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373 results for “Chloroplast”
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.
Alignments of chloroplast noncoding regions for context-dependency analysis
<p>Substitutions between closely related noncoding chloroplast DNA sequences are studied with respect to the composition of the three bases on each side of the substitution, that is the hexanucleotide context. There is about 100-fold variation in rate, amongst the contexts, particularly on substitutions of A and T. Rate heterogeneity of transitions differs from that of transversions, resulting in a more than 200-fold variation in the transitions:transversion bias. The data are consistent with a CpG effect, and it is shown that both the A+T content and the arrangement of purines/pyrimidines along the same DNA strand are correlated with rate variation. Expected equilibrium A+T content ranges from 36.4% to 82.8% across contexts, while G-C skew ranges from -77.4 to 72.2 and A-T skew from -63.9 to 68.2. The predicted equilibria are associated with specific features of the content of the hexanucleotide context, and also show close agreement with the observed context-dependent compositions. Finally, by controlling for the content of nucleotides closer to the substitution site it is shown that both the third and fourth nucleotide removed on each side of the substitution directly influence substitution dynamics at that site. Overall, the results demonstrate that noncoding sites in different contexts are evolving along very different evolutionary trajectories and that substitution dynamics are far more complex than typically assumed. This has important implications for a number of types of sequence analysis, particularly analyses of natural selection, and the context-dependent substitution matrices developed here can be applied in future analyses.</p>
Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia
<p>Ecotypes are distinct populations within a species that are adapted to specific environmental conditions. Understanding how these ecotypes become established, and how they interact when reunited, is fundamental to elucidating how ecological adaptations are maintained. This study focuses on Themeda triandra, a dominant grassland species across Asia, Africa and Australia. It is the most widespread plant in Australia, where it has distinct ecotypes that are usually restricted to either wetter and cooler coastal regions or the drier and hotter interior. We generate a de novo reference genome for T. triandra and use whole genome sequencing for over 80 Themeda accessions to reconstruct the evolutionary history of T. triandra and related taxa. Organelle phylogenies confirm that Australia was colonised by T. triandra twice, with the division between ecotypes predating their arrival in Australia. The nuclear genome provides evidence of differences in the dominant ploidal level and gene-flow among the ecotypes. In northern Queensland there appears to be a hybrid zone between ecotypes with admixed nuclear genomes and shared chloroplast haplotypes. Conversely, in the cracking claypans of Western Australia, there is cytonuclear discordance with individuals possessing the coastal chloroplast and interior clade nuclear genome. This chloroplast capture is potentially a result of adaptive introgression, with selection detected in the rpoC2 gene which is associated with water use efficiency. The reason why T. triandra is the most widespread plant in Australia appears to be a result of distinct ecotypic genetic variation and genome duplication, with the importance of each depending on the geographic scale considered.</p>
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
<p><span>This study aimed to reveal the evolutionary timescale and processes underlying the diversity of <em>Rubus</em> in the Japanese Archipelago. We conducted molecular phylogenetic analyses of most native species (35 species), along with previously published data from 116 foreign species, based on nuclear ribosomal internal transcribed spacer (ITS) and chloroplast DNA sequences. Most of the northern species of Japan, that is, <em>R. chamaemorus</em>, <em>R. pedatus</em>, <em>R. vernus</em>, <em>R. pseudojaponicus</em>, and <em>R. ikenoensis</em>, were found to belong to anciently diverged lineages; in particular, <em>R. ikenoensis</em> formed a unique lineage distinct from other species. The other species diverged into two evolutionary groups. One included subg. <em>Malachobatus</em>, <em>Chamaebatus</em>, and sects. <em>Pungentes</em>, <em>Idaeanthi</em>, and <em>Parvifolii</em> (subg. <em>Idaeobatus</em>), which was further divided into two clades in the chloroplast phylogenies. Although the phylogenetic structures within this group were unresolved, <em>R. sieboldii</em> has been proven to be recently derived. The second group represented a well-supported clade, comprising sects. <em>Microphylli</em>, <em>Corchorifolii</em>, <em>Peltati</em>, and <em>Rosifolii</em> (subg. <em>Idaeobatus</em>), and suggested early Miocene diversification of this Asian lineage associated with character specialization in vegetative reproduction and leaf shape. This clade was further resolved into lower clades primarily representing the sectional classifications, although the placement of the earliest diverged species, <em>R. sumatranus</em>, <em>R. peltatus</em>, <em>R. corchorifolius</em>, and <em>R. chingii</em>, was incongruent among gene trees. At the lower taxonomic levels, <em>R. illecebrosus</em>, <em>R. grayanus</em>, and the thornless species of sect. <em>Microphylli</em> showed earlier divergence.</span></p>
Supplementary material 9 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Maximum likelihood phylogram inferred from psbK–psbI sequence data : Explanation note: ML bootstrap support is recorded along branches. No support is shown for branches with bootstrap support <50%.
Supplementary material 8 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Maximum likelihood phylogram inferred from atpF–atpH sequence data : Explanation note: ML bootstrap support is recorded along branches. No support is shown for branches with bootstrap support <50%.
Supplementary material 2 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Supplementary material 2 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Supplementary material 19 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Supplementary material 19 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Supplementary material 4 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Maximum likelihood phylogram inferred from ITS sequence data : Explanation note: ML bootstrap support is recorded along branches. No support is shown for branches with bootstrap support <50%. Source information for previously published sequences is provided in Suppl. material 2.
Supplementary material 5 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Maximum likelihood phylogram inferred from ETS sequence data : Explanation note: ML bootstrap support (left) and BI posterior probabilities (right) are recorded along branches. No support is shown for branches with bootstrap support <50% and posterior probability <0.5. Source information for previously published sequences is provided in Suppl. material 2.
Supplementary material 11 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Maximum likelihood phylogram inferred from trnL–trnF sequence data : Explanation note: ML bootstrap support is recorded along branches. No support is shown for branches with bootstrap support <50%. Source information for previously published sequences is provided in Suppl. material 2.
Supplementary material 15 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Supplementary material 15 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Supplementary material 18 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Supplementary material 18 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Supplementary material 7 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Maximum likelihood phylogram inferred from matK sequence data : Explanation note: ML bootstrap support is recorded along branches. No support is shown for branches with bootstrap support <50%. Source information for previously published sequences is provided in Suppl. material 2.
Supplementary material 6 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Maximum likelihood phylogram inferred from combined plastid (atpF–atpH, matK, psbA–rps19–trnH, psbK–psbI, trnL–trnF) sequence data : Explanation note: ML bootstrap support is recorded along branches. No support is shown for branches with bootstrap support <50%.
Supplementary material 3 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Maximum likelihood phylogram inferred from combined ITS+ETS sequence data : Explanation note: ML bootstrap support is recorded along branches. No support is shown for branches with bootstrap support <50%.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.
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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.