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67 results for “plastid DNA”
FIGURE 4 in The non-monophyly of Dasymaschalon dasymaschalum (Annonaceae) revealed by a plastid DNA phylogeny, with D. halabalanum sp. nov. from Thailand and D. argenteum comb. nov.
FIGURE 4. Holotype of Dasymaschalon halabalanum at CMUB.
Data from: Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid
PREMISE OF THE STUDY: We explored the phylogenetic utility of entire plastid DNA sequences in Daucus and compared the results with prior phylogenetic results using plastid and nuclear DNA sequences. METHODS: We used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20 Daucus taxa and outgroups, analyzed the data with phylogenetic methods, and examined evidence for mitochondrial DNA transfer to the plastid (DcMP). KEY RESULTS: Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. Subsets of the data, including regions traditionally used as phylogenetically informative regions, provide various degrees of soft congruence with the entire data set. There are areas of hard incongruence, however, with phylogenies using nuclear data. We extended knowledge of a mitochondrial to plastid DNA insertion sequence previously named DcMP and identified the first instance in flowering plants of a sequence of potential nuclear genome origin inserted into the plastid genome. There is a relationship of inverted repeat junction classes and repeat DNA to phylogeny, but no such relationship with nonsynonymous mutations. CONCLUSIONS: Our data have allowed us to (1) produce a well-resolved plastid phylogeny of Daucus, (2) evaluate subsets of the entire plastid data for phylogeny, (3) examine evidence for plastid and nuclear DNA phylogenetic incongruence, and (4) examine mitochondrial and nuclear DNA insertion into the plastid.
Data from: Patterns of morphological and plastid DNA variation in the Corallorhiza striata species complex (Orchidaceae)
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Data from: Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid
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Fig. 2 in Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences
Fig. 2 Phylogenetic tree for Ranunculus species based on plastid regions (rpl32-trnL, rps16-trnQ, trnK-matK, ycf6-psbM). a Consensus tree inferred from the two most parsimonious trees (CI=0.76; RI=0.93). Numbers above branches show bootstrap values (3,000 replicates). b
FIGURE 3 in Plastid DNA fingerprinting of the rare Fritillaria moggridgei (Liliaceae) reveals population differentiation and genetic isolation within the Fritillaria tubiformis complex
FIGURE 3. Median-joining (MJ) network for the combined plastid DNA data set of Fritillaria tubiformis s.l. A. MJ network based on indel repeats at locus 4, 7, 8, 9, 10. Haplotypes (Ha, Hb1 and Hb2) are indicated by circles, the size of each circle being proportional to the observed frequency of each haplotype. B. MJ network for the combined plastid DNA data set of Fritillaria tubiformis s.l. based on all ten microsatellites. Median vectors are labelled mv1, mv2, mv3 and mv4. Number of changes required to explain transitions among haplotypes is indicated along the lines of the networks, except for connections that required only a single change. Information on type and number of repeat motifs contributing to the network is provided for the two main clusters (A and B) corresponding to var. burnatii and subsp. moggridgei.
pTAC3 and pTAC14 are required for binding of Plastid Encoded RNA Polymerase to DNA
GEO Series GSE259283. Arabidopsis thaliana. 36 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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