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64 results for “chloroplast sequence”
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>
Rhizophora complete chloroplast genome sequences
<p>Historical processes of long-distance migration and ocean-wide expansion feature the global biogeographic pattern of <i>Rhizophora</i> species. Throughout the Indian Ocean, <i>R. stylosa</i> and <i>R. mucronata</i> appear as a young phylogenetic group with expansion of <i>R. mucronata</i> towards the Western Indian Ocean (WIO) driven by the South Equatorial Current. Nuclear microsatellites revealed genetic patterns and breaks, however, estimating propagule dispersal routes requires maternally inherited cytoplasmic markers. Here, we examine the phylogeography of 21 <i>R. mucronata</i> provenances across a >4,200 km coastal stretch in the WIO using <i>R. stylosa</i> as outgroup. Full length chloroplast genome (164,474 bp) and nuclear ribosomal RNA cistron (8,033 bp) sequences were assembled. Boundaries, junction point, sequence orientation and stretch between LSC/IRb/SSC/IRa/LSC showed no differences with the <i>R. stylosa</i> chloroplast genome. A total of 58 mutations in <i>R. mucronata</i> encompassing transitions/transversions, insertion-deletions and mononucleotide repeats revealed three major haplogroups. Haplonetwork, Bayesian ML and Approximate Bayesian Computation (ABC) analyses supported discrete historical migration events. An ancient haplogroup A in the Seychelles and eastern Madagascar was as divergent from other <i>R. mucronata</i> haplogroups as it was from <i>R. stylosa</i>. A star-like haplonetwork referred to recent range expansion of haplogroup B from northern Madagascar towards the African mainland coastline, including a single variant spanning >1,800 km across the Mozambique Channel Area. Populations south of Delagoa Bight contained haplogroup C and originate from a unique bottleneck dispersal event. Divergence estimates of pre- and post-Last Glacial Maximum illustrated a recent emergence of WIO <i>Rhizophora </i>mangroves compared to other oceans. Connectivity patterns could be aligned with directionality of major ocean currents. Madagascar and the Seychelles each harbored haplogroups A and B, albeit among spatially separated populations, explained from a different migration era. Likewise, the Aldabra Atoll harbored spatially distinct haplotypes. Nuclear ribosomal cistron (8,033bp) variants corresponded to haplogroups and confirmed admixtures in the Seychelles and Aldabra. These findings shed new light on the origins and dispersal routes of <i>R. mucronata</i> lineages that have shaped their contemporary populations in large regions of the WIO, which may be important information for defining marine conservation units, both at ocean scale and at level of small islands.</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: Assemblage Accumulation Curves: A framework for resolving species accumulation in biological communities using chloroplast genome sequences
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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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DNA sequences for six chloroplast loci concatenated, representing haplotypes found in Colocasia esculenta, and closely related Araceae
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Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny
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Rhizophora complete chloroplast genome sequences
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Figure 3 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460
Figure 3 Undated 18S–26S nuclear DNA repeat region BEAST 2 phylogeny of Pennantia, under the Birth-Death model. The tree was rooted to make P. cunninghamii sister to the other species of Pennantia, in accordance with the chloroplast DNA tree and the ITS tree of Keeling et al. (2004). Node posterior probability is shown next to the corresponding node. The sequences downloaded from GenBank have their accession number in round brackets; the others were generated from the samples used in this study.
Supplementary material 2 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460
BEAST2 and RAxML files
Figure 2 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460
Figure 2 Dated chloroplast DNA BEAST 2 phylogeny of Pennantia, under the Birth-Death model. Mean node age and 95% HPD (in My) is given in the table embedded in the figure under the corresponding letter code. 95% HPD is also represented by blue bars. All node posterior probabilities are equal to 1 except if indicated otherwise. The calibrated nodes (see text) are indicated by red dots.
Supplementary material 1 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460
Figs S1–S5; Tables S1–S3
Figure 1 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460
Figure 1 General distribution of the four Pennantia species. TKI = Three Kings Islands. Generated in QGIS 3.0.1 from Google Satellite data obtained through the XYZ Tiles tool (https://mt1.google.com/vt/lyrs=s&x={x}&y={y}&z={z}).
Data from: Congruent deep relationships in the grape family (Vitaceae) based on sequences of chloroplast genomes and mitochondrial genes via genome skimming
Vitaceae is well-known for having one of the most economically important fruits, i.e., the grape (Vitis vinifera). The deep phylogeny of the grape family was not resolved until a recent phylogenomic analysis of 417 nuclear genes from transcriptome data. However, it has been reported extensively that topologies based on nuclear and organellar genes may be incongruent due to differences in their evolutionary histories. Therefore, it is important to reconstruct a backbone phylogeny of the grape family using plastomes and mitochondrial genes. In this study, next-generation sequencing data sets of 27 species were obtained using genome skimming with total DNAs from silica-gel preserved tissue samples on an Illumina HiSeq 2500 instrument. Plastomes were assembled using the combination of de novo and reference genome (of V. vinifera) methods. Sixteen mitochondrial genes were also obtained via genome skimming using the reference genome of V. vinifera. Extensive phylogenetic analyses were performed using maximum likelihood and Bayesian methods. The topology based on either plastome data or mitochondrial genes is congruent with the one using hundreds of nuclear genes, indicating that the grape family did not exhibit significant reticulation at the deep level. The results showcase the power of genome skimming in capturing extensive phylogenetic data: especially from chloroplast and mitochondrial DNAs.
Data from: Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution
Chloroplast sequence data are widely used to infer phylogenies of plants and algae. With the increasing availability of complete chloroplast genome sequences, the opportunity arises to resolve ancient divergences that were heretofore problematic. On the flip side, properly analyzing large multi-gene data sets can be a major challenge, as these data may be riddled with systematic biases and conflicting signals. Our study contributes new data from nine complete and four fragmentary chloroplast genome sequences across the green algal order Sphaeropleales. Our phylogenetic analyses of a 56-gene data set show that analyzing these data on a nucleotide level yields a well-supported phylogeny – yet one that is quite different from a corresponding amino acid analysis. We offer some possible explanations for this conflict through a range of analyses of modified data sets. In addition, we characterize the newly sequenced genomes in terms of their structure and content, thereby further contributing to the knowledge of chloroplast genome evolution.
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OpenNeuro
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