Biology of Frankia strains, actinomycete symbionts of actinorhizal plants, Microbiol Rev, vol.57, pp.293-319, 1993. ,
Chloroplast gene sequence data suggest a single origin of the predisposition for symbiotic nitrogen fixation in angiosperms, Proc Natl Acad Sci, vol.92, pp.2647-2651, 1995. ,
Phylogenetic perspectives on the origins of nodulation, Mol Plant Microbe Interact, vol.24, pp.1289-1295, 2011. ,
A single evolutionary innovation drives the deep evolution of symbiotic N 2 -fixation in angiosperms, Nature Commun, vol.5, p.4087, 2014. ,
Three keys to the radiation of angiosperms into freezing environments, Nature, vol.506, pp.89-92, 2014. ,
Direct characterization of Frankia and of close phyletic neighbors from an Alnus viridis rhizosphere, Physiol Plant, vol.99, pp.722-731, 1997. ,
URL : https://hal.archives-ouvertes.fr/hal-02553861
Molecular phylogeny of the genus Frankia and related genera and emendation of family Frankiaceae, Int J Syst Bacteriol, vol.46, pp.1-9, 1996. ,
16S-23S rRNA intergenic spacer region variability in the genus Frankia, Microb Ecol, vol.60, pp.487-495, 2010. ,
Phylogeny of members of the Frankia genus based on gyrB, nifH and glnII sequences, Antonie Van Leeuwenhoek, vol.100, pp.579-587, 2011. ,
Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders 'Frankiales' and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov, Int J Syst Evol Microbiol, vol.64, pp.3821-332, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01182770
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography, Genome Res, vol.17, pp.7-15, 2007. ,
URL : https://hal.archives-ouvertes.fr/halsde-00140365
What stories can the Frankia genomes start to tell us?, J Biosci, vol.38, pp.719-726, 2013. ,
Draft genome sequence of Frankia sp, strain BMG5, vol.12, 2013. ,
, Genome Announc, vol.1, pp.468-481
Draft genome sequence of Frankia sp. strain QA3, a nitrogen-fixing actinobacterium isolated from the root nodule of Alnus nitida, Genome Announc, vol.1, p.1031, 2013. ,
Draft genome Sequence of Frankia sp. strain BCU110501, a nitrogen-fixing actinobacterium isolated from nodules of Discaria trinevis, Genome Announc, vol.1, pp.503-516, 2013. ,
Low genetic diversity among Frankia spp. strains nodulating sympatric populations of actinorhizal species of Rosaceae, Ceanothus (Rhamnaceae) and Datisca glomerata (Datiscaceae) west of the Sierra Nevada (California), Can J Microbiol, vol.50, pp.989-1000, 2004. ,
The role of Dryas drummondii in vegetation development following ice recession at Glacier Bay, Alaska, with special reference to its nitrogen fixation by root nodules, J Ecol, vol.55, pp.793-813, 1967. ,
The results of the IBP survey of root nodule formation in non-leguminous angiosperms, Symbiotic Nitrogen Fixation in Plants, pp.443-474, 1976. ,
Morphological statis and molecular divergence in the intercontinal disjunct genus Datisca (Datiscaceae), Aliso, vol.12, pp.525-542, 1989. ,
Molecular phylogeny of Coriaria, with special emphasis on the disjunct distribution, Mol Phylogenet Evol, vol.14, pp.11-19, 2000. ,
The genome of Candidatus Frankia datiscae Dg1, the uncultured microsymbiont from nitrogen-fixing root nodules of the dicot Datisca glomerata, J Bacteriol, vol.193, pp.7017-7018, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02540431
Evolution of signal transduction in intracellular symbiosis, Trends Plant Sci, vol.7, pp.511-518, 2002. ,
Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza, Nature, vol.469, pp.58-63, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00577122
LysM-type mycorrhizal receptor recruited for Rhizobium symbiosis in nonlegume Parasponia, Science, vol.331, pp.909-912, 2010. ,
Speak, friend, and enter: signalling systems that promote beneficial symbiotic associations in plants, Nat Rev Microbiol, vol.11, pp.252-263, 2013. ,
Functional adaptation of a plant receptor-kinase paved the way for the evolution of intracellular root symbioses with bacteria, PLoS Biol, vol.6, p.68, 2008. ,
SymRK defines a common genetic basis for plant root endosymbioses with arbuscular mycorrhiza fungi, rhizobia, and Frankia bacteria, Proc Natl Acad Sci, vol.105, pp.4928-4932, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-02666106
The independent acquisition of plant root nitrogen-fixing symbiosis in Fabids recruited the same genetic pathway for nodule organogenesis, PLoS One, vol.8, p.64515, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-02651288
Transcriptomics of actinorhizal symbioses reveals homologs of the whole common symbiotic signaling cascade, Plant Physiol, vol.156, pp.700-711, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00599363
Comparison of the nodule vs. root transcriptome of the actinorhizal plant Datisca glomerata: actinorhizal nodules contain a specific class of defensins, PLoS One, vol.8, p.72442, 2013. ,
Short-chain chitin oligomers from arbuscular mycorrhizal fungi trigger nuclear Ca 2+ spiking in Medicago truncatula roots and their production is enhanced by strigolactone, New Phytol, vol.198, pp.190-202, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-02651472
Structural and functional comparison of Frankia root hair deforming factor and rhizobia Nod factor, Can J Bot, vol.77, pp.1293-1301, 1999. ,
Legumes symbioses: Absence of nod genes in photosynthetic bradyrhizobia, Science, vol.316, pp.1307-1312, 2007. ,
URL : https://hal.archives-ouvertes.fr/halsde-00151340
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucl Acids Res, vol.32, pp.1792-1797, 2004. ,
PAUP 4.0: Phylogenetic analysis using parsimony (and other methods). Sunderland, 1999. ,
Confidence limits on phylogenies: An approach using the bootstrap, Evolution, vol.39, pp.783-791, 1985. ,
, GenBank. Nucl Acids Res, vol.41, pp.36-42, 2013.
ProtTest: Selection of best-fit models of protein evolution, Bioinformatics, vol.21, pp.2104-2105, 2005. ,
New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0, Syst Biol, vol.59, pp.307-321, 2010. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00511784
Using the quantitative genetic threshold model for inferences between and within species, Philos Trans R Soc Lond B Biol Sci, vol.360, pp.1427-1434, 2005. ,
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol, vol.10, p.25, 2009. ,
The Sequence Alignment/ Map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009. ,
Integrative Genomics Viewer, Nature Biotechnol, vol.29, pp.24-26, 2011. ,
, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2008.
fitdistrplus: help to fit of a parametric distribution to non-censored or censored data, vol.1, pp.0-2, 2013. ,
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases, Nucl Acids Res, vol.38, pp.473-479, 2010. ,
Pathway Tools version 13.0: Integrated software for pathway/genome informatics and systems biology, Brief Bioinform, vol.11, pp.40-79, 2010. ,
A new mathematical model for relative quantification in real-time RT-PCR, Nucl Acids Res, vol.29, 2001. ,
, ABI PRISM 7700 Sequence Detection System, User Bulletin, vol.2, 2007.
anti-SMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences, Nucl Acids Res, vol.39, pp.339-346, 2011. ,
EDGAR: a software framework for the comparative analysis of prokaryotic genomes, BMC Bioinformat, vol.10, p.154, 2009. ,
MaGe: a microbial genome annotation system supported by synteny results, Nucl Acids Res, vol.34, pp.53-65, 2006. ,
De novo identification of repeat families in large genomes, Bioinformatics, vol.21, pp.351-358, 2005. ,
Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis, BMC Genomics, 2014. ,
ISfinder: the reference centre for bacterial insertion sequences, Nucl Acids Res, vol.34, pp.32-36, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00021179
Genetic diversity of Datisca-compatible Frankia strains determined by sequence analysis of PCR-amplified 16S rRNA gene, Appl Environ Microbiol, vol.60, pp.2371-2376, 1994. ,
Rapid denoising of pyrosequencing amplicon data: exploiting the rankabundance distribution, Nature Methods, vol.7, pp.668-669, 2010. ,
QIIME allows analysis of high-throughput community sequencing data, Nat Methods, vol.7, pp.335-336, 2010. ,
Basic local alignment search tool, J Mol Biol, vol.215, pp.403-410, 1990. ,
MAFFT: iterative refinement and additional methods, Methods Mol Biol, vol.1079, pp.131-146, 2014. ,
Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, 2003. ,
Identification of genes and gene products involved in the nodulation of peas by Rhizobium leguminosarum, Mol Gen Genet, vol.198, pp.255-262, 1985. ,
Broad-host-range expression vectors with tightly regulated promoters and their use to examine the influence of TraR and TraM expression on Ti plasmid quorum sensing, Appl Environ Microbiol, vol.74, pp.5053-5062, 2008. ,
High-efficiency transformation of Rhizobium leguminosarum by electroporation, Appl Environ Microbiol, vol.65, pp.2802-2804, 1999. ,
The infection of clover root hairs by nodule bacteria studied by simple glass technique, J Gen Microbiol, vol.16, pp.374-381, 1957. ,
R factor transfer in Rhizobium leguminosarum, J Gen Microbiol, vol.84, pp.188-198, 1974. ,
Significant natural product biosynthetic potential of actinorhizal symbionts of the genus Frankia, as revealed by comparative genomic and proteomic analyses, Appl Environ Microbiol, vol.77, pp.3617-3625, 2011. ,
Distribution, formation and regulation of gas vesicles, Nat Rev Microbiol, vol.10, pp.705-715, 2012. ,
Bacterial insertion sequences: their genomic impact and diversity, FEMS Microbiol Rev, vol.38, pp.865-891, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01117881
Insertion sequences, Microbiol Mol Biol Rev, vol.62, pp.725-774, 1998. ,
URL : https://hal.archives-ouvertes.fr/hal-00021179
Genomic changes following host restriction in bacteria, Curr Opin Genet Dev, vol.14, pp.627-633, 2004. ,
Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia, BMC Genom, vol.10, p.468, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-02555039
Tracing the evolution of gene loss in obligate bacterial symbionts, Curr Opin Microbiol, vol.6, pp.512-518, 2003. ,
Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium, PLoS One, vol.5, p.11486, 2010. ,
Complete genome sequence of Geodermatophilus obscurus type strain (G-20), Stand Genomic Sci, vol.2, pp.158-167, 2010. ,
Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations, Genome Res, vol.19, pp.1033-1043, 2009. ,
URL : https://hal.archives-ouvertes.fr/halsde-00526039
Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21), Stand Genomic Sci, vol.1, pp.234-241, 2009. ,
Complete genome sequence of Nakamurella multipartita type strain (Y-104), Stand Genomic Sci, vol.2, pp.168-175, 2010. ,
The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571, BMC Genomics, vol.9, p.271, 2008. ,
From ?-to ?-proteobacteria: the origin and evolution of rhizobial nodulation genes nodIJ, Mol Biol Evol, vol.30, pp.2494-2508, 2013. ,
Multiple origins of endosymbiosis within the Enterobacteriaceae (?-Proteobacteria): convergence of complex phylogenetic approaches, BMC Biol, vol.9, p.87, 2011. ,
The genome of Rhizobium leguminosarum has recognizable core and accessory components, Genome Biol, vol.7, p.34, 2006. ,
G+C3 structuring along the genome: a common feature in prokaryotes, Mol Biol Evol, vol.20, pp.471-483, 2003. ,
URL : https://hal.archives-ouvertes.fr/hal-00427485
The Frankia alni symbiotic transcriptome, Mol Plant Microbe Interact, vol.23, pp.593-607, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00599356
The diversity of actinorhizal symbiosis, Protoplasma, vol.249, pp.967-979, 2012. ,
Mycobacteria in water, soil, plants and air: a review, Veterinarni Medicina, vol.57, pp.623-679, 2012. ,
Peptidoglycan from Bacillus cereus mediates commensalism with rhizosphere bacteria from the Cytophaga-Flavobacterium group, Appl Env Microbiol, vol.72, pp.5421-5427, 2006. ,
Multilocus sequence analysis of phytopathogenic species of the genus Streptomyces, Int J Syst Evol Microbiol, vol.61, pp.2525-2531, 2010. ,
Dyadobacter fermentans gen. nov., sp. nov., a novel Gram-negative bacterium isolated from surface-sterilized Zea mays stems, Int J Syst Evol Microbiol, vol.50, pp.751-758, 2000. ,
Novel root nodule bacteria belonging to the genus Caulobacter, Lett Appl Microbiol, vol.53, pp.587-591, 2011. ,
Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses, Int J Syst Evol Microbiol, vol.51, pp.1405-1417, 2001. ,
Methylophilus rhizosphaerae sp. nov., a restricted facultative methylotroph isolated from rice rhizosphere soil, Int J Syst Evol Microbiol, vol.59, pp.2904-2908, 2009. ,
, Symbiosis. Curr Biol, vol.16, pp.866-871, 2006.
Evolution of organellar genomes, Curr Opin Genet Dev, vol.9, pp.678-687, 1999. ,
Glomalean fungi from the Ordovician, Science, vol.289, pp.1920-1921, 2000. ,
Estimation of the Glomus intraradices nuclear DNA content, New Phytol, vol.192, pp.794-797, 2011. ,
First report on the occurrence of the uncultivated cluster 2 Frankia microsymbionts in soil outside the native actinorhizal host range area, J Biosci, vol.38, pp.695-698, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-02522200
Spores of Frankia strain HFPCcI3 nodulate Casuarina equisetifolia after passage through the digestiv tracts of captive parakeets (Melopsittacus undulatus), Can J Bot, vol.73, pp.1527-1530, 1995. ,
River and lake sediments as sources of infective Frankia (Alnus), Plant Soil, vol.197, pp.35-39, 1997. ,
Diversity of Frankia strains in root nodules of plants from the families Elaeagnaceae and Rhamnaceae, Appl Environ Microbiol, vol.64, pp.3539-3543, 1998. ,
Draft genome sequence of Frankia sp. strain CN3, an atypical, noninfective (Nod -) ineffective (Fix -) isolate from Coriaria nepalensis, Genome Announc, vol.1, p.8513, 2013. ,
Draft genome sequence of Frankia sp. strain CcI6, a salt-tolerant nitrogen-fixing actinobacterium isolated from the root nodule of Casuarina cunninghamiana, Genome Announc, vol.2, pp.1205-1218, 2014. ,
Mammalian cell entry genes in Streptomyces may provide clues to the evolution of bacterial virulence, Sci Rep, vol.3, p.1109, 2013. ,
PCR-amplified 16S ribosomal RNA sequence analysis to confirm nodulation of Datisca cannabina by the endophyte of Coriaria nepalensis Wall, Plant Soil, vol.160, pp.147-152, 1994. ,
Suppression of nodulation gene expression in bacteroids of Rhizobium leguminosarum biovar viciae, J Bacteriol, vol.173, pp.4277-4287, 1991. ,
Formation of organelle-like N 2 -fixing symbiosomes in legume root nodules is controlled by DMI2, Proc Natl Acad Sci, vol.102, pp.10375-10380, 2005. ,
Novel expression pattern of cytosolic glutamine synthetase in nitrogen-fixing root nodules of the actinorhizal host, Datisca glomerata, Plant Physiol, vol.135, pp.1849-1862, 2004. ,
New perspectives on nodule nitrogen assimilation in actinorhizal symbioses, Funct Plant Biol, vol.38, pp.645-652, 2011. ,
Legumes regulate Rhizobium bacteroid development and persistence by the supply of branched-chain amino acids, Proc Natl Acad Sci, vol.106, pp.12477-12482, 2009. ,
Biosynthesis of branched-chain amino acids is essential for effective symbioses between ?-rhizobia and Mimosa pudica, Microbiology, vol.158, pp.1758-1766, 2012. ,
Hopanoid lipids compose the Frankia vesicle envelope, presumptive barrier of oxygen diffusion to nitrogenase, Proc Natl Acad Sci, vol.90, pp.6091-6094, 1993. ,
Arbuscular mycorrhiza: the mother of plant root endosymbioses, Nat Rev Microbiol, vol.6, pp.763-775, 2008. ,
Evolutionary genomics of LysM genes in land plants, BMC Evol Biol, vol.9, p.183, 2009. ,
Proof that Burkholderia strains form effective symbioses with legumes: a study of novel Mimosa-nodulating strains from South America, Appl Environ Microbiol, vol.71, pp.7461-7471, 2005. ,
Burkholderia species are ancient symbionts of legumes, Mol Ecol, vol.19, pp.44-52, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-01655679
Nod factors integrate spontaneously in biomembranes and transfer rapidly between membranes and to root hairs, but transbilayer flip-flop does not occur, Biochem, vol.38, pp.10898-10907, 1999. ,
The molecular phylogeny and systematics of the actinomycetes, Annu Rev Microbiol, vol.48, pp.257-289, 1994. ,