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91 results for “chloroplast genome”
Data from: Analysis of chloroplast genomes of ten Central Asian Fritillaria species and their phylogenetic relationships
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Comparative chloroplast genome and phylogenetic analysis of Central Asian Tulips
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The complete chloroplast genome of Mimusops elengi (Sapotaceae)
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A Pleistocene legacy of gene pools, ecodemes and admixtures of Stuckenia pectinata (L.) Börner as evidenced from microsatellites, complete chloroplast genomes and ribosomal RNA cistron (Europe, Africa)
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Comparative analysis of chloroplast genomes of Sanguisorba species and insights into phylogenetic implications and molecular dating
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Chloroplast genome of the critically endangered ginger Zingiber odoriferum Blume from Java, Indonesia: Characterization, comparison, and conservation insights
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Supplementary data of chloroplast genome of a centennial olive tree from the Peruvian coast
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The data of complete chloroplast genome sequence of Sorbus amabilis (Rosaceae) in China
<p>This dataset includes the complete chloroplast genome of <em>Sorbus amabilis </em> in China.</p>
Chloroplast genome of Phyllostachys glauca
<p><span><i>Phyllostachys glauca</i> is a dominant species in limestone mountains endemic to China. Here, we characterized its complete chloroplast genome. It is a circular DNA molecule of 139689 bp in length, including a pair of 21798 bp inverted repeats (IRs), a 12872 bp small single-copy (SSC) region and an 83221 bp large single-copy (LSC) region. The total GC content of <i>P. glauca</i> chloroplast genome was 38.9%, and it encodes a total of 137 functional genes, including 89 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. The phylogenetic analysis shows that <i>P. glauca</i> is highly clustered in the <i>Phyllostachys</i> clade (V), sister to the lineage of <i>P. nigra</i> var. <i>henonis</i> + <i>P. sulphurea</i>.</span></p>
Data from: Assemblage Accumulation Curves: A framework for resolving species accumulation in biological communities using chloroplast genome sequences
The timing and tempo of the processes involved in community assembly are of substantial concern to community ecologists and conservation managers. The fossil record is a valuable source of data for studying past changes in community composition, but it is not always detailed enough to allow the process of community assembly to be resolved at regional or site scales while tracing the trajectories of known species with associated known traits. We present a three‐step framework for studying present‐day species accumulation through time: DNA sampling from multiple individuals from multiple species within a community; estimates of coalescence times for each species using molecular dating methods; and plotting the accumulation of present‐day species through time using the inferred population ages. Our approach is illustrated using whole chloroplast genomes from plants from three rainforest communities in eastern Australia. Expected times to coalescence for multiple species in each community were inferred from pooled high‐throughput sequence libraries. Local assemblage accumulation curves for each community were constructed. We also explored the variation in assemblage accumulation curves of species with different functional traits. Models of equilibrium species richness informed our null hypothesis and largely explained the shape of the assemblage accumulation curves and indicated that the complexities of the accumulation process should be explored with additional parameters, for example allowing species classes with different extinction rates. The assemblage accumulation curves for the study sites showed evidence of recent population expansions within each of the communities. This signal of recent accumulation is consistent with the increase in suitable rainforest habitat that followed the Last Glacial Maximum. Our method of constructing assemblage accumulation curves provides a simple approach for visualizing species‐accumulation data. It can be used to test hypotheses such as the relative survival potential of species‐specific ecological attributes. Although our example used single‐nucleotide polymorphisms derived from whole‐chloroplast sequencing, this framework can be applied to mitochondrial genomes and to communities of other organisms.
Chloroplast genome of the invasive Pyrus calleryana
<p>The complete chloroplast genome of Pyrus calleryana (BioSample SAMC013142) was developed by de novo assembly from whole-genome sequencing data. Reference-guided (P.<b> </b>phaeocarpa<b>) </b>read<b> </b>mapping and assembly were followed by annotation and phylogenetic comparisons. The Pyrus calleryana chloroplast genome of 159,965 bp in length (36,56% of GC content) represents a classical quadripartite architecture, with two inverted repeats regions (IRs; each 26,392 bp in length) separating the large single-copy region (LSC; 87,942 bp) and the small single-copy region (SSC; 19.239 bp). In total, 115 unique genes were predicted and annotated in that genome, including 81 protein coding genes, 30 tRNA coding genes, and 4 rRNA coding genes. Phylogenetic analyses based on the whole chloroplast genome sequences places the P. calleryana among other Rosaceae plants, specifically among the Asian species of Pyrus.</p>
FIGURE 4 in Indocalamus chongzhouensis (Poaceae: Bambusoideae), a new synonym of I. emeiensis: evidence from morphology and complete chloroplast genome data
FIGURE 4. Micromophology of leaf abaxial epidermis under SEM. A–D. Indocalamus chongzhouensis (Chongzhou, Sichuan, China); E–H. I. emeiensis (E'mei, Sichuan, China). Abbreviations: ep, elongated papillae; sp, short papillae; mi, microhairs; sb, silica bodies; pr, prickles. (Scale bars = 5 μm [B, D, F & H]; 10 μm [C & G]; 50 μm [A & E]).
FIGURE 3 in Indocalamus chongzhouensis (Poaceae: Bambusoideae), a new synonym of I. emeiensis: evidence from morphology and complete chloroplast genome data
FIGURE 3. Morphological comparison between Indocalamus chongzhouensis (A–F) and I. emeiensis (G–L). A and G. Part of young culm, showing white-powdery and hirsute infranodal region; B and H. Culm sheath; C and I. Sheath auricle and oral setae; D and J. Branching node; E and K. Longitudinal section of branching node; F and L. part of ultimate leafy branch, showing leaf sheath, auricles, and oral setae. (Scale bars=1 cm).
FIGURE 1. Indocalamus chongzhouensis. A in Indocalamus chongzhouensis (Poaceae: Bambusoideae), a new synonym of I. emeiensis: evidence from morphology and complete chloroplast genome data
FIGURE 1. Indocalamus chongzhouensis. A. Syntype (Yi 03014, SIFS); B. Culm sheath; C. Leaf sheath, auricles and oral setae; D. Sheath auricles, oral setae and the base of sheath blade; E. Culm sheath, sheath auricle and oral setae. (Scale bars=1 cm).
FIGURE 6. Indocalamus emeiensis. A and B in Indocalamus chongzhouensis (Poaceae: Bambusoideae), a new synonym of I. emeiensis: evidence from morphology and complete chloroplast genome data
FIGURE 6. Indocalamus emeiensis. A and B. Habitat and habit; C and D. Rhizome and new shoot; E. Apex of new shoot, showing sheath auricle, oral setae and ligule; F. Infranodal region of young culm; G–J. Culm sheath; K. Part of ultimate leafy branch, showing leaf auricle and oral setae; L. Branching node; M. Longitudinal section of branching node. (Scale bars=1 m [A & B]; 1 cm [C–M]).
FIGURE 5 in Indocalamus chongzhouensis (Poaceae: Bambusoideae), a new synonym of I. emeiensis: evidence from morphology and complete chloroplast genome data
FIGURE 5. Phylogeny of Arundinarieae inferred from maximum likelihood (ML) analysis based on complete chloroplast genomes of 44 representative bamboos. Colored branches indicate 11 accepted lineages of Arundinarieae (I–XI). Numbers associated with branches indicate the bootstrap value and the posterior probability, respectively. Asterisks indicate 100% bootstrap support or 1.0 posterior probability. Hyphens indicate the bootstrap support or the posterior probability lower than 50% or 0.5.
Chloroplast genome-based molecular baraminology analysis of Proteales
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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 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.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.