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193 results for “Vitaceae”
Ampelopsis arborea (Vitaceae) - stem - showing leaf bases
Image of Ampelopsis arborea (Vitaceae) - stem - showing leaf bases
Ampelopsis arborea (Vitaceae) - stem - showing leaf bases
Image of Ampelopsis arborea (Vitaceae) - stem - showing leaf bases
Ampelopsis arborea (Vitaceae) - fruit - as borne on the plant
Image of Ampelopsis arborea (Vitaceae) - fruit - as borne on the plant
Ampelopsis arborea (Vitaceae) - leaf - basal or on lower stem
Image of Ampelopsis arborea (Vitaceae) - leaf - basal or on lower stem
Ampelopsis arborea (Vitaceae) - whole plant - in fruit
Image of Ampelopsis arborea (Vitaceae) - whole plant - in fruit
Ampelopsis arborea (Vitaceae) - whole plant - in fruit
Image of Ampelopsis arborea (Vitaceae) - whole plant - in fruit
Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
<p>With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated the optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 datasets with different sequencing coverage <i>in silico</i>. We tested the performance of four datasets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of the <i>Vitis</i> clade at the genus level and Vitaceae at the family level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10× coverage. Without the steps of synthesizing baits and enrichment experiments, coupled with incredibly low sequencing costs, we showcase that deep genome skimming (DGS) is as effective for capturing large datasets of SCNs as the widely used Hyb-Seq approach, in addition to capturing plastomes, mtDNA, and entire nrDNA repeats. DGS may serve as an efficient and economical alternative and may be superior to the popular target enrichment/Hyb-Seq approach.</p>
Phylogenomic analyses using a new 1013-gene Vitaceae bait-set support major groups of North American Vitis
<p class="p1">A set of newly designed Vitaceae baits targeting 1013 genes was employed to explore phylogenetic relationships among North American <em>Vitis</em>. Eurasian <em>Vitis</em> taxa including <em>Vitis vinifera</em> were found to be nested within North American <em>Vitis</em> subgenus <em>Vitis</em>. North American <em>Vitis</em> subgenus <em>Vitis</em> can be placed into nine main groups: the Monticola group, the Occidentales group, the Californica group, the Vinifera group (introduced from Eurasia), the Mustangensis group, the Palmata group, the Aestivali group, the Labrusca group, and the Cinerea group. Strong cytonuclear discordances were detected in North American <em>Vitis</em>, with many species non-monophyletic in the plastid phylogeny, while monophyletic in the nuclear phylogeny. The phylogenomic analyses support recognizing four distinct species in the <em>Vitis cinerea </em>complex in North America: <em>V. cinerea</em>, <em>V. baileyana</em>, <em>V. berlandieri</em>, and <em>V. simpsonii</em>. Such treatment will better serve the conservation of wild <em>Vitis</em> diversity in North America.</p>
Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
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Resolving the Tetrastigma loheri s.l. species complex (Vitaceae) in the Philippines: No evidence for recognizing more than one species
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Data from: Dispersal is associated with morphological innovation, but not increased diversification, in Cyphostemma (Vitaceae)
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Phylogenomic analyses using a new 1013-gene Vitaceae bait-set support major groups of North American Vitis
Open the record for dataset details and reuse information.
Data from: X-rays and virtual taphonomy resolve the first Cissus (Vitaceae) macrofossils from Africa as early diverging members of the genus
PREMISE OF THE STUDY: Fossilized seeds similar to Cissus (Vitaceae) have been recognized from the Miocene of Kenya, though some were previously assigned to the Menispermaceae. We undertook a comparative survey of extant African Cissus seeds to identify the fossils and consider their implications for the evolution and biogeography of Cissus and for African early Miocene paleoenvironments. METHODS: Micro-computed tomography (µCT) and synchrotron-based X-ray tomographic microscopy (SRXTM) were used to study seed morphology and anatomy. Virtual taphonomy, using SRXTM data sets, produced digital fossils to elucidate seed taphonomy. Phylogenetic relationships within Cissus were reconstructed using existing and newly produced DNA sequences for African species. Paleobiology and paleoecology were inferred from African nearest living relatives. KEY RESULTS: The fossils were assigned to four new Cissus species, related to four modern clades. The fossil plants were interpreted as climbers inhabiting a mosaic of riverine woodland and forest to more open habitats. Virtual taphonomy explained how complex mineral infill processes concealed key seed features, causing the previous taxonomic misidentification. Newly sampled African species, with seeds most similar to the fossils, belong to four clades within core Cissus, two of which are early diverging. CONCLUSIONS: Virtual taphonomy, combined with X-ray imaging, has enabled recognition of the first fossil Cissus and Vitaceae from Africa. Early-divergent members of the core Cissus clade were present in Africa by at least the early Miocene, with an African origin suggested for the Cissus sciaphila clade. The fossils provide supporting evidence for mosaic paleoenvironments inhabited by early Miocene hominoids.
FIGURE 1 in Tydeid and triophtydeid mites (Acari: Tydeoidea) associated with grapevine (Vitaceae: Vitis spp.) in Brazil, with the descriptions of species of Prelorryia (André, 1980) and Tydeus Koch, 1835
FIGURE 1. Triophtydeus lebruni (Female) A. Dorsal view; B. Anogenital area; C. Palp; D. Leg I; E. Leg IV.
FIGURE 8 in Tydeid and triophtydeid mites (Acari: Tydeoidea) associated with grapevine (Vitaceae: Vitis spp.) in Brazil, with the descriptions of species of Prelorryia (André, 1980) and Tydeus Koch, 1835
FIGURE 8. Pretydeus henriandrei (Female) A. Dorsal view; B. Seta c1 on dorsal idiosoma. C. Palp; D. Cheliceral stilettos; E. Leg I; F. Leg II.
FIGURE 6 in Tydeid and triophtydeid mites (Acari: Tydeoidea) associated with grapevine (Vitaceae: Vitis spp.) in Brazil, with the descriptions of species of Prelorryia (André, 1980) and Tydeus Koch, 1835
FIGURE 6. Tydeus manoi sp. nov. (Female) A. Dorsal view; B. Anogenital area; C. Palp; D. Leg I; E. Leg II; F. Leg III.
FIGURE 2. A in Cyphostemma mendesii (Vitaceae), a new species from Angola
FIGURE 2. A plant of Cyphostemma mendesii before the growth of new stems (Photo E.J.Mendes, taken in 1955).
Supplementary material 1 from: van Nieukerken EJ, Geertsema H (2015) A new leafminer on grapevine and Rhoicissus (Vitaceae) in South Africa within an expanded generic concept of Holocacista (Insecta, Lepidoptera, Heliozelidae). ZooKeys 507: 41-97. https://doi.org/10.3897/zookeys.507.9536
All material examined and used for DNA barcoding: Explanation note: The dataset comprises all material examined and identified to a certain extent for this study. All specimens used for the descriptions of genus and listed species are included, as are all DNA barcoded specimens, including those that were published earlier.
FIGURE 4. A in Morphological studies on leaf epidermis in six species of Nekemias Raf. (Vitaceae) from China
FIGURE 4. A maximum likelihood tree showing the types of anticlinal wall of both leaf sides and habitats.
FIGURE 3 in Morphological studies on leaf epidermis in six species of Nekemias Raf. (Vitaceae) from China
FIGURE 3. The hair types of Nekemias and its related species of Ampelopsis. A. N. hypoglauca (Chu 206); B. N. chaffanjonii (Nie 4544). C–F: The venations and epidermal cells with sparsely pubescent, C. N. cantoniensis (Chu 007), D. N. grossedentata (Chu 001); E. N. megalophylla (Chu 401), F. Ampelopsis delavayana (Nie 4438), G–H: the epidermal cells with bending villous. G. N. rubifolia (Chu 238), H. N. rubifolia (Chu 025). Scale bar = 50μm.
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Allen Brain Atlas
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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
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.