Genome Biology

Budar F, Roux F (2011). The role of organelle genomes in plant adaptation: time to get to work!. Plant Signal Behav, 6:635-639. PubMed | DOI

Llorens C, Futami R, Covelli L, Dominguez-Escriba L, Viu JM, Tamarit D, Aguilar-Rodriguez J, Vicente-Ripolles M, Fuster G, Bernet GP, Maumus F, Munoz-Pomer A, Sempere JM, Latorre A, Moya A (2011). The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res, 39:D70-74. PubMed | DOI

Renny-Byfield S, Chester M, Kovarik A, Le Comber SC, Grandbastien MA, Deloger M, Nichols RA, Macas J, Novak P, Chase MW, Leitch AR (2011). Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs. Mol Biol Evol, 28:2843-2854. PubMed | DOI

Géry C, Zuther E, Schulz E, Legoupi J, Chauveau A, Mckhann H, Hincha DK, Téoulé E (2011). Natural variation in the freezing tolerance of Arabidopsis thaliana: effects of RNAi-induced CBF depletion and QTL localisation vary among accessions. Plant Sci, 180:12-23. PubMed | DOI

Lefebvre V, Fortabat MN, Ducamp A, North HM, Maia-Grondard A, Trouverie J, Boursiac Y, Mouille G, Durand-Tardif M (2011). ESKIMO1 disruption in Arabidopsis alters vascular tissue and impairs water transport. PLoS One, 6:e16645. PubMed | DOI

Trontin C, Tisne S, Bach L, Loudet O (2011). What does Arabidopsis natural variation teach us (and does not teach us) about adaptation in plants?. Curr Opin Plant Biol, 14:225-231. PubMed | DOI

Schaefer DG, Delacote F, Charlot F, Vrielynck N, Guyon-Debast A, Le Guin S, Neuhaus JM, Doutriaux MP, Nogué F (2010). RAD51 loss of function abolishes gene targeting and de-represses illegitimate integration in the moss Physcomitrella patens. DNA Repair (Amst), 9:526-533. PubMed | DOI

Jauvion V, Elmayan T, Vaucheret H (2010). The conserved RNA trafficking proteins HPR1 and TEX1 are involved in the production of endogenous and exogenous small interfering RNA in Arabidopsis. Plant Cell, 22:2697-2709. PubMed | DOI

Mallory A, Vaucheret H (2010). Form, function, and regulation of ARGONAUTE proteins. Plant Cell, 22:3879-3889. PubMed | DOI

Marin E, Jouannet V, Herz A, Lokerse AS, Weijers D, Vaucheret H, Nussaume L, Crespi MD, Maizel A (2010). miR390, Arabidopsis TAS3 tasiRNAs, and their AUXIN RESPONSE FACTOR targets define an autoregulatory network quantitatively regulating lateral root growth. Plant Cell, 22:1104-1117. PubMed | DOI

Yu B, Bi L, Zhai J, Agarwal M, Li S, Wu Q, Ding SW, Meyers BC, Vaucheret H, Chen X (2010). siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis. Nucleic Acids Res, 38:5844-5850. PubMed | DOI

Ainouche ML, Jenczewski E (2010). Focus on polyploidy. New Phytol, 186:1-4. PubMed | DOI

Baarends WM, Mercier R (2010). Sisters dancing in meiosis. EMBO Rep, 11:76-78. PubMed | DOI

Chelysheva L, Grandont L, Vrielynck N, Le Guin S, Mercier R, Grelon M (2010). An easy protocol for studying chromatin and recombination protein dynamics during Arabidopsis thaliana meiosis: immunodetection of cohesins, histones and MLH1. Cytogenet Genome Res, 129:143-153. PubMed | DOI

Cifuentes M, Eber F, Lucas MO, Lode M, Chevre AM, Jenczewski E (2010). Repeated polyploidy drove different levels of crossover suppression between homoeologous chromosomes in Brassica napus allohaploids. Plant Cell, 22:2265-2276. PubMed | DOI

Cifuentes M, Grandont L, Moore G, Chevre AM, Jenczewski E (2010). Genetic regulation of meiosis in polyploid species: new insights into an old question. New Phytol, 186:29-36. PubMed | DOI

D'erfurth I, Cromer L, Jolivet S, Girard C, Horlow C, Sun Y, To JP, Berchowitz LE, Copenhaver GP, Mercier R (2010). The cyclin-A CYCA1;2/TAM is required for the meiosis I to meiosis II transition and cooperates with OSD1 for the prophase to first meiotic division transition. PLoS Genet, 6:e1000989. PubMed | DOI

Leflon M, Grandont L, Eber F, Huteau V, Coriton O, Chelysheva L, Jenczewski E, Chevre AM (2010). Crossovers get a boost in Brassica allotriploid and allotetraploid hybrids. Plant Cell, 22:2253-2264. PubMed | DOI

Szadkowski E, Eber F, Huteau V, Lode M, Huneau C, Belcram H, Coriton O, Manzanares-Dauleux MJ, Delourme R, King GJ, Chalhoub B, Jenczewski E, Chevre AM (2010). The first meiosis of resynthesized Brassica napus, a genome blender. New Phytol, 186:102-112. PubMed | DOI

Hernandez Mora JR, Rivals E, Mireau H, Budar F (2010). Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo). BMC Plant Biol, 10:35. PubMed | DOI

Moison M, Roux F, Quadrado M, Duval R, Ekovich M, Le DH, Verzaux M, Budar F (2010). Cytoplasmic phylogeny and evidence of cyto-nuclear co-adaptation in Arabidopsis thaliana. Plant J, 63:728-738. PubMed | DOI

Parisod C, Alix K, Just J, Petit M, Sarilar V, Mhiri C, Ainouche M, Chalhoub B, Grandbastien MA (2010). Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytol, 186:37-45. PubMed | DOI

Petit M, Guidat C, Daniel J, Denis E, Montoriol E, Bui QT, Lim KY, Kovarik A, Leitch AR, Grandbastien MA, Mhiri C (2010). Mobilization of retrotransposons in synthetic allotetraploid tobacco. New Phytol, 186:135-147. PubMed | DOI

Kronholm I, Loudet O, De Meaux J (2010). Influence of mutation rate on estimators of genetic differentiation--lessons from Arabidopsis thaliana. BMC Genet, 11:33. PubMed | DOI

Platt A, Horton M, Huang YS, Li Y, Anastasio AE, Mulyati NW, Agren J, Bossdorf O, Byers D, Donohue K, Dunning M, Holub EB, Hudson A, Le Corre V, Loudet O, Roux F, Warthmann N, Weigel D, Rivero L, Scholl R, Nordborg M, Bergelson J, Borevitz JO (2010). The scale of population structure in Arabidopsis thaliana. PLoS Genet, 6:e1000843. PubMed | DOI

Vlad D, Rappaport F, Simon M, Loudet O (2010). Gene transposition causing natural variation for growth in Arabidopsis thaliana. PLoS Genet, 6:e1000945. PubMed | DOI

De Muyt A, Pereira L, Vezon D, Chelysheva L, Gendrot G, Chambon A, Laine-Choinard S, Pelletier G, Mercier R, Nogué F, Grelon M (2009). A high throughput genetic screen identifies new early meiotic recombination functions in Arabidopsis thaliana. PLoS Genet, 5:e1000654. PubMed | DOI

Gallois JL, Guyon-Debast A, Lécureuil A, Vezon D, Carpentier V, Bonhomme S, Guerche P (2009). The Arabidopsis proteasome RPT5 subunits are essential for gametophyte development and show accession-dependent redundancy. Plant Cell, 21:442-459. PubMed | DOI

Ben Amor B, Wirth S, Merchan F, Laporte P, D'aubenton-Carafa Y, Hirsch J, Maizel A, Mallory A, Lucas A, Deragon JM, Vaucheret H, Thermes C, Crespi M (2009). Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res, 19:57-69. PubMed | DOI

Elmayan T, Adenot X, Gissot L, Lauressergues D, Gy I, Vaucheret H (2009). A neomorphic sgs3 allele stabilizing miRNA cleavage products reveals that SGS3 acts as a homodimer. FEBS J, 276:835-844. PubMed | DOI

Mallory AC, Hinze A, Tucker MR, Bouché N, Gasciolli V, Elmayan T, Lauressergues D, Jauvion V, Vaucheret H, Laux T (2009). Redundant and specific roles of the ARGONAUTE proteins AGO1 and ZLL in development and small RNA-directed gene silencing. PLoS Genet, 5:e1000646. PubMed | DOI

Mallory AC, Vaucheret H (2009). ARGONAUTE 1 homeostasis invokes the coordinate action of the microRNA and siRNA pathways. EMBO Rep, 10:521-526. PubMed | DOI

Vaucheret H (2009). AGO1 homeostasis involves differential production of 21-nt and 22-nt miR168 species by MIR168a and MIR168b. PLoS One, 4:e6442. PubMed | DOI

Curtis MJ, Belcram K, Bollmann SR, Tominey CM, Hoffman PD, Mercier R, Hays JB (2009). Reciprocal chromosome translocation associated with TDNA-insertion mutation in Arabidopsis: genetic and cytological analyses of consequences for gametophyte development and for construction of doubly mutant lines. Planta, 229:731-745. PubMed | DOI

D'erfurth I, Jolivet S, Froger N, Catrice O, Novatchkova M, Mercier R (2009). Turning meiosis into mitosis. PLoS Biol, 7:e1000124. PubMed | DOI

Duroc Y, Hiard S, Vrielynck N, Ragu S, Budar F (2009). The Ogura sterility-inducing protein forms a large complex without interfering with the oxidative phosphorylation components in rapeseed mitochondria. Plant Mol Biol, 70:123-137. PubMed | DOI

Muyt A, Mercier R, Mézard C, Grelon M (2009). Meiotic recombination and crossovers in plants. Genome Dyn, 5:14-25. PubMed | DOI

Nicolas SD, Leflon M, Monod H, Eber F, Coriton O, Huteau V, Chevre AM, Jenczewski E (2009). Genetic regulation of meiotic cross-overs between related genomes in Brassica napus haploids and hybrids. Plant Cell, 21:373-385. PubMed | DOI

Manetti ME, Rossi M, Nakabashi M, Grandbastien MA, Van Sluys MA (2009). The Tnt1 family member Retrosol copy number and structure disclose retrotransposon diversification in different Solanum species. Mol Genet Genomics, 281:261-271. PubMed | DOI

Maumus F, Allen AE, Mhiri C, Hu H, Jabbari K, Vardi A, Grandbastien MA, Bowler C (2009). Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. BMC Genomics, 10:624. PubMed | DOI

Parisod C, Salmon A, Zerjal T, Tenaillon M, Grandbastien MA, Ainouche M (2009). Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina. New Phytol, 184:1003-1015. PubMed | DOI

Tam SM, Lefebvre V, Palloix A, Sage-Palloix AM, Mhiri C, Grandbastien MA (2009). LTR-retrotransposons Tnt1 and T135 markers reveal genetic diversity and evolutionary relationships of domesticated peppers. Theor Appl Genet, 119:973-989. PubMed | DOI

Zerjal T, Joets J, Alix K, Grandbastien MA, Tenaillon MI (2009). Contrasting evolutionary patterns and target specificities among three Tourist-like MITE families in the maize genome. Plant Mol Biol, 71:99-114. PubMed | DOI

Balasubramanian S, Schwartz C, Singh A, Warthmann N, Kim MC, Maloof JN, Loudet O, Trainer GT, Dabi T, Borevitz JO, Chory J, Weigel D (2009). QTL mapping in new Arabidopsis thaliana advanced intercross-recombinant inbred lines. PLoS One, 4:e4318. PubMed | DOI

Bikard D, Patel D, Le Mette C, Giorgi V, Camilleri C, Bennett MJ, Loudet O (2009). Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana. Science, 323:623-626. PubMed | DOI

Lefebvre V, Kiani SP, Durand-Tardif M (2009). A focus on natural variation for abiotic constraints response in the model species Arabidopsis thaliana. Int J Mol Sci, 10:3547-3582. PubMed | DOI

Alboresi A, Caffarri S, Nogué F, Bassi R, Morosinotto T (2008). In silico and biochemical analysis of Physcomitrella patens photosynthetic antenna: identification of subunits which evolved upon land adaptation. PLoS One, 3:e2033. PubMed | DOI

Lienard D, Durambur G, Kiefer-Meyer MC, Nogué F, Menu-Bouaouiche L, Charlot F, Gomord V, Lassalles JP (2008). Water transport by aquaporins in the extant plant Physcomitrella patens. Plant Physiol, 146:1207-1218. PubMed | DOI

Mercier R, Jolivet S, Vignard J, Durand S, Drouaud J, Pelletier G, Nogué F (2008). Outcrossing as an explanation of the apparent unconventional genetic behavior of Arabidopsis thaliana hth mutants. Genetics, 180:2295-2297. PubMed | DOI

Daxinger L, Hunter B, Sheikh M, Jauvion V, Gasciolli V, Vaucheret H, Matzke M, Furner I (2008). Unexpected silencing effects from T-DNA tags in Arabidopsis. Trends Plant Sci, 13:4-6. PubMed | DOI