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9 results for “ycf1”
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: 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.
Data from: Primer development for the plastid region ycf1 in Annonaceae and other magnoliids
PREMISE OF THE STUDY: Primers were developed for a portion of the ycf1 plastid gene in magnoliid taxa to investigate the utility of ycf1 in phylogenetic analyses. METHODS AND RESULTS: Twenty-six species across six families within the magnoliid group (Canellales, Piperales, Laurales, and Magnoliales) were sampled to examine the ability to amplify ycf1. Additionally, 29 accessions of Asimina and Deeringothamnus (Annonaceae) were sequenced to assess levels of variation in ycf1 compared to matK and trnL-F. CONCLUSIONS: Results indicate that ycf1 is easily amplifi ed and sequenced. In Annonaceae, ycf1 provides more informative phylogenetic characters than commonly used markers such as matK and trnL-F .
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.
Data from: Primer development for the plastid region ycf1 in Annonaceae and other magnoliids
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Data from: Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK
Open the record for dataset details and reuse information.
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