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25 results for “matK”
FIG. 1 in Position taxonomique de Hemiperis micrantha (Frapp. ex Cordem.) Schltr. (Orchidaceae; Orchidoideae; Habenariinae), par séquençage des gènes ITS et matK
FIG. 1. — Arbre phylogénétique à maximum de vraisemblance déduit de l'analyse matK (A) et ITS (B). La prise en charge du bootstrap à partir des analyses du maximum de vraisemblance (MV) supérieures à 50% est indiquée au-dessus des branches. Le symbole (*) représente les espèces types des genres Cynorkis Thouars et Benthamia A. Rich. et le symbole (+) positionne Cynorkis micrantha (Frapp. ex Cordem.) Schltr. dans les arbres.
FIG. 3 in Position taxonomique de Hemiperis micrantha (Frapp. ex Cordem.) Schltr. (Orchidaceae; Orchidoideae; Habenariinae), par séquençage des gènes ITS et matK
FIG. 3. — Cynorkis micrantha (Frapp. ex Cordem.) Schltr. photographié in situ (photographies de Frédéric Henze): A, fleur vue de face; B, fleur vue de profil; C, inflorescence; D, feuille.
Genus level DNA sequence data for three genes (matK, rbcL, trnH-psbA) for the paper: A comprehensive, genus-level time-calibrated phylogeny of the tree flora of Mediterranean Europe and an assessment of its vulnerability
<p>This data file contains the consensus DNA sequences in fasta format, of 64 tree genera found in Mediterranean Europe, following the checklist of Médail et al. (2019). </p> <p>The data are used in a manuscript submitted for publication to Botany Letters and currently under revision. The manuscript is entitled: "<em>A comprehensive, genus-level time-calibrated phylogeny of the tree flora of Mediterranean Europe and an assessment of its vulnerability</em>". Its authors are: Marwan Cheikh Albassatneh, Marcial Escudero, Loic Ponge<sup>*</sup>, Anne-Christine Monnet, Juan Arroyo, Toni Nikolic, Gianluigi Bacchetta, Francesca Bagnoli, Panayotis Dimopoulos, Agathe Leriche, Frédéric Médail, Anne Roig, Ilaria Spanu, Giovanni Giuseppe Vendramin, Arndt Hampe, Bruno Fady.</p>
FIG. 2 in Position taxonomique de Hemiperis micrantha (Frapp. ex Cordem.) Schltr. (Orchidaceae; Orchidoideae; Habenariinae), par séquençage des gènes ITS et matK
FIG. 2. — Néotype de Cynorkis micrantha (Frapp. ex Cordem.) Schltr. hébergé à REU (REU007364).
Data from: Megaphylogenetic specimen-level approaches to the Carex (Cyperaceae) phylogeny using ITS, ETS, and matK sequences: implications for classification
We present the first large-scale phylogenetic hypothesis for the genus Carex based on 996 of the 1983 accepted species (50.23%). We used a supermatrix approach using three DNA regions: ETS, ITS and matK. Every concatenated sequence was derived from a single specimen. The topology of our phylogenetic reconstruction largely agreed with previous studies. We also gained new insights into the early divergence structure of the two largest clades, core Carex and Vignea clades, challenging some previous evolutionary hypotheses about inflorescence structure. Most sections were recovered as non-monophyletic. Homoplasy of characters traditionally selected as relevant for classification, historical misunderstanding of how morphology varies across Carex, and regional rather than global views of Carex diversity seem to be the main reasons for the high levels of polyphyly and paraphyly in the current infrageneric classification.
FIGURE. Bayesian tree based on combined plastid (matK, trnL-trnF) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches in Hedysarum sunhangii (Fabaceae, Hedysareae), a new species from Pamir-Alay (Babatag Ridge - Uzbekistan)
FIGURE. Bayesian tree based on combined plastid (matK, trnL-trnF) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches
FIGURE. (A) Summary phylogeny showing relations between genera in tribe Phyllantheae from Bayesian and Maximum Likelihood analysis of five markers (ITS, PHYC, accD–psaI, trnS–trnG, matK), modified from Appendix 1. Classification is shown of genera (right column), subgenera (middle column) and sections (except for the genus Phyllanthus. Sections not included in phylogenetic analyses and those for the genus Flueggea were omitted. (B) summary phylogeny of the genus Phyllanthus as envisioned here with subgenera and sections of groups included in phylogenetic studies shown. in A revised phylogenetic classification of tribe Phyllantheae (Phyllanthaceae)
FIGURE. (A) Summary phylogeny showing relations between genera in tribe Phyllantheae from Bayesian and Maximum Likelihood analysis of five markers (ITS, PHYC, accD–psaI, trnS–trnG, matK), modified from Appendix 1. Classification is shown of genera (right column), subgenera (middle column) and sections (except for the genus Phyllanthus. Sections not included in phylogenetic analyses and those for the genus Flueggea were omitted. (B) summary phylogeny of the genus Phyllanthus as envisioned here with subgenera and sections of groups included in phylogenetic studies shown.
FIGURE 4. Bulbophyllum cambodianum. Two Bulbophyllum cambodianum specimens with different flower morphology. B. cambodianum I in Molecular phylogenetics of species of Bulbophyllum sect. Trias (Orchidaceae; Epidendroideae; Malaxidae) based on nrITS and plastid rbcL and matK
FIGURE 4. Bulbophyllum cambodianum. Two Bulbophyllum cambodianum specimens with different flower morphology. B. cambodianum I (A) has pale yellow flower with purple dots on the sepals, both edges of petals and proximal half of the lip, with the top sepal and the lateral sepals shapes being slightly different and the top being slightly slender than the lateral. B. cambodianum II (B), on the other hand, has equally shaped sepals, with purple dots on its flower that are slightly darker and more densely distributed in the proximal end of sepals than in the apex and having darker purple dots that cover the petals including the lip very densely with its dorsal sepal bent forward at almost a 90–degree angle.
FIGURE 1 in Molecular phylogenetics of species of Bulbophyllum sect. Trias (Orchidaceae; Epidendroideae; Malaxidae) based on nrITS and plastid rbcL and matK
FIGURE 1. Phylogenetic tree of Trias and Bulbophyllum based on nuclear ITS sequence. The Bayesian tree of Trias species, Drymoda and 32 Bulbophyllum species with five outgroup species. Numbers above branches are maximum likelihood bootstrap percentage (BP), numbers below branches are Bayesian posterior probabilities (PP). A dash (-) above branches are values below 50 BP. Clades of Trias and Bulbophyllum are indicated. Trias photographs represent vegetative morphological characters unique to each Trias clade.
FIGURE 3 in Molecular phylogenetics of species of Bulbophyllum sect. Trias (Orchidaceae; Epidendroideae; Malaxidae) based on nrITS and plastid rbcL and matK
FIGURE 3. The species tree of Trias and Bulbophyllum based on ITS and plastid matK–rbcL sequences. The species tree constructed by StatBEAST utilizing ITS, matK, and rbcL for eight Trias species, Drymoda and 18 Bulbophyllum species with four outgroup species: Dendrobium pullchellum, D. parciflorum, D. rosellum and D. mariae. Numbers above branches are posterior probabilities (PP). Clades of Trias and Bulbophyllum are indicated.
FIGURE 2 in Molecular phylogenetics of species of Bulbophyllum sect. Trias (Orchidaceae; Epidendroideae; Malaxidae) based on nrITS and plastid rbcL and matK
FIGURE 2. The phylogenetic tree of Trias and Bulbophyllum based on plastid matK–rbcL sequence. The Bayesian tree of Trias species, Drymoda and 18 Asian Bulbophyllum species with four outgroup species: Dendrobium pullchellum, D. parciflorum, D. rosellum and D. mariae. Numbers above branches are maximum likelihood bootstrap percentage (BP), numbers below branches are Bayesian posterior probabilities (PP). Clades of Trias and Bulbophyllum are indicated.
FIGURE 4. trnK-matK mrBayes 50 in Wadithamnus, a new monotypic genus in Amaranthaceae
FIGURE 4. trnK-matK mrBayes 50% majority-rule consensus tree. Bayesian posterior probabilities and maximum likelihood bootstrap are given above and below the branches respectively. An arrow indicates the position of Aerva artemisioides; major clades within Amaranthaceae are labeled on the right.
FIGURE. Maximum clade credibility tree of a post-burnin Bayesian analysis (100 million generations), based on nuclear (agt1, ETS, g3pdh, phyC, rpb2) and plastid (atpB–rbcL, matK, rps16, ycf1 pos. 1113-2103, ycf1 pos. 4492-5440) data. Above the branches, Bayesian posterior probabilities (PP) and maximum-likelihood bootstrap support (BS) are shown (PP/BS). The scale bar below the tree shows the branch length for 0.004 substitutions per nucleotide position. Capital letters at the branches are referred to in the tree description. in Re-evaluation of the Amazonian Hylaeaicum (Bromeliaceae: Bromelioideae) based on neglected morphological traits and molecular evidence
FIGURE. Maximum clade credibility tree of a post-burnin Bayesian analysis (100 million generations), based on nuclear (agt1, ETS, g3pdh, phyC, rpb2) and plastid (atpB–rbcL, matK, rps16, ycf1 pos. 1113-2103, ycf1 pos. 4492-5440) data. Above the branches, Bayesian posterior probabilities (PP) and maximum-likelihood bootstrap support (BS) are shown (PP/BS). The scale bar below the tree shows the branch length for 0.004 substitutions per nucleotide position. Capital letters at the branches are referred to in the tree description.
Data from: Megaphylogenetic specimen-level approaches to the Carex (Cyperaceae) phylogeny using ITS, ETS, and matK sequences: implications for classification
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Data from: Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae
Background: The plastid maturase MatK has been implicated as a possible model for the evolutionary "missing link" between prokaryotic and eukaryotic splicing machinery. This evolutionary implication has sparked investigations concerning the function of this unusual maturase. Intron targets of MatK activity suggest that this is an essential enzyme for plastid function. The matK gene, however, is described as a pseudogene in many photosynthetic orchid species due to presence of premature stop codons in translations, and its high rate of nucleotide and amino acid substitution. Results: Sequence analysis of the matK gene from orchids identified an out-of-frame alternative AUG initiation codon upstream from the consensus initiation codon used for translation in other angiosperms. We demonstrate translation from the alternative initiation codon generates a conserved MatK reading frame. We confirm that MatK protein is expressed and functions in sample orchids currently described as having a matK pseudogene using immunodetection and reverse-transcription methods. We demonstrate using phylogenetic analysis that this alternative initiation codon emerged de novo within the Orchidaceae, with several reversal events at the basal lineage and deep in orchid history. Conclusion: These findings suggest a novel evolutionary shift for expression of matK in the Orchidaceae and support the function of MatK as a group II intron maturase in the plastid genome of land plants including the orchids.
Data from: Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK
Plastid DNA sequences have been widely used by systematists for reconstructing plant phylogenies. The utility of any DNA region for phylogenetic analysis is determined by ease of amplification and sequencing, confidence of assessment in phylogenetic character alignment, and by variability across broad taxon sampling. Often, a compromise must be made between using relatively highly conserved coding regions or highly variable introns and intergenic spacers. Analyses of a combination of these types of DNA regions yield phylogenetic structure at various levels of a tree (i.e., along the spine and at the tips of the branches). Here, we demonstrate the phylogenetic utility of a heretofore unused portion of a plastid protein-coding gene, hypothetical chloroplast open reading frame 1 (ycf1), in orchids. All portions of ycf1 examined are highly variable, yet alignable across Orchidaceae, and are phylogenetically informative at the level of species. In Orchidaceae, ycf1 is more variable than matK both in total number of parsimony informative characters and in percent variability. The nrITS region is more variable than ycf1, but is more difficult to align. Although we only demonstrate the phylogenetic utility of ycf1 in orchids, it is likely to be similarly useful among other plant taxa.
Figure 3 from: Sulistyo B, Boos R, Cootes J, Gravendeel B (2015) Dendrochilum hampelii (Coelogyninae, Epidendroideae, Orchidaceae) traded as 'Big Pink' is a new species, not a hybrid: evidence from nrITS, matK and ycf1 sequence data. PhytoKeys 56: 83-97. https://doi.org/10.3897/phytokeys.56.5432
Figure 3 - Dendrochilum hampelii: a habit b floral bract c flower d flower (sepals and petals removed) e dorsal sepal f petal g lateral sepal h labellum i column, front view j anther k pollinia. Drawing by Esmee Winkel based on Hort. bot. Leiden 20130654 (L! [spirit no. WAG0116920]).
Figure 2 from: Sulistyo B, Boos R, Cootes J, Gravendeel B (2015) Dendrochilum hampelii (Coelogyninae, Epidendroideae, Orchidaceae) traded as 'Big Pink' is a new species, not a hybrid: evidence from nrITS, matK and ycf1 sequence data. PhytoKeys 56: 83-97. https://doi.org/10.3897/phytokeys.56.5432
Figure 2 - Above: alignment of nrITS sequences of the ingroup species from our phylogenetic analyses. For 'Big Pink' (Dendrochilum hampelii) and its apparently closest relatives among our study species, electropherograms are shown in red boxes. The electropherograms show clear distinct peaks; the species-specific mutation of 'Big Pink' is indicated by a red arrow. Below: electropherogram of 'Big Pink' (Dendrochilum hampelii) covering a larger region of nrITS; the distinct single peaks in both the forward and reverse sequences suggest this is a wild species rather than an artificial hybrid (see text for details).
Figure 1 from: Sulistyo B, Boos R, Cootes J, Gravendeel B (2015) Dendrochilum hampelii (Coelogyninae, Epidendroideae, Orchidaceae) traded as 'Big Pink' is a new species, not a hybrid: evidence from nrITS, matK and ycf1 sequence data. PhytoKeys 56: 83-97. https://doi.org/10.3897/phytokeys.56.5432
Figure 1 - Phylogenetic relationships amongst the sampled species of Dendrochilum, created using BEAST and PAUP*. The values on the nodes represent posterior probabilities, whereas branch lengths indicate to the relative number of changes: A comparison between topologies based on nrITS and matK + ycf1 matrices B topology resulting from the combined nrITS + matK + ycf1 data matrices.
Figure 4 from: Sulistyo B, Boos R, Cootes J, Gravendeel B (2015) Dendrochilum hampelii (Coelogyninae, Epidendroideae, Orchidaceae) traded as 'Big Pink' is a new species, not a hybrid: evidence from nrITS, matK and ycf1 sequence data. PhytoKeys 56: 83-97. https://doi.org/10.3897/phytokeys.56.5432
Figure 4 - Dendrochilum hampelii: A portion of inflorescence of cultivated pinkish salmon-coloured form B habit. Photographs by Lubbert Westra of Hort. bot. Leiden 20130654 (L! [spirit no. WAG0116920]) C portion of inflorescence of pale yellow-coloured form of a plant growing in the wild in the Philippines in the Misamis Oriental province of the island of Mindanao. Photograph by James Cootes.
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