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373 results for “Chloroplast”
FIGURE 6 in Liu, H.J., Ding, C.H., He, J., Cheng, J., Pei, L.Y. & Xie, L. (2018) Complete chloroplast genomes of Archiclematis, Naravelia and Clematis (Ranunculaceae), and their phylogenetic implications. Phytotaxa 343 (3): 214-226.
FIGURE 6. Phylogeny of Clematis s.l. species inferred from complete chloroplast genome sequences. Bayesian phylograms are shown with MP bootstrap values/PP values at each node.
FIGURE 2 in Iris tibetica, a new combination in I. ser. Lacteae (Iridaceae) from China: evidence from morphological and chloroplast DNA analyses
FIGURE 2. Median-joining network based on combined sequences of four cpDNA regions, depicting the relationships among haplotypes of 136 individuals from 59 localities across the geographic range of Iris ser. Lacteae. Each white circle represents a haplotype and the size of the circle is proportional to the number of individuals with that haplotype. Haplotype codes correspond to those in Table 1. Black dots indicate missing haplotypes (extinct or not sampled). Haplotypes of A, B, and C haplogroups are encircled with thin lines.
FIGURE 4 in Complete chloroplast genomes of Archiclematis, Naravelia and Clematis (Ranunculaceae), and their phylogenetic implications
FIGURE 4. Sliding window analysis of the whole plastid genomes of eight Clematis s.l. samples. Lines parallel to the x-axis show the positions of the LSC, SSC, and IR regions. The vertical blue line shows the value of nucleotide diversity (Pi) in a sliding window analysis of window size 600 bp with step size 50 bp. The value is inserted at its mid-point.
FIGURE 3 in Complete chloroplast genomes of Archiclematis, Naravelia and Clematis (Ranunculaceae), and their phylogenetic implications
FIGURE 3. Sequence alignment of eight plastomes of Clematis s.l. in the mVISTA program. Clematis terniflora was used as a reference. A cut-off of 70% similarity was used for the plot. The Y-scale represents the percent similarity (50–100%). Blue represents coding regions, and pink represents non-coding regions.
FIGURE 1 in Complete chloroplast genomes of Archiclematis, Naravelia and Clematis (Ranunculaceae), and their phylogenetic implications
FIGURE 1. Map of the chloroplast genomes of Clematis s.l. Genes shown outside the circle are transcribed clockwise, whereas those inside the circle are transcribed counterclockwise. Genes belonging to different functional groups are colored. The dashed area in the inner circle indicates the GC content of the plastomes.
FIGURE 5 in Complete chloroplast genomes of Archiclematis, Naravelia and Clematis (Ranunculaceae), and their phylogenetic implications
FIGURE 5. Analyses of repeated sequences in Clematis s.l. chloroplast genomes. A: Number of each repeat type; B: frequency of direct repeats by length; C: frequency of reverse repeats by length; D: frequency of palindromic repeats by length; E: location of repeats.
FIGURE 2 in Complete chloroplast genomes of Archiclematis, Naravelia and Clematis (Ranunculaceae), and their phylogenetic implications
FIGURE 2. Comparison of the LSC, IRs and SSC borders among Clematis s.l. samples used in this study.
FIGURE 4 in Iris tibetica, a new combination in I. ser. Lacteae (Iridaceae) from China: evidence from morphological and chloroplast DNA analyses
FIGURE 4. Phylogenetic analysis of Iris ser. Lacteae based on psbA–trnH/rps4–trnS/trnS–trnG/trnL–trnF sequences. Neighbour-joining tree is shown with bootstrap values in 1000 replicates for NJ/MP/ML analyses (shown only when> 50%) above the branches and Bayesian posterior probabilities more than PP = 0.90 below the branches. Clades I and II within I. ser. Lacteae are indicated. Haplotypes and locality codes are given in Table 1.
FIGURE 1 in Iris tibetica, a new combination in I. ser. Lacteae (Iridaceae) from China: evidence from morphological and chloroplast DNA analyses
FIGURE 1. Map showing the locations of Iris ser. Lacteae samples analyzed in the present study (created with http://www. spatialepidemiology.net). The locality codes are given in Table 1.
FIGURE 3 in Iris tibetica, a new combination in I. ser. Lacteae (Iridaceae) from China: evidence from morphological and chloroplast DNA analyses
FIGURE 3. Genetic clustering of Iris ser. Lacteae haplotypes from 136 individuals inferred with the program BAPS. Each vertical column corresponds to one haplotype, and black vertical lines separate haplotypes from the different localities. Locality codes are given in Table 1. Different colours represent the different genetic cluster (blue-cluster 1, red-cluster 2, green-cluster 3). (a) Mixture clustering results revealing three clusters with a posterior marginal probability of 0.80; (b) Bar plot from the admixture results. The vertical bars are split into several colours when there is evidence for the admixture (P <0.05). Localities are ordered according to latitude, from south to north.
Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization
<p>Assembled sequence alignments and phylogenetic trees for plastomes and nuclear loci for 24 samples of Crataegus.</p>
FIGURE 2. Notothylas yunnanensis T.Peng & R.L.Zhu 1. Thalli with mature orange-red sporophytes. 2. Dorsal thallus epidermis, showing each cell containing a single chloroplast with central pyrenoid. 3 in A revision of the genus Notothylas (Notothyladaceae, Anthocerotophyta) in China
FIGURE 2. Notothylas yunnanensis T.Peng & R.L.Zhu 1. Thalli with mature orange-red sporophytes. 2. Dorsal thallus epidermis, showing each cell containing a single chloroplast with central pyrenoid. 3. Two Nostoc colonies within ventral side of solid thallus in transverse section. 4. Four antheridia with orange chromoplasts in irregularly arranged jacket cells. 5. Transverse section of capsule wall. 6. Dehiscing sporophyte with yellowish spores and columella. 7. Epidermis of capsule wall. 8. Three spores and a pseudoelater. 9. Capsule wall showing slightly thick-walled, sub-quadrate to sub-rectangular, irregularly arranged epidermal cells. All from T. Peng et al. 20120715-7 (holotype HSNU).
FIGURE 2 in Molecular phylogeny of Faberia (Asteraceae: Cichorieae) based on nuclear and chloroplast sequences
FIGURE 2. Strict consensus tree of Faberia and relatives based ITS sequences. Tree length = 1227 steps, CI = 0.50, RI = 0.55, and RC = 0.28. Bootstrap values greater than 50% are above the lines and Bayesian posterior probabilities are below the lines.
FIGURE 1 in Molecular phylogeny of Faberia (Asteraceae: Cichorieae) based on nuclear and chloroplast sequences
FIGURE 1. Distribution of Faberia in central and southwestern China based on field observations and herbarium collections.
FIGURE 4 in Molecular phylogeny of Faberia (Asteraceae: Cichorieae) based on nuclear and chloroplast sequences
FIGURE 4. Phylogram of Faberia and relatives derived from internal transcribed spacer (ITS) nrDNA data. Values above each branch are branch length.
FIGURE 3 in Molecular phylogeny of Faberia (Asteraceae: Cichorieae) based on nuclear and chloroplast sequences
FIGURE 3. Strict consensus tree of Faberia and relatives based on the combined chloroplast sequences. Tree length = 624, CI = 0.83, RI = 0.67, and RC = 0.56. Bootstrap values greater than 50% are above the lines and Bayesian posterior probabilities are below the lines.
Comparative Analysis of Complete Chloroplast Genomes and Multiple DNA Sequences Reveals Interspecific Relationships of C. bretschneideri and Related Species in China
<p><strong> ITS, and <em>LEAFY</em> intron 1 sequencing of 36 Crataegus accessions.</strong></p>
FIGURE 1. Percentage Potentially Informative Character values for all 11 chloroplast regions. For the regions rps16 in A new genus and a major temperate bamboo lineage of the Arundinarieae (Poaceae: Bambusoideae) from Sri Lanka based on a multi-locus plastid phylogeny
FIGURE 1. Percentage Potentially Informative Character values for all 11 chloroplast regions. For the regions rps16–trnQ, trnC– rpoB, trnD–trnT, trnT–trnL and ndhF 3' the PIC values include the outgroups. For the regions psbD-trnT, psbJ-petA and ycf6- psbM the PIC values include only the ingroup species.
Supplementary material 1 from: Duan L, Han L-N, Sirichamorn Y, Wen J, Compton JA, Deng S-W, Arslan E, Ertuğrul K, Schrire B, Chen H-F (2021) Proposal to recognise the tribes Adinobotryeae and Glycyrrhizeae (Leguminosae subfamily Papilionoideae) based on chloroplast phylogenomic evidence. PhytoKeys 181: 65-77. https://doi.org/10.3897/phytokeys.181.71259
Voucher information, characters of chloroplast (cp) genomes and GenBank BioSample accession of genome skimming raw reads in this study
Supplementary material 2 from: Duan L, Han L-N, Sirichamorn Y, Wen J, Compton JA, Deng S-W, Arslan E, Ertuğrul K, Schrire B, Chen H-F (2021) Proposal to recognise the tribes Adinobotryeae and Glycyrrhizeae (Leguminosae subfamily Papilionoideae) based on chloroplast phylogenomic evidence. PhytoKeys 181: 65-77. https://doi.org/10.3897/phytokeys.181.71259
Chloroplast protein coding sequences (cpCDSs) and their corresponding substitution models generated from PartitionFinder 2
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