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12 results for “nrITS”
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 1. Maximum Likelihood phylogram obtained from the general nrITS and RPB2 in Inocybe cervenianensis (Agaricales, Inocybaceae), a new species in the I. flavoalbida clade from Italy
FIGURE 1. Maximum Likelihood phylogram obtained from the general nrITS and RPB2 sequence alignment of Inocybe spp. Mallocybe arthrocystis and Mallocybe leucoblema were used as outgroup taxa. Only MLB values ≥70% and BPP values ≥0.95 are given above clade branches. Newly sequenced collections are in bold. For each collection, the specific epithet (as present in GenBank), voucher, GenBank accession numbers of the RPB2/ITS sequences are reported. The /- notation indicates the sequence as missing for that collection.
Chloroplast haplotypes and main haplotypes of nrITS clones of Gentiana crassicaulis
<p>The Himalaya-Hengduan Mountain region is one of the hotspots of biodiversity research. The uplift of the Qinghai-Tibetan Plateau (QTP) and the Quaternary glaciation caused great environmental changes in this region, and the responses of many species in the QTP to the Quaternary climate are still largely unknown. The genetic structure and phylogeographical history of Gentiana crassicaulis Duthie ex Burk, an endemic Chinese alpine species in this area, were investigated based on four chloroplast fragments and internal transcribed spacer region of the nuclear ribosomal DNA (nrITS) sequences of 11 populations. The populations with highly diverse chloroplast haplotypes were mainly found at the edge of the QTP. There were two main haplotypes of nrITS clones, one shared by the Yunnan and Guizhou populations, and the other by the remaining populations. The population with the highest diversity was the Gansu population, located at the edge of the plateau. Based on molecular dating, the diversification of G. crassicaulis at the edge of the plateau occurred before the Last Glacial Maximum (LGM), and the species may have completed its expansion from the edge to the platform. Ecological Niche Models were conducted to predict the distributional ranges of G. crassicaulis at present, during the LGM, and during the last interglacial (LIG) period. The results demonstrated that G. crassicaulis survived on the QTP platform and at the edge during the LGM but afterward retreated from the platform to the southern edge, followed by expansion to the platform.</p>
Chloroplast haplotypes and main haplotypes of nrITS clones of Gentiana crassicaulis
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Figure 1 from: Chen H, Al-Shehbaz IA, Yue J, Sun H (2018) New insights into the taxonomy of tribe Euclidieae (Brassicaceae), evidence from nrITS sequence data. PhytoKeys 100: 125-139. https://doi.org/10.3897/phytokeys.100.24756
Figure 1 Phylogenetic tree resulting from Bayesian analysis of the ITS sequences of the 88 Brassicaceae species, of which 28 genera and 82 species in Euclidieae. Posterior probabilities are indicated above branches. Bootstrap support values (>50%) are noted below branches.
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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