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351 results for “gene tree”
Gene profiling in arbuscular mycorrhizal symbiosis between the actinorhizal tree Casuarina glauca and the fungus Glomus intraradices.
GEO Series GSE36676. Casuarina glauca. 6 samples. Type: Expression profiling by array.
Sequence alignments and tree file for wsp gene.
<p>Alignment of <em>wsp</em> dataset was constructed on the GUIDANCE2 Server based on codons using the MAFFT algorithm, and ambiguous alignments with the confidence score below 0.7 were excluded. The maximum likelihood tree was built using <em>RAxML</em> program.</p>
Phylogenetic trees of diatom genes of horizontal descent
<p>Supplemental dataset accompanying the paper: Comprehensive and functional analysis of horizontal gene transfer events in diatoms, Vancaester et al. MBE (<a href="https://doi.org/10.1093/molbev/msaa182">https://doi.org/10.1093/molbev/msaa182</a>).<br> <br> This dataset contains all maximum-likelihood phylogenetic trees produced using IQTree (version 1.6.5) of diatom gene families which were deemed to contain horizontal gene transfer. Additionally, a file containing the gene family, donor, acceptor, the genes of the nine diatoms and the support for all events is given.</p> <p>The dataset containing the generated gene expression matrices and the defined co-expression clusters for <em>Phaeodactylum tricornutum</em> can be found on <a href="https://zenodo.org/record/3964792#.XyCCM-dCdPY">(https://zenodo.org/record/3964792#.XyCCM-dCdPY)</a></p> <p> </p>
Trees and Roary output for Adaptation by ancient horizontal acquisition of butyrate metabolism genes in Aggregatibacter actinomycetemcomitans
<p>Supporting data for publication. </p> <ol> <li>Raw Trees for Figure 1 and supplementary figures 2 and 3.</li> <li>Roary presence absence output.</li> </ol>
The Bayesian trees of the nuclear gene DMC1 and the chloroplast gene rps16 sequences
<p>Some plants with low fertility are morphologically intermediate between <i>Roegneria stricta</i><i> </i>and<i> Roegneria</i> <i>turczaninovii</i>, and were suspected to be natural hybrids between these species. In this study, karyotype analysis showed that natural hybrids and its putative parents were tetraploids (2n = 4x = 28). Meiotic pairing in natural hybrids is more irregular than its putative parents. Results of genomic <i>in situ</i> hybridization and fluorescence <i>in situ</i> hybridization indicate that natural hybrids contain the same genome as its putative parents. The nuclear gene DNA meiotic recombinase 1 (<i>DMC</i>1) and the chloroplast gene <i>rps</i>16 of natural hybrids and its putative parents were analyzed for evidence of hybridization. The results from molecular data supported by morphology and cytology demonstrated that the plants represent natural hybrids between <i>R. stricta</i><i> </i>and<i> R.</i> <i>turczaninovii</i>. The study is important understanding species evolution in the genus since it demonstrates for the first time the existence of populations of natural homoploid hybrids in <i>Roegneria. </i>The study also reports for the first time that the composition of the genomic formula of <i>R.</i> <i>turczaninovii </i>is <b>StY</b>, confirming that the current taxonomic status is correct.</p> <p> </p>
Differences in Human Germinal Center B Cell Selection Revealed by Analysis of IgVH Gene Hypermutation and Lineage Trees in Inflammatory Bowel Disease
ClinicalTrials.gov study NCT00291681. IPD Sharing: Not stated. Countries: 1. Publications: 0.
The Bayesian trees of the nuclear gene DMC1 and the chloroplast gene rps16 sequences
Open the record for dataset details and reuse information.
Genome-Wide Analysis Reveals Divergent Patterns of Gene Expression During Zygotic and Somatic Embryo Maturation of Theobroma cacao L., The Chocolate Tree
GEO Series GSE55476. Theobroma cacao. 6 samples. Type: Expression profiling by array.
Gene expression in Citrus sinensis fruit tissues harvested from huanglongbing-infected trees: comparison with girdled fruit
GEO Series GSE33373. Citrus sinensis. 67 samples. Type: Expression profiling by array.
Laccaria bicolor gene expression in different tissues and with different host trees
GEO Series GSE32559. Laccaria bicolor S238N-H82; Pseudotsuga menziesii; Populus deltoides; Populus trichocarpa. 12 samples. Type: Expression profiling by array.
Transcriptome sequencing and analysis of rubber tree (Hevea brasiliensis Muell.) to discover putative genes associated with tapping panel dryness (TPD)
GEO Series GSE67214. Hevea brasiliensis. 2 samples. Type: Expression profiling by high throughput sequencing.
FIGURE 57. ITS2 gene tree. G in Crickets of the genus Gryllus in the United States (Orthoptera: Gryllidae: Gryllinae)
FIGURE 57. ITS2 gene tree. G. veintinueve samples: S02-39 (G134); S07-21 (G1139); S07-27 (G1140, G1211); S09-71 (G1451); OK, Love Co., Hwy 32 at Boggy Creek (2015-055). G. vernalis samples: S03-56 (G27, G1739); S03-62 (G31, G33). G. fultoni samples: S03-62 (G32, G34); S03-64 (G35), S07-22 (G1138). G. veletis samples: S03-58 (G39); S03-60 (G30); S15-9 (G2939); S15-16 (G2927, G2934); S15-21 (G2899); S15-24 (G2936); S15-25 (G2963, G2968, G2983); S15-53 (G3304, G3343).
FIGURE 54. ITS2 gene tree. G in Crickets of the genus Gryllus in the United States (Orthoptera: Gryllidae: Gryllinae)
FIGURE 54. ITS2 gene tree. G. multipulsator sample: S03-41 (G577); G. assimilis samples: S10-64 (G1901); S16-12 (G3367, G3373); G. locorojo sample: type locality (Rainbow Mealworms); G. veintinueve samples: S02-39 (G134); S07-21 (G1139); S07-27 (G1140, G1211); S09-71 (G1451); OK, Love Co., Hwy 32 at Boggy Creek (2015-055).
FIGURE 30. ITS2 gene tree. G in Crickets of the genus Gryllus in the United States (Orthoptera: Gryllidae: Gryllinae)
FIGURE 30. ITS2 gene tree. G. firmus samples: S03-85 (G60, G61, G62); S07-25 (G1073, G1074); S07-26 (G1186, G1235); S10-63 (G1920, G1922); S10-67 (G1915); S11-29 (G2165, G2029, G2034); S13-41 (G2709); S13-59 (G2716); G. pennsylvanicus samples: S08-74 (G709, G710); S11-107 (G2208); S11-108 (G2211).
FIGURE 19. Mapped COI gene tree. COI barcode tree from Fig. 18 visualized against a in Thirteen new species of Chilecicada Sanborn, 2014 (Hemiptera: Auchenorrhyncha: Cicadidae: Tibicininae) expand the highly endemic cicada fauna of Chile
FIGURE 19. Mapped COI gene tree. COI barcode tree from Fig. 18 visualized against a map of specimen localities using web application TreeToM (See methods). Colors represent described species.
FIGURE 174. ITS2 gene tree. Collection stop numbers for G in Crickets of the genus Gryllus in the United States (Orthoptera: Gryllidae: Gryllinae)
FIGURE 174. ITS2 gene tree. Collection stop numbers for G. lineaticeps samples: S00-15, Guadalupe Island, Mexico (G273); S04-64 (G352); S05-39 (G463); S09-28 (G1303); S09-37 (G1315). Collection stop numbers for G. personatus samples: S99- 84, Durango, Mexico (G393); S03-127, from Coahuila, Mexico (G75, G76); S07-41 (G1014); S09-58 (G1372); S09-151, from near Janos, Mexico (G1462, G1463); S16-6 (G3371). Collection stop numbers for G. staccato samples: S04-121 (G376); S09- 54 (G1397); S09-103 (G1407); S11-102 (G2186). See also Gray et al. (2016b).
FIGURE 132. ITS2 gene tree. G in Crickets of the genus Gryllus in the United States (Orthoptera: Gryllidae: Gryllinae)
FIGURE 132. ITS2 gene tree. G. planeta samples: S15-61 (G3088, G3094, G3114, G3135, G3344, G3345, G3347); S15-63 (G3130). G. veletis samples: S03-58 (G39); S03-60 (G30); S15-9 (G2939); S15-13 (G2884, G2929); S15-16 (G2927, G2934); S15-21 (G2894, G2895, G2896, G2899, G2942); S15-24 (G2936); S15-25 (G2963, G2968, G2983); S15-53 (G3304, G3343); S15-62 (G3131, G3134); S15-67 (G3137, G3144); S15-78 (G3145, G3147); Salt Lake City, UT (2009-013). Most ITS2 sequenced western US G. veletis samples match closely with the two eastern US samples from near the type locality, but a few samples from eastern NV, central NM, and west TX are genetically somewhat divergent. G. montis Clade 1 ITS2 sequences fall within this Group, but alternative placements are supported by different genes and analysis methods (see under G. montis, page 201, for discussion).
FIGURE 2 in Combined multi-gene backbone tree for the genus Coniochaeta with two new species from Uzbekistan
FIGURE 2. Maximum likelihood tree revealed by RAxML from an analysis of the combined LSU-ITS rDNA matrix of Coniochaeta, showing the phylogenetic position of C. acaciae and C. coluteae. MP, ML bootstrap supports (≥50%) and Bayesian posterior probabilities (≥0.9PP) support are given above or below the branches respectively. The tree was rooted with Chaetosphaeria garethjonesii (MFLUCC 15-1012) and C. jonesii (MFLUCC 15-1015). New species proposed in this study are indicated in red, and type strains are in boldface.
Figure 8 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 8. Ebiscothyris bellonensis gen. et sp. nov., cruise EBISCO, Coral Sea, South-West Pacific, SEM micrographs: A, inner view of ventral valve to show symphytium with a weak line of junction, and small teeth, paratype, CP 2616, 786–836 m depth, IB-2013-4; B–E, inner, tilted, posterior, and side views of dorsal valve to show brachidium and cardinalia, paratype, CP 2557, 800–923 m depth, IB-2013-5; F, inner view of posterior part of complete specimen to show tubular pedicle collar and cardinal process, paratype, CP 2616, 786–836 m depth, IB-2013-6. Scale bars: 1 mm.
Figure 5. A, topological similarities between gene trees. A in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
Figure 5. A, topological similarities between gene trees. A non-metric multidimensional ordination plot, based on the Robinson–Foulds (RF) distance between each pair of genes, is used to visualize the topological similarity among the 208 single gene trees. Pairs of gene trees with similar topologies are closer together in the two-dimensional space. Colours represent RF distances between individual gene trees and the extended majority-rule consensus (MRE) phylogeny. B, identifying optimal subsets of genes with the least topological incongruence. The graph shows the Tree Certainty (TC) values from Salichos & Rokas (2013). Information theory approach using the MRE phylogeny as a reference tree, where higher values represent greater congruency between the gene trees and the MRE tree. The x-axis represents the number of genes sampled, following an iterative procedure beginning with the first two genes in the respective ranking and progressively adding genes according to their order in the list. The five ranking criteria all outperformed random gene orders.
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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
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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
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