The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation, Am J Bot, vol.99, issue.9, pp.1513-1523, 2012. ,
Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms, Mol Biol Evol, vol.31, issue.12, pp.3095-3112, 2014. ,
Tribe Neottieae, vol.4, 2005. ,
Nutritional regulation in mixotrophic plants: new insights from Limodorum abortivum, Oecologia, vol.175, issue.3, pp.875-885, 2014. ,
Isotopic evidence of partial mycoheterotrophy in Burmannia coelestis (Burmanniaceae), Plant Species Biol, vol.32, issue.1, pp.74-80, 2017. ,
Mauve: multiple alignment of conserved genomic sequence with rearrangements, Genome Res, vol.14, issue.7, pp.1394-1403, 2004. ,
Orchid mycorrhizas: molecular ecology, physiology, evolution and conservation aspects, 2012. ,
, , pp.207-230
Lineage-specific reductions of plastid genomes in an orchid tribe with partially and fully mycoheterotrophic species, 2016. ,
, Genome Biol Evol, vol.8, issue.7, pp.2164-2175
An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution, Biochem Genet, vol.4, issue.5, pp.579-593, 1970. ,
Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii, BMC Plant Biol, vol.7, p.45, 2007. ,
15 N and 13 C natural abundance of autotrophic and myco-heterotrophic orchids provides insight into nitrogen and carbon gain from fungal association, New Phytol, vol.160, issue.1, pp.209-223, 2003. ,
Inefficient photosynthesis in the Mediterranean orchid Limodorum abortivum is mirrored by specific association to ectomycorrhizal Russulaceae, Mol Ecol, vol.15, issue.2, pp.491-504, 2006. ,
Phylogenetic insights on adaptive radiation, Annu Rev Ecol Evol Syst, vol.41, issue.1, pp.251-270, 2010. ,
Photosynthesis in perennial mixotrophic Epipactis spp. (Orchidaceae) contributes more to shoot and fruit biomass than to hypogeous survival, J Ecol, vol.102, issue.5, pp.1183-1194, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01908416
Phylogenetic relationships within Orchidaceae based on a low-copy nuclear coding gene, Xdh: congruence with organellar and nuclear ribosomal DNA results, Mol Phylogenet Evol, vol.56, issue.2, pp.784-795, 2010. ,
Plastomes on the edge: the evolutionary breakdown of mycoheterotroph plastid genomes, New Phytol, vol.214, issue.1, pp.48-55, 2017. ,
Two distinct plastid genome configurations and unprecedented intraspecies length variation in the accD coding region in Medicago truncatula, DNA Res, vol.21, pp.417-427, 2014. ,
Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina, R Soc Open Sci, vol.4, issue.10, p.171095, 2017. ,
The physiological ecology of mycoheterotrophy, Mycoheterotrophy: the biology of plants living on fungi, pp.297-342, 2013. ,
Mycorrhizal associations and trophic modes in coexisting orchids: an ecological continuum between auto-and mixotrophy, Front Plant Sci, vol.8, p.1497, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01589851
The evolution of floral deception in Epipactis veratrifolia (Orchidaceae): from indirect defense to pollination, BMC Plant Biol, vol.14, p.63, 2014. ,
Mixotrophy in orchids: insights from a comparative study of green individuals and nonphotosynthetic individuals of Cephalanthera damasonium, New Phytol, vol.166, issue.2, pp.639-653, 2005. ,
ModelFinder: fast model selection for accurate phylogenetic estimates, Nat Methods, vol.14, issue.6, pp.587-589, 2017. ,
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization, Brief Bioinform bbx, p.108, 2017. ,
Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics, vol.28, issue.12, pp.1647-1649, 2012. ,
Sequencing of the plastome in the leafless green mycoheterotroph Cymbidium macrorhizon helps us to understand an early stage of fully mycoheterotrophic plastome structure, Plant Syst Evol, vol.304, issue.2, pp.245-258, 2018. ,
Seven new complete plastome sequences reveal rampant independent loss of the ndh gene family across orchids and associated instability of the inverted repeat/small single-copy region boundaries, PLoS One, vol.10, issue.11, p.142215, 2015. ,
Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants, DNA Res, vol.11, issue.4, pp.247-261, 2004. ,
The 13 C content of the orchid Epipactis palustris (L.) Crantz responds to light as in autotrophic plants, Bot Lett, vol.165, pp.265-273, 2018. ,
The elusive predisposition to mycoheterotrophy in Ericaceae, New Phytol, vol.212, issue.2, pp.314-319, 2016. ,
Mixotrophic orchids do not use photosynthates for perennial underground organs, New Phytol, vol.221, issue.1, pp.12-17, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02124763
The biology of myco-heterotrophic ('saprophytic') plants, New Phytol, vol.127, issue.2, pp.171-216, 1994. ,
Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids, Plant J, vol.90, pp.994-1006, 2017. ,
Comparative chloroplast genomes of photosynthetic orchids: insights into evolution of the Orchidaceae and development of molecular markers for phylogenetic applications, PLoS One, vol.9, issue.6, p.99016, 2014. ,
Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta, BMC Plant Biol, vol.7, p.57, 2007. ,
Taxonomy and classification, Mycoheterotrophy: the biology of plants living on fungi, pp.19-101, 2013. ,
Evolution and diversification, Mycoheterotrophy: the biology of plants living on fungi, pp.215-244, 2013. ,
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol Biol Evol, vol.32, issue.1, pp.268-274, 2015. ,
Variation in synonymous substitution rates among mammalian genes and the correlation between synonymous and nonsynonymous divergences, J Mol Evol, vol.41, issue.6, pp.717-720, 1995. ,
Plastome evolution in hemiparasitic mistletoes, Genome Biol Evol, vol.7, issue.9, pp.2520-2532, 2015. ,
Genome reports: contracted genes and dwarfed plastome in mycoheterotrophic Sciaphila thaidanica, 2018. ,
, Genome Biol Evol, vol.10, issue.3, pp.976-981
Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components, Plant Mol Biol Rep, vol.15, issue.1, pp.8-15, 1997. ,
, R: a language and environment for statistical computing, 2007.
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space, Syst Biol, vol.61, issue.3, pp.539-542, 2012. ,
Two mycoheterotrophic orchids from Thailand tropical dipterocarpacean forests associate with a broad diversity of ectomycorrhizal fungi, BMC Biol, vol.7, p.51, 2009. ,
Why do mixotrophic plants stay green? A comparison between green and achlorophyllous orchid individuals in situ, Ecol Monogr, vol.83, pp.95-117, 2013. ,
Exploiting mycorrhizas in broad daylight: partial mycoheterotrophy is a common nutritional strategy in meadow orchids, J Ecol, vol.106, issue.1, pp.168-178, 2018. ,
Mixotrophy everywhere on land and in water: the grand ecart hypothesis, Ecol Lett, vol.20, issue.2, pp.246-263, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01624074
Do chlorophyllous orchids heterotrophically use mycorrhizal fungal carbon?, Trends Plant Sci, vol.19, issue.11, pp.683-685, 2014. ,
Green plants that feed on fungi: facts and questions about mixotrophy, Trends Plant Sci, vol.14, issue.2, pp.64-70, 2009. ,
Communities and populations of sebacinoid basidiomycetes associated with the achlorophyllous orchid Neottia nidus-avis (L.) L.C.M. Rich. and neighbouring tree ectomycorrhizae, Mol Ecol, vol.11, issue.9, pp.1831-1844, 2002. ,
Mycorrhizal symbiosis, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-01268065
Partial mycoheterotrophy in the leafless orchid Cymbidium macrorhizon, Am J Bot, vol.105, issue.9, pp.1595-1596, 2018. ,
Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference, Syst Biol, vol.64, pp.778-791, 2015. ,
Mixotrophy in Land Plants: why to Stay Green?, Trends Plant Sci, vol.23, issue.8, pp.656-659, 2018. ,
Symbiotic germination capability of four Epipactis species (Orchidaceae) is broader than expected from adult ecology, Am J Bot, vol.99, issue.6, pp.1020-1032, 2012. ,
Two widespread green Neottia species (Orchidaceae) show mycorrhizal preference for Sebacinales in various habitats and ontogenetic stages, Mol Ecol, vol.24, issue.5, pp.1122-1134, 2015. ,
Analysis of plastid and nuclear DNA data in plant phylogenetics-evaluation and improvement, Sci China Life Sci, vol.57, issue.3, pp.280-286, 2014. ,
, World checklist of selected plant families. Facilitated by the Royal Botanic Gardens, February, vol.17, 2018.
RELAX: detecting relaxed selection in a phylogenetic framework, Mol Biol Evol, vol.32, issue.3, pp.820-832, 2015. ,
Molecular evolution of plastid genomes in parasitic flowering plants, Advances in botanical research, vol.85, pp.315-347, 2018. ,
Disproportional plastome-wide increase of substitution rates and relaxed purifying selection in genes of carnivorous Lentibulariaceae, Mol Biol Evol, vol.31, issue.3, pp.529-545, 2014. ,
Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants, Proc Natl Acad Sci U S A, vol.113, issue.32, pp.9045-9050, 2016. ,
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment, BMC Bioinformatics, vol.16, p.322, 2015. ,
Using DECIPHER v2.0 to analyze big biological sequence data in R. R, J, vol.8, issue.1, pp.352-359, 2016. ,
Phylogenetic placement of the enigmatic orchid genera Thaia and Tangtsinia: evidence from molecular and morphological characters, Taxon, vol.61, issue.1, pp.45-54, 2012. ,
Fungal partner shifts during the evolution of mycoheterotrophy in Neottia, Am J Bot, vol.103, issue.9, pp.1630-1641, 2016. ,
Phylogenetic Analysis by Maximum Likelihood, Mol Biol Evol, vol.4, issue.8, pp.1586-1591, 2007. ,
Molecular systematics and the evolution of mycoheterotrophy of tribe Neottieae (Orchidaceae, Epidendroideae), PhytoKeys, vol.94, pp.39-49, 2018. ,