan L, Zhu S, Hou J, Cheng Y, Wang C. Characterization and utilization of a cytoplasmic male sterility line of Wucai (Brassica campestris L.). Hortic. Environ. Biotechnol. 2019;60(3):373–82.
Google Scholar
Xiao H, Xu Y, Ni C, Zhang Q, Zhong F, Huang J, Liu W, Peng L, Zhu Y, Hu J. A rice dual-localized pentatricopeptide repeat protein is involved in organellar RNA editing together with OsMORFs. J Exp Bot. 2018;69(12):2923–36.
CAS
PubMed
PubMed Central
Google Scholar
Xiao H, Zhang Q, Qin X, Xu Y, Ni C, Huang J, Zhu L, Zhong F, Liu W, Yao G, et al. Rice PPS1 encodes a DYW motif-containing pentatricopeptide repeat protein required for five consecutive RNA-editing sites of nad3 in mitochondria. New Phytol. 2018;220(3):878–92.
Article
CAS
PubMed
Google Scholar
O'Toole N, Hattori M, Andres C, Iida K, Lurin C, Schmitz-Linneweber C, Sugita M, Small I. On the expansion of the pentatricopeptide repeat gene family in plants. Mol Biol Evol. 2008;25(6):1120–8.
Article
CAS
PubMed
Google Scholar
Barkan A, Small I. Pentatricopeptide repeat proteins in plants. Annu Rev Plant Biol. 2014;65:415–42.
Article
CAS
PubMed
Google Scholar
Tang QY, Zhang CX. Data processing system (DPS) software with experimental design, statistical analysis and data mining developed for use in entomological research. Insect Sci. 2013;20(2):254–60.
Article
PubMed
Google Scholar
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35(6):1547–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heazlewood JL, Howell KA, Whelan J, Millar AH. Towards an analysis of the rice mitochondrial proteome. Plant Physiol. 2003;132(1):230–42.
Article
CAS
PubMed
PubMed Central
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
CAS
PubMed
PubMed Central
Google Scholar
Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 2005;33(Web Server issue):W686–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lohse M, Drechsel O, Kahlau S, Bock R. OrganellarGenomeDRAW--a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 2013;41(W1):W575–81.
Article
PubMed
PubMed Central
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.
Article
CAS
PubMed
Google Scholar
Darling AE, Mau B, Perna NT. ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010;5(6):e11147.
Article
PubMed
PubMed Central
CAS
Google Scholar
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG. Primer3--new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115.
Article
CAS
PubMed
PubMed Central
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
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
CAS
PubMed
Google Scholar
Guo W, Grewe F, Mower JP. Variable frequency of plastid RNA editing among ferns and repeated loss of uridine-to-cytidine editing from vascular plants. PLoS One. 2015;10(1):e0117075.
Article
PubMed
PubMed Central
CAS
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. Genome project data processing S. the sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article
PubMed
PubMed Central
CAS
Google Scholar