J. D. Palmer and L. A. Herbon, Unicircular structure of the Brassica hirta mitochondrial genome, Curr. Genet, vol.11, pp.565-570, 1987.

D. B. Sloan, A. J. Alverson, J. P. Chuckalovcak, M. Wu, D. E. Mccauley et al., Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates, PLoS Biol, vol.10, p.1001241, 2012.

A. J. Alverson, X. Wei, D. W. Rice, D. B. Stern, K. Barry et al., Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae), Mol. Biol. Evol, vol.27, pp.1436-1448, 2010.

L. Rodríguez-moreno, V. M. González, A. Benjak, M. C. Martí, P. Puigdomènech et al., 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 Genom, vol.12, pp.424-424, 2011.

S. A. Morley and B. L. Nielsen, Plant mitochondrial DNA, vol.15, p.17, 2017.

A. O. Richardson and J. D. Palmer, Horizontal gene transfer in plants, J. Exp. Bot, vol.58, pp.1-9, 2006.

A. J. Bendich, Reaching for the ring: The study of mitochondrial genome structure, Curr. Genet, vol.24, pp.279-290, 1993.

D. J. Oldenburg and A. J. Bendich, Size and structure of replicating mitochondrial DNA in cultured tobacco cells, Plant Cell, vol.8, pp.447-461, 1996.

M. Manchekar, K. Scissum-gunn, D. Song, F. Khazi, S. L. Mclean et al., DNA recombination activity in soybean mitochondria, J. Mol. Biol, vol.356, pp.288-299, 2006.

J. M. Gualberto, D. Mileshina, C. Wallet, A. K. Niazi, F. Weber-lotfi et al., The plant mitochondrial genome: Dynamics and maintenance, Biochimie, vol.100, pp.107-120, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00965626

A. J. Alverson, D. W. Rice, S. Dickinson, K. Barry, and J. D. Palmer, Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber, Plant Cell, vol.23, pp.2499-2513, 2011.

D. B. Sloan, One ring to rule them all? Genome sequencing provides new insights into the 'master circle' model of plant mitochondrial DNA structure, New Phytol, pp.978-985, 0200.

J. I. Davila, M. P. Arrieta-montiel, Y. Wamboldt, J. Cao, J. Hagmann et al., Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis, BMC Biol, vol.9, p.64, 2011.

J. R. Shearman, C. Sonthirod, C. Naktang, W. Pootakham, T. Yoocha et al., The two chromosomes of the mitochondrial genome of a sugarcane cultivar: Assembly and recombination analysis using long PacBio reads, Sci. Rep, vol.6, p.31533, 2016.

T. Kazama and K. Toriyama, Whole mitochondrial genome sequencing and re-examination of a cytoplasmic male sterility-associated gene in Boro-taichung-type cytoplasmic male sterile rice, PLoS ONE, vol.11, p.159379, 2016.

M. Tsujimura, T. Kaneko, T. Sakamoto, S. Kimura, M. Shigyo et al., Multichromosomal structure of the onion mitochondrial genome and a transcript analysis, vol.46, pp.179-186, 2019.

Z. Wu, J. M. Cuthbert, D. R. Taylor, and D. B. Sloan, The massive mitochondrial genome of the angiosperm Silene noctiflora is evolving by gain or loss of entire chromosomes, Proc. Natl. Acad. Sci, vol.112, pp.10185-10191, 2015.

C. Halldén, C. Lind, and T. Bryngelsson, Minicircle variation in Beta mitochondrial DNA, Theor. Appl. Genet, vol.77, pp.337-342, 1989.

J. M. Warren, M. P. Simmons, Z. Wu, and D. B. Sloan, Linear plasmids and the rate of sequence evolution in plant mitochondrial genomes, Genome Biol. Evol, vol.8, pp.364-374, 2016.

S. Backert, R-loop-dependent rolling-circle replication and a new model for DNA concatemer resolution by mitochondrial plasmid mp1, EMBO J, vol.21, pp.3128-3136, 2002.

A. C. Christensen, Plant mitochondrial genome evolution can be explained by DNA repair mechanisms, Genome Biol. Evol, vol.5, pp.1079-1086, 2013.

J. M. Gualberto and K. J. Newton, Plant mitochondrial genomes: Dynamics and mechanisms of mutation, Annu. Rev. Plant Biol, vol.68, pp.225-252, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01521803

R. Horn, K. J. Gupta, and N. Colombo, Mitochondrion role in molecular basis of cytoplasmic male sterility, vol.19, pp.198-205, 2014.

Z. Chen, N. Zhao, S. Li, C. E. Grover, H. Nie et al., Plant mitochondrial genome evolution and cytoplasmic male sterility, Crit. Rev. Plant Sci, vol.36, pp.55-69, 2017.

Y. Kim and D. Zhang, Molecular control of male fertility for crop hybrid breeding, Trends Plant Sci, vol.23, pp.53-65, 2018.

M. Takenaka, J. A. Van-der-merwe, D. Verbitskiy, J. Neuwirt, A. Zehrmann et al., RNA Editing in Plant Mitochondria, RNA Editing

H. U. Göringer, , pp.105-122, 2008.

M. Takenaka, D. Verbitskiy, J. A. Van-der-merwe, A. Zehrmann, and A. Brennicke, The process of RNA editing in plant mitochondria, Mitochondrion, vol.8, pp.35-46, 2008.

T. Sun, S. Bentolila, and M. R. Hanson, The Unexpected Diversity of Plant Organelle RNA Editosomes, Trends Plant Sci, vol.21, pp.962-973, 2016.

W. Tang and C. Luo, Molecular and Functional Diversity of RNA Editing in Plant Mitochondria, Mol. Biotechnol, vol.60, pp.935-945, 2018.

B. Oldenkott, Y. Yang, E. Lesch, V. Knoop, and M. Schallenberg-rüdinger, Plant-type pentatricopeptide repeat proteins with a DYW domain drive C-to-U RNA editing in Escherichia coli, Commun. Biol, vol.2, p.85, 2019.

M. A. Hardigan, F. P. Laimbeer, L. Newton, E. Crisovan, J. P. Hamilton et al., Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato, Proc. Natl. Acad. Sci, vol.114, p.9999, 2017.

, Genome sequence and analysis of the tuber crop potato, Nature, p.189, 2011.

C. E. Mcgregor, C. A. Lambert, M. M. Greyling, J. H. Louw, and L. Warnich, A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm, Euphytica, vol.113, pp.135-144, 2000.

M. Ghislain, D. Andrade, F. Rodríguez, R. J. Hijmans, and D. M. Spooner, Genetic analysis of the cultivated potato Solanum tuberosum L. Phureja Group using RAPDs and nuclear SSRs, Theor. Appl. Genet, vol.113, pp.1515-1527, 2006.

D. M. Spooner, J. Núñez, G. Trujillo, M. Del-rosario-herrera, F. Guzmán et al., Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification, Proc. Natl. Acad. Sci, vol.104, pp.19398-19403, 2007.

S. A. Peters, J. W. Bargsten, D. Szinay, J. Van-de-belt, R. G. Visser et al., Structural homology in the Solanaceae: Analysis of genomic regions in support of synteny studies in tomato, potato and pepper, Plant J, vol.71, pp.602-614, 2012.

P. Smyda-dajmund, J. ?liwka, I. Wasilewicz-flis, H. Jakuczun, and E. Zimnoch-guzowska, Genetic composition of interspecific potato somatic hybrids and autofused 4x plants evaluated by DArT and cytoplasmic DNA markers, Plant Cell Rep, vol.35, pp.1345-1358, 2016.

J. Berdugo-cely, R. I. Valbuena, E. Sánchez-betancourt, L. S. Barrero, and R. Yockteng, Genetic diversity and association mapping in the Colombian Central Collection of Solanum tuberosum L. Andigenum group using SNPs markers, PLoS ONE, vol.12, p.173039, 2017.

T. Cardi, T. Bastia, L. Monti, and E. D. Earle, Organelle DNA and male fertility variation in Solanum spp. and interspecific somatic hybrids, Theor. Appl. Genet, vol.99, pp.819-828, 1999.

A. Lössl, N. Adler, R. Horn, U. Frei, and G. Wenzel, Chondriome-type characterization of potato: Mt ?, ?, ??? and novel plastid-mitochondrial configurations in somatic hybrids, Theor. Appl. Genet, vol.99, pp.1-10, 1999.

N. Scotti, L. Monti, and T. Cardi, Organelle DNA variation in parental Solanum spp. genotypes and nuclearcytoplasmic interactions in Solanum tuberosum (+) S. commersonii somatic hybrid-backcross progeny, Theor. Appl. Genet, vol.108, pp.87-94, 2003.

N. Scotti, S. Cozzolino, and T. Cardi, Mitochondrial DNA variation in cultivated and wild potato species (Solanum spp.), Genome, vol.50, pp.706-713, 2007.

A. Lössl, M. Götz, A. Braun, and G. Wenzel, Molecular markers for cytoplasm in potato: Male sterility and contribution of different plastid-mitochondrial configurations to starch production, Euphytica, vol.116, pp.221-230, 2000.

P. Brandt, M. Unseld, U. Eckert-ossenkopp, and A. Brennicke, An rps14 pseudogene is transcribed and edited in Arabidopsis mitochondria, Curr. Genet, vol.24, pp.330-336, 1993.

V. Quiñones, S. Zanlungo, A. Moenne, I. Gómez, L. Holuigue et al., The rpl5-rps 14-cob gene arrangement in Solanum tuberosum: rps14 is a transcribed and unedited pseudogene, Plant Mol. Biol, vol.31, pp.937-943, 1996.

N. Scotti, L. Maréchal-drouard, and T. Cardi, The rpl5-rps14 mitochondrial region: A hot spot for DNA rearrangements in Solanum spp. somatic hybrids, Curr. Genet, vol.45, pp.378-382, 2004.

P. Figueroa, I. Gómez, L. Holuigue, A. Araya, and X. Jordana, Transfer of rps14 from the mitochondrion to the nucleus in maize implied integration within a gene encoding the iron-sulphur subunit of succinate dehydrogenase and expression by alternative splicing, Plant J, vol.18, pp.601-609, 1999.

H. C. Ong and J. D. Palmer, Pervasive survival of expressed mitochondrial rps14 pseudogenes in grasses and their relatives for 80 million years following three functional transfers to the nucleus, BMC Evol. Biol, vol.6, pp.55-55, 2006.

T. Bastia, N. Scotti, and T. Cardi, Organelle DNA analysis of Solanum and Brassica somatic hybrids by PCR with'universal primers, Theor. Appl. Genet, vol.102, pp.1265-1272, 2001.

L. Maréchal-drouard, P. Guillemaut, A. Cosset, M. Arbogast, F. Weber et al., Transfer RNAs of potato (Solanum tuberosum) mitochondria have different genetic origins, Nucleic Acids Res, vol.18, pp.3689-3696, 1990.

A. Dietrich, C. Wallet, R. K. Iqbal, J. M. Gualberto, and F. Lotfi, Organellar non-coding RNAs: Emerging regulation mechanisms, Biochimie, vol.117, pp.48-62, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01213794

D. H. Kim, J. G. Kang, and B. Kim, Isolation and characterization of the cytoplasmic male sterilityassociated orf456 gene of chili pepper (Capsicum annuum L.), Plant Mol. Biol, vol.63, pp.519-532, 2007.

J. Fey and L. Maréchal-drouard, Compilation and Analysis of Plant Mitochondrial Promoter Sequences: An Illustration of a Divergent Evolution between Monocot and Dicot Mitochondria, Biochem. Biophys. Res. Commun, vol.256, pp.409-414, 1999.

K. Kühn, A. Weihe, and T. Börner, Multiple promoters are a common feature of mitochondrial genes in Arabidopsis, Nucleic Acids Res, vol.33, pp.337-346, 2005.

K. Kühn, A. Bohne, K. Liere, A. Weihe, and T. Börner, Arabidopsis phage-type RNA polymerases: Accurate in vitro transcription of organellar genes, Plant Cell, vol.19, pp.959-971, 2007.

J. Forner, B. Weber, S. Thuss, S. Wildum, and S. Binder, Mapping of mitochondrial mRNA termini in Arabidopsis thaliana: T-elements contribute to 5' and 3' end formation, Nucleic Acids Res, vol.35, pp.3676-3692, 2007.

J. D. Palmer and L. A. Herbon, Plant mitochondrial DNA evolved rapidly in structure, but slowly in sequence, J. Mol. Evol, vol.28, pp.87-97, 1988.

S. Zanlungo, V. Quinones, A. Moenne, L. Holuigue, and X. Jordana, Splicing and editing of rps10 transcripts in potato mitochondria, Curr. Genet, vol.27, pp.565-571, 1995.

S. Zanlungo, V. Quiñones, L. Holuigue, and X. Jordana, Identification of the RPS10 polypeptide encoded by the mitochondrial genome in Solanum tuberosum: Translation initiates at a genomic-encoded AUG and not at a conserved AUG codon created by RNA editing, Physiol. Plant, vol.110, pp.256-261, 2000.

V. Quiñones, S. Zanlungo, L. Holuigue, S. Litvak, and X. Jordana, The cox1 initiation codon is created by RNA editing in potato mitochondria, Plant Physiol, vol.108, p.1327, 1995.

P. Dell'orto, A. Moenne, P. V. Graves, and X. Jordana, The potato mitochondrial ATP synthase subunit 9: Gene structure, RNA editing and partial protein sequence, Plant Sci, vol.88, pp.45-53, 1993.

M. D. Hunt and K. J. Newton, The NCS3 mutation: Genetic evidence for the expression of ribosomal protein genes in Zea mays mitochondria, EMBO J, vol.10, pp.1045-1052, 1991.

M. Takemura, K. Oda, K. Yamato, E. Ohta, Y. Nakamura et al., Gene clusters for ribosomal proteins in the mitochondrial genome of a liverwort, Marchantia polymorpha, Nucleic Acids Res, vol.20, pp.3199-3205, 1992.

P. Giegé and A. Brennicke, RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs, Proc. Natl. Acad. Sci, vol.96, pp.15324-15329, 1999.

L. Marechal-drouard, A. Cosset, C. Remacle, D. Ramamonjisoa, and A. Dietrich, A single editing event is a prerequisite for efficient processing of potato mitochondrial phenylalanine tRNA, Mol. Cell. Biol, vol.16, pp.3504-3510, 1996.

J. Fey, K. Tomita, M. Bergdoll, and L. Maréchal-drouard, Evolutionary and functional aspects of C-to-U editing at position 28 of tRNACys(GCA) in plant mitochondria, RNA, vol.6, pp.470-474, 2000.

M. Ngu, K. Massel, and L. Bonen, Group II introns in wheat mitochondria have degenerate structural features and varied splicing pathways, Int. J. Biochem. Cell Biol, vol.91, pp.156-167, 2017.

V. Cognat, G. Morelle, C. Megel, S. Lalande, J. Molinier et al., The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic, Nucleic Acids Res, vol.45, pp.3460-3472, 2016.

W. Guo, A. Zhu, W. Fan, and J. P. Mower, Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns, New Phytol, vol.213, pp.391-403, 2017.

K. L. Adams, D. O. Daley, J. Whelan, and J. D. Palmer, Genes for two mitochondrial ribosomal proteins in flowering plants are derived from their chloroplast or cytosolic counterparts, Plant Cell, vol.14, pp.931-943, 2002.

Y. Notsu, S. Masood, T. Nishikawa, N. Kubo, G. Akiduki et al., The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: Frequent DNA sequence acquisition and loss during the evolution of flowering plants, Mol. Genet. Genom, vol.268, pp.434-445, 2002.

D. Aubert, C. Bisanz-seyer, and M. Herzog, Mitochondrial rps14 is a transcribed and edited pseudogene in Arabidopsis thaliana, Plant Mol. Biol, vol.20, pp.1169-1174, 1992.

M. Unseld, J. R. Marienfeld, P. Brandt, and A. Brennicke, The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides, Nat. Genet, vol.15, pp.57-61, 1997.

N. Kubo, K. Harada, A. Hirai, and K. Kadowaki, A single nuclear transcript encoding mitochondrial RPS14 and SDHB of rice is processed by alternative splicing: Common use of the same mitochondrial targeting signal for different proteins, Proc. Natl. Acad. Sci, vol.96, pp.9207-9211, 1999.

A. Mohanty, J. P. Martín, L. M. González, and I. Aguinagalde, Association between chloroplast DNA and mitochondrial DNA haplotypes in Prunus spinosa L. (Rosaceae) populations across Europe, Ann. Bot, vol.92, pp.749-755, 2003.

G. Bartoszewski, S. Malepszy, and M. J. Havey, Mosaic (MSC) cucumbers regenerated from independent cell cultures possess different mitochondrial rearrangements, Curr. Genet, vol.45, pp.45-53, 2004.

P. Sandoval, G. León, I. Gómez, R. Carmona, P. Figueroa et al., Transfer of RPS14 and RPL5 from the mitochondrion to the nucleus in grasses, Gene, vol.324, pp.139-147, 2004.

K. L. Adams, Y. Qiu, M. Stoutemyer, and J. D. Palmer, 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, vol.99, pp.9905-9912, 2002.

U. Bergthorsson, K. L. Adams, B. Thomason, and J. D. Palmer, Widespread horizontal transfer of mitochondrial genes in flowering plants, Nature, vol.424, pp.197-201, 2003.

S. Park, F. Grewe, A. Zhu, T. A. Ruhlman, J. Sabir et al., Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers, New Phytol, vol.208, pp.570-583, 2015.

H. Handa, The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): Comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana, Nucleic Acids Res, vol.31, pp.5907-5916, 2003.

S. W. Clifton, P. Minx, C. M. Fauron, M. Gibson, J. O. Allen et al., Sequence and comparative analysis of the maize NB mitochondrial genome, Plant Physiol, vol.136, pp.3486-3503, 2004.

D. Luo, H. Xu, Z. Liu, J. Guo, H. Li et al., A detrimental mitochondrial-nuclear interaction causes cytoplasmic male sterility in rice, Nat. Genet, p.573, 2013.

C. Osman, C. Wilmes, T. Tatsuta, and T. Langer, Prohibitins interact genetically with Atp23, a novel processing peptidase and chaperone for the F1Fo-ATP synthase, Mol. Biol. Cell, vol.18, pp.627-635, 2007.

X. Zeng, W. Neupert, and A. Tzagoloff, The metalloprotease encoded by ATP23 has a dual function in processing and assembly of subunit 6 of mitochondrial ATPase, Mol. Biol. Cell, vol.18, pp.617-626, 2007.

T. D. Fox, Mitochondrial protein synthesis, import, and assembly, Genetics, vol.192, pp.1203-1234, 2012.

M. Kimura and T. Ohta, On some principles governing molecular evolution, Proc. Natl. Acad. Sci, vol.71, pp.2848-2852, 1974.

J. Echave, S. J. Spielman, and C. O. Wilke, Causes of evolutionary rate variation among protein sites, Nat. Rev. Genet, vol.17, pp.109-121, 2016.

A. Darracq, J. Varré, L. Maréchal-drouard, A. Courseaux, V. Castric et al., Structural and content diversity of mitochondrial genome in beet: A comparative genomic analysis, Genome Biol. Evol, vol.3, pp.723-736, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00616508

H. A. Aljohi, W. Liu, Q. Lin, Y. Zhao, J. Zeng et al., Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome, PLoS ONE, vol.11, p.163990, 2016.

C. Bi, A. H. Paterson, X. Wang, Y. Xu, D. Wu et al., Analysis of the Complete Mitochondrial Genome Sequence of the Diploid Cotton Gossypium raimondii by Comparative Genomics Approaches, BioMed Res. Int, 2016.

X. Wang, F. Cheng, D. Rohlsen, C. Bi, C. Wang et al., Organellar genome assembly methods and comparative analysis of horticultural plants, Hortic. Rese, vol.5, p.3, 2018.

R. G. Olmstead, L. Bohs, H. A. Migid, E. Santiago-valentin, V. F. Garcia et al., A Molecular Phylogeny of the Solanaceae, Taxon, vol.57, pp.1159-1181, 2008.

C. Pujol, M. Bailly, D. Kern, L. Maréchal-drouard, H. Becker et al., Dual-targeted tRNAdependent amidotransferase ensures both mitochondrial and chloroplastic Gln-tRNAGln synthesis in plants, Proc. Natl. Acad. Sci, vol.105, pp.6481-6485, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00356301

N. Scotti, T. Cardi, and L. Marechaldrouard, Mitochondrial DNA and RNA isolation from small amounts of potato tissue, Plant Mol. Biol. Rep, vol.19, pp.67-67, 2001.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: A flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2120, 2014.

D. R. Zerbino and E. Birney, Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Res, vol.18, pp.821-829, 2008.

A. Bashir, A. Klammer, W. P. Robins, C. Chin, D. Webster et al., A hybrid approach for the automated finishing of bacterial genomes, Nat. Biotechnol, vol.30, pp.701-707, 2012.

R. Luo, B. Liu, Y. Xie, Z. Li, W. Huang et al., SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler, vol.1, p.18, 2012.

S. Koren, B. P. Walenz, K. Berlin, J. R. Miller, N. H. Bergman et al., Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation, Genome Res, vol.27, pp.722-736, 2017.

K. E. Holt, M. B. Schultz, R. R. Wick, and J. Zobel, Bandage: Interactive visualization of de novo genome assemblies, Bioinformatics, vol.31, pp.3350-3352, 2015.

T. Vincent, A. Vingadassalon, E. Ubrig, K. Azeredo, O. Srour et al., A genome-scale analysis of mRNAs targeting to plant mitochondria: Upstream AUGs in 5' untranslated regions reduce mitochondrial association, vol.92, pp.1132-1142, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01700910

D. Kim, B. Langmead, and S. L. Salzberg, HISAT: A fast spliced aligner with low memory requirements, Nat. Methods, vol.12, p.357, 2015.

K. Katoh and D. M. Standley, MAFFT multiple sequence alignment software version 7: Improvements in performance and usability, Mol. Biol. Evol, vol.30, pp.772-780, 2013.

A. Stamatakis, RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, pp.1312-1313, 2014.