S. Aubourg, N. Boudet, M. Kreis, and A. Lecharny, In Arabidopsis thaliana, 1% of the genome codes for a novel protein family unique to plants, Plant Molecular Biology, vol.42, issue.4, pp.603-616, 2000.
DOI : 10.1023/A:1006352315928

I. Small and N. Peeters, The PPR motif ?????? a TPR-related motif prevalent in plant organellar proteins, Trends in Biochemical Sciences, vol.25, issue.2, pp.46-47, 2000.
DOI : 10.1016/S0968-0004(99)01520-0

M. Magniette, H. Mireau, N. Peeters, J. Renou, B. Szurek et al., Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis, Plant Cell, issue.8, pp.162089-103, 2004.

O. Toole, N. Hattori, M. Andres, C. Iida, K. Lurin et al., On the expansion of the pentatricopeptide repeat gene family in plants, Mol Biol Evol, issue.6, pp.251120-251128, 2008.

D. Saha, A. Prasad, and R. Srinivasan, Pentatricopeptide repeat proteins and their emerging roles in plants, Plant Physiology and Biochemistry, vol.45, issue.8, pp.521-555, 2007.
DOI : 10.1016/j.plaphy.2007.03.026

C. Schmitz-linneweber and I. Small, Pentatricopeptide repeat proteins: a socket set for organelle gene expression, Trends in Plant Science, vol.13, issue.12, pp.663-70, 2008.
DOI : 10.1016/j.tplants.2008.10.001

C. Andres, C. Lurin, and I. Small, The multifarious roles of PPR proteins in plant mitochondrial gene expression, Physiologia Plantarum, vol.14, issue.1, pp.14-22, 2007.
DOI : 10.1074/jbc.270.31.18227

D. Fisk, M. Walker, and A. Barkan, Molecular cloning of the maize gene crp1 reveals similarity between regulators of mitochondrial and chloroplast gene expression, The EMBO Journal, vol.18, issue.9, pp.2621-2651, 1999.
DOI : 10.1093/emboj/18.9.2621

M. Uyttewaal, N. Arnal, M. Quadrado, A. Martin-canadell, N. Vrielynck et al., Characterization of Raphanus sativus Pentatricopeptide Repeat Proteins Encoded by the Fertility Restorer Locus for Ogura Cytoplasmic Male Sterility, THE PLANT CELL ONLINE, vol.20, issue.12, pp.203331-203376, 2008.
DOI : 10.1105/tpc.107.057208

A. Falcon-de-longevialle, E. Meyer, C. Andres, N. Taylor, C. Lurin et al., The Pentatricopeptide Repeat Gene OTP43 Is Required for trans-Splicing of the Mitochondrial nad1 Intron 1 in Arabidopsis thaliana, Plant Cell, issue.10, pp.193256-3265, 2007.

K. Meierhoff, S. Felder, T. Nakamura, N. Bechtold, and G. Schuster, HCF152, an Arabidopsis RNA Binding Pentatricopeptide Repeat Protein Involved in the Processing of Chloroplast psbB-psbT-psbH-petB-petD RNAs, THE PLANT CELL ONLINE, vol.15, issue.>6, pp.151480-95, 2003.
DOI : 10.1105/tpc.010397

C. Schmitz-linneweber, R. Williams-carrier, P. Williams-voelker, T. Kroeger, A. Vichas et al., A Pentatricopeptide Repeat Protein Facilitates the trans-Splicing of the Maize Chloroplast rps12 Pre-mRNA, THE PLANT CELL ONLINE, vol.18, issue.10, pp.182650-63, 2006.
DOI : 10.1105/tpc.106.046110

S. Beick, C. Schmitz-linneweber, R. Williams-carrier, B. Jensen, and A. Barkan, The Pentatricopeptide Repeat Protein PPR5 Stabilizes a Specific tRNA Precursor in Maize Chloroplasts, Molecular and Cellular Biology, vol.28, issue.17, pp.5337-5384, 2008.
DOI : 10.1128/MCB.00563-08

M. Hattori, H. Miyake, and M. Sugita, A Pentatricopeptide Repeat Protein Is Required for RNA Processing of clpP Pre-mRNA in Moss Chloroplasts, Journal of Biological Chemistry, vol.282, issue.14, pp.10773-82, 2007.
DOI : 10.1074/jbc.M608034200

J. Robbins, W. Heller, and M. Hanson, A comparative genomics approach identifies a PPR-DYW protein that is essential for C-to-U editing of the Arabidopsis chloroplast accD transcript, RNA, vol.15, issue.6, pp.1142-53, 2009.
DOI : 10.1261/rna.1533909

E. Kotera, M. Tasaka, and T. Shikanai, A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts, Nature, vol.101, issue.7023, pp.326-356, 2005.
DOI : 10.1073/pnas.96.26.15324

K. Okuda, F. Myouga, R. Motohashi, K. Shinozaki, and T. Shikanai, Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing, Proceedings of the National Academy of Sciences, vol.104, issue.19, pp.8178-83, 2007.
DOI : 10.1073/pnas.0700865104

K. Okuda, A. Chateigner-boutin, T. Nakamura, E. Delannoy, M. Sugita et al., Pentatricopeptide Repeat Proteins with the DYW Motif Have Distinct Molecular Functions in RNA Editing and RNA Cleavage in Arabidopsis Chloroplasts, THE PLANT CELL ONLINE, vol.21, issue.1, pp.146-56, 2009.
DOI : 10.1105/tpc.108.064667

A. Chateigner-boutin, M. Ramos-vega, A. Guevara-garcia, C. Andres, L. Gutierrez-nava et al., a pentatricopeptide repeat protein required for editing of rpoA and clpP chloroplast transcripts, Plant J, vol.56, issue.4, pp.19590-602, 2008.

W. Zhou, Y. Cheng, A. Yap, A. Chateigner-boutin, E. Delannoy et al., The Arabidopsis gene YS1 encoding a DYW protein is required for editing of rpoB transcripts and the rapid development of chloroplasts during early growth, The Plant Journal, vol.283, issue.1, 2008.
DOI : 10.1111/j.1365-313X.2008.03766.x

A. Zehrmann, D. Verbitskiy, M. Van-der, J. Brennicke, A. Takenaka et al., A DYW Domain-Containing Pentatricopeptide Repeat Protein Is Required for RNA Editing at Multiple Sites in Mitochondria of Arabidopsis thaliana, THE PLANT CELL ONLINE, vol.21, issue.2, pp.558-67, 2009.
DOI : 10.1105/tpc.108.064535

E. Rivals, C. Bruyere, C. Toffano-nioche, and A. Lecharny, Formation of the Arabidopsis Pentatricopeptide Repeat Family, PLANT PHYSIOLOGY, vol.141, issue.3, pp.825-864, 2006.
DOI : 10.1104/pp.106.077826

URL : https://hal.archives-ouvertes.fr/lirmm-00109042

DOI : 10.1093/pcp/pcg121

M. Havey, The Use of Cytoplasmic Male Sterility for Hybrid Seed Production, Molecular Biology and Biotechnology of Plant Organelles SpringerDaniell H, pp.623-634, 2004.
DOI : 10.1007/978-1-4020-3166-3_23

C. Chase, Cytoplasmic male sterility: a window to the world of plant mitochondrial???nuclear interactions, Trends in Genetics, vol.23, issue.2, pp.81-90, 2007.
DOI : 10.1016/j.tig.2006.12.004

S. Bentolila, A. Alfonso, and M. Hanson, A pentatricopeptide repeatcontaining gene restores fertility to cytoplasmic male-sterile plants, Proc Natl Acad Sci, issue.16, pp.9910887-92, 2002.

T. Kazama and K. Toriyama, A pentatricopeptide repeat-containing gene that promotes the processing of aberrant atp6 RNA of cytoplasmic malesterile rice, FEBS Lett, vol.544, pp.1-399, 2003.

T. Komori, S. Ohta, N. Murai, Y. Takakura, Y. Kuraya et al., L.), The Plant Journal, vol.79, issue.3, pp.315-340, 2004.
DOI : 10.1046/j.1365-313X.2003.01961.x

H. Akagi, A. Nakamura, Y. Yokozeki-misono, A. Inagaki, H. Takahashi et al., Positional cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondria-targeting PPR protein, Theor Appl Genet, vol.108, issue.8, pp.1449-57, 2004.

G. Brown, N. Formanova, H. Jin, R. Wargachuk, C. Dendy et al., restorer gene of Ogura cytoplasmic male sterility encodes a protein with multiple pentatricopeptide repeats, The Plant Journal, vol.4, issue.2, pp.262-72, 2003.
DOI : 10.1046/j.1365-313X.2003.01799.x

S. Desloire, H. Gherbi, W. Laloui, S. Marhadour, V. Clouet et al., , in radish, as a member of the pentatricopeptide-repeat protein family, EMBO reports, vol.22, issue.6, pp.588-594, 2003.
DOI : 10.1038/sj.embor.embor848

N. Koizuka, R. Imai, H. Fujimoto, T. Hayakawa, Y. Kimura et al., Genetic characterization of a pentatricopeptide repeat protein gene, orf687, that restores fertility in the cytoplasmic male-sterile Kosena radish, The Plant Journal, vol.143, issue.4, pp.407-415, 2003.
DOI : 10.1007/BF00193143

H. Kato, K. Tezuka, Y. Feng, T. Kawamoto, H. Takahashi et al., Structural diversity and evolution of the Rf-1 locus in the genus Oryza, Heredity, vol.22, issue.5, pp.99516-99540, 2007.
DOI : 10.1007/BF00226900

Z. Wang, Y. Zou, X. Li, Q. Zhang, L. Chen et al., Cytoplasmic Male Sterility of Rice with Boro II Cytoplasm Is Caused by a Cytotoxic Peptide and Is Restored by Two Related PPR Motif Genes via Distinct Modes of mRNA Silencing, THE PLANT CELL ONLINE, vol.18, issue.3, pp.676-87, 2006.
DOI : 10.1105/tpc.105.038240

P. Touzet and F. Budar, Unveiling the molecular arms race between two conflicting genomes in cytoplasmic male sterility?, Trends in Plant Science, vol.9, issue.12, pp.568-70, 2004.
DOI : 10.1016/j.tplants.2004.10.001

R. Michelmore and B. Meyers, Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process, Genome Res, vol.8, issue.11, pp.1113-1143, 1998.

B. Meyers, A. Kozik, A. Griego, H. Kuang, and R. Michelmore, Genome-Wide Analysis of NBS-LRR-Encoding Genes in Arabidopsis, THE PLANT CELL ONLINE, vol.15, issue.4, pp.809-843, 2003.
DOI : 10.1105/tpc.009308

R. Geddy and G. Brown, Genes encoding pentatricopeptide repeat (PPR) proteins are not conserved in location in plant genomes and may be subject to diversifying selection, BMC Genomics, vol.8, issue.1, p.130, 2007.
DOI : 10.1186/1471-2164-8-130

A. Bonnet, Breeding in France of a radish F1 hybrid obtained by use of cytoplasmic male sterility, Eucarpia Cruciferae Newslett, vol.2, p.5, 1977.

L. Noe and G. Kucherov, YASS: enhancing the sensitivity of DNA similarity search, 33 Web Server, pp.540-543, 2005.
DOI : 10.1093/nar/gki478

URL : https://hal.archives-ouvertes.fr/inria-00100004

C. Burge and S. Karlin, Finding the genes in genomic DNA, Current Opinion in Structural Biology, vol.8, issue.3, pp.346-54, 1998.
DOI : 10.1016/S0959-440X(98)80069-9

S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.253389-402, 1997.
DOI : 10.1093/nar/25.17.3389

I. Small, N. Peeters, F. Legeai, and C. Lurin, Predotar: A tool for rapidly screening proteomes forN-terminal targeting sequences, PROTEOMICS, vol.4, issue.6, pp.1581-90, 2004.
DOI : 10.1002/pmic.200300776

O. Emanuelsson, S. Brunak, G. Von-heijne, and H. Nielsen, Locating proteins in the cell using TargetP, SignalP and related tools, Nature Protocols, vol.22, issue.4, pp.953-71, 2007.
DOI : 10.1038/nprot.2007.131

G. Etherington, J. Dicks, and I. Roberts, Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination, Bioinformatics, vol.21, issue.3, pp.278-81, 2005.
DOI : 10.1093/bioinformatics/bth500

S. Giancola, Y. Rao, S. Chaillou, S. Hiard, A. Martin-canadell et al., Cytoplasmic suppression of Ogura cytoplasmic male sterility in European natural populations of Raphanus raphanistrum, Theoretical and Applied Genetics, vol.103, issue.3, pp.1141333-1141376, 2007.
DOI : 10.1007/s00122-007-0520-6

Y. Zhang, Y. Cheng, D. Bi, K. Palma, and X. Li, MOS2, a Protein Containing G-Patch and KOW Motifs, Is Essential for Innate Immunity in Arabidopsis thaliana, Current Biology, vol.15, issue.21, pp.1936-1978, 2005.
DOI : 10.1016/j.cub.2005.09.038

S. Seah, A. Telleen, and V. Williamson, Introgressed and endogenous Mi-1 gene clusters in tomato differ by complex rearrangements in flanking sequences and show sequence exchange and diversifying selection among homologues, Theoretical and Applied Genetics, vol.98, issue.7, pp.1289-302, 2007.
DOI : 10.1007/s00122-007-0519-z

L. Noel, T. Moores, E. Biezen-van-der, M. Parniske, M. Daniels et al., Pronounced Intraspecific Haplotype Divergence at the RPP5 Complex Disease Resistance Locus of Arabidopsis, THE PLANT CELL ONLINE, vol.11, issue.11, pp.2099-112, 1999.
DOI : 10.1105/tpc.11.11.2099

T. Wicker, N. Yahiaoui, and B. Keller, Illegitimate recombination is a major evolutionary mechanism for initiating size variation in plant resistance genes, The Plant Journal, vol.95, issue.4, pp.631-672, 2007.
DOI : 10.1111/j.1365-313X.2007.03164.x

D. Peterson, J. Tomkins, D. Frisch, R. Wing, and A. Paterson, Construction of plant bacterial artificial chromosome (BAC) libraries: an illustrated guide, Journal of Agricultural Genomics, vol.5, 2000.

J. Dellaporta, J. Wood, and J. Hicks, A plant DNA minipreparation: Version II, Plant Molecular Biology Reporter, vol.3, issue.4, pp.19-21, 1983.
DOI : 10.1007/BF02712670

C. Burge and S. Karlin, Prediction of complete gene structures in human genomic DNA, Journal of Molecular Biology, vol.268, issue.1, pp.78-94, 1997.
DOI : 10.1006/jmbi.1997.0951

R. Uricaru, L. Bréhélin, and E. Rivals, A new type of Hidden Markov Models to predict complex motif organization in protein sequences, Proceeding of Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), pp.97-102, 2007.
URL : https://hal.archives-ouvertes.fr/lirmm-00120171

A. Dereeper, V. Guignon, G. Blanc, S. Audic, S. Buffet et al., Phylogeny.fr: robust phylogenetic analysis for the non-specialist, 36 Web Server, pp.465-474, 2008.
DOI : 10.1093/nar/gkn180

URL : https://hal.archives-ouvertes.fr/lirmm-00324099

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1799, 2004.
DOI : 10.1093/nar/gkh340

J. Castresana, Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, vol.17, issue.4, pp.540-52, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026334

M. Anisimova and O. Gascuel, Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative, Systematic Biology, vol.55, issue.4, pp.539-52, 2006.
DOI : 10.1080/10635150600755453

URL : https://hal.archives-ouvertes.fr/lirmm-00136658

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

A. Waterhouse, J. Procter, D. Martin, M. Clamp, and G. Barton, Jalview Version 2--a multiple sequence alignment editor and analysis workbench, Bioinformatics, vol.25, issue.9, pp.1189-91, 2009.
DOI : 10.1093/bioinformatics/btp033

F. Chevenet, C. Brun, A. Banuls, B. Jacq, and C. R. , TreeDyn: towards dynamic graphics and annotations for analyses of trees, BMC Bioinformatics, vol.7, issue.1, p.439, 2006.
DOI : 10.1186/1471-2105-7-439

URL : https://hal.archives-ouvertes.fr/hal-00321061