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274 results for “nuclear sequence”
Figure 1 in Molecular dating and diversification of the South American lizard genus Liolaemus (subgenus Eulaemus) based on nuclear and mitochondrial DNA sequences
Figure 1. Fifty per cent majority rule phylogram from the partitioned BEAST analyses of the combined data set (cytochrome b, 12S, CMOS, and MXRA5). Numbers above and below the nodes represent posterior probability values and mean estimates of divergence dates (in millions of years), respectively.
FIGURE 1 in Reinstatement of Alysicarpus pokleanus (Leguminosae, Papilionoideae: Desmodieae) based on ITS sequences of nuclear ribosomal DNA
FIGURE 1. Best ML tree obtained after analyzing 41 accessions from previous study (Gholami et al. 2017) including 3 outgroups using RaXML (Stamatakis 2014) on CIPRES Science gateway (Miller et al. 2010).
Sequences of nuclear ribosomal internal transcribed spacer (ITS) for five Toxicodendron vernicifluum individuals
<p>This dataset includes the aligned sequences of nuclear ribosomal internal transcribed spacer (ITS) for five <em>Toxicodendron vernicifluum</em> individuals sampled from China.</p>
Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data
<span>Background</span> <p><em><span>Abies koreana</span></em><span> E. H. Wilson is an endangered evergreen coniferous tree that is native to high altitudes in South Korea and susceptible to the effects of climate change. Hybridization and reticulate evolution have been reported in the genus; therefore, multigene datasets from nuclear and cytoplasmic genomes are needed to better understand its evolutionary history.</span></p> <span>Results</span> <p><span>Using Illumina NovaSeq6000 and Oxford Nanopore Technologies (ONT) PromethION platforms, we generated complete mitochondrial (1,174,803 bp) and plastid (121,341 bp) genomes from <em>A. koreana</em>. The mitochondrial genome is highly dynamic, transitioning from cis- to trans-splicing and breaking the conserved gene clusters. In the case of the plastome, the ONT reads revealed two structural conformations of <em>A. koreana</em>. The short inverted repeats (1,186 bp) of the <em>A. koreana</em> plastome are associated with the different structural types. Transcriptomic sequencing revealed 1,356 sites of C-to-U RNA editing in the 41 mitochondrial genes. Using <em>A. koreana</em> as a reference, we additionally produced nuclear ribosomal DNA and organelle genomic sequences from eight Abies species and generated multiple datasets for maximum likelihood and network analyses. Three sections (<em>Balsamea</em>, <em>Momi</em>, and <em>Pseudopicea</em>) were well grouped in the nuclear phylogeny, but the phylogenomic relationships showed conflicting signals in the mitochondrial and plastid genomes, indicating a complicated evolutionary history that may have included introgressive hybridization.</span></p> <span>Conclusions</span> <p><span>These results illustrate that phylogenomic analyses based on the sequences from differently inherited organelle genomes resulted in conflicting trees. Organellar capture, organellar genome recombination, and incomplete lineage sorting in an ancestral heteroplasmic individual can contribute to phylogenomic discordance. We provide strong support for the relationships within <em>Abies</em> and new insights into the phylogenomic complexity of this genus.</span></p>
FIG. 2 in A Molecular Systematic Study of the Lampranthus Group (Aizoaceae) Based on the Chloroplast TrnL-trnF and Nuclear ITS and 5S NTS Sequence Data
FIG. 2. Strict consensus tree of the 30,000 most parsimonious trees based on the combined trnL-F, ITS and 5S spacer sequence data recovered during simultaneous analysis 1 (not weighted) including 58 taxa; Length = 524, CI = 0.479, RI = 0.601, RC = 0.288. Values above the internodes give the jackknife values. Members of the Lampranthus group are underlined.
FIG. 1 in A Molecular Systematic Study of the Lampranthus Group (Aizoaceae) Based on the Chloroplast TrnL-trnF and Nuclear ITS and 5S NTS Sequence Data
FIG. 1. Strict consensus tree of the 30,000 most parsimonious trees based on the 5S spacer sequence data recoverd during heuristic Search 3 for 56 taxa; Length = 231, CI = 0.519, RI = 0.743, RC = 0.386. Values above the internodes give the jackknife values (where absent, the jackknife values are less than 50%). Members of the Lampranthus group are underlined.
FIG. 3 in A Molecular Systematic Study of the Lampranthus Group (Aizoaceae) Based on the Chloroplast TrnL-trnF and Nuclear ITS and 5S NTS Sequence Data
FIG. 3. Strict consensus tree of the 167 most parsimonious trees based on the combined and successively weighted trnL-F, ITS and 5S spacer sequence data recovered during simultaneous analysis 4 including 51 taxa; CI = 0.599, RI = 0.841, RC = 0.504. Values above the internodes give the jackknife values. Members of the Lampranthus group are underlined.
Data from: Host associated genetic differentiation in a seed parasitic weevil Rhinusa antirrhini (Coleptera: Curculionidae) revealed by mitochondrial and nuclear sequence data
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Data from: Rapid allopolyploid radiation of moonwort ferns (Botrychium ; Ophioglossaceae) revealed by PacBio sequencing of homologous and homeologous nuclear regions
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Data from: Development of nuclear microsatellite loci and mitochondrial single nucleotide polymorphisms for the natterjack toad, Bufo (Epidalea) calamita (Bufonidae), using next generation sequencing and Competitive Allele Specific PCR (KASPar)
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Data from: Nuclear and mitochondrial sequence data reveal and conceal different demographic histories and population genetic processes in Caribbean reef fishes
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Monotropoid Ericaceae 102-locus nuclear sequences matrices and plastid locus sequence matrix
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Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data
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Data from: Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma
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Data from: Phylogenetic systematics of subtribe Spiranthinae (Orchidaceae: Orchidoideae: Cranichideae) based on nuclear and plastid DNA sequences of a nearly complete generic sample
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Data from: DISCOMARK: nuclear marker discovery from orthologous sequences using draft genome data
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Data from: Phylogenetic inferences using nuclear ribosomal ITS and chloroplast sequences provide insights into the biogeographic origins, diversification timescales and trait evolution of Rubus in the Japanese Archipelago
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Integrative taxonomic analysis to reveal the species status of Bombus flavidus, combining COI and nuclear sequencing, wing morphometrics and secretions used for mate attraction as well as patterns of color polymorphism
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Data from: Phylogenetic relationships and timing of diversification in gonorynchiform fishes inferred using nuclear gene DNA sequences (Teleostei: Ostariophysi)
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Data from: Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus
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