Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
46
datasets available to search
ShareScore release 0.9.0
Dataset results
46 results for “Sophora”
Dataset for the genome of medicinal plant Sophora flavescens has undergone significant expansion of both transposons and genes
<p><em>Sophora flavescens</em> is a medicinal plant in the genus Sophora of the Fabaceae family. The root of <em>S. flavescens</em> is known in China as Kushen and has a long history of wide use in multiple formulations of Traditional Chinese Medicine (TCM). However, there is little genomic information available for <em>S. flavescens</em>, which has greatly hindered the breeding of <em>S. flavescens</em> and characterisation of bioactive compounds. Therefore, in this study, we used third-generation Nanopore long-read sequencing technology combined with Hi-C scaffolding technology to <em>de novo</em> assemble the <em>S. flavescens</em> genome. We obtained a chromosomal level high-quality <em>S. flavescens</em> draft genome. The draft genome size is approximately 2.08 Gb, with more than 80% annotated as Transposable Elements (TEs). We also annotated 60,485 genes and examined their expression profiles in leaf, stem and root tissues. We also characterised the genes and pathways involved in the biosynthesis of major bioactive compounds, including alkaloids, flavonoids and isoflavonoids. The assembled genome provides valuable resources for conservation, genetic research and breeding of <em>S. flavescens</em>.</p>
FIGURE 24 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 24. Length and width dimensions for coprolites investigated for cuticle in this work (red dots), overlain on a summary of Wood and Wilmshurst (2014, fig. 3). The blue curve contains the range of genetically confirmed moa coprolites in their study, and the small yellow dot indicates the size of their one genetically determined kakapo coprolite, and the green are those of their 'putative' kakapo coprolites. There is a clear group of coprolites in the present study which are well beyond the range of even 'putative' kakapo, and are regarded as moa (Coprolites-11, 14, 15, 16, 25, 26, 27, 28, 29, 51, 58, 60, 62, 78, 110, 111).
FIGURE 23 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 23. Coprolites regarded here as moa, based on their size (scale bar equals 30 mm). A. Coprolite-25, containing Poaceae (Shelter-32). B. Coprolite-26, containing Pseudopanax ferox, Pittosporum tennuifolium, Sophora microphylla (Shelter-32). C. Coprolite-15, containing Coprosma sp., Olearia sp, Pittosporum tennuifolium, Pseudopanax ferox, Rubus sp., Sophora microphylla (Shelter-102). D. Coprolite-111, containing Sophora microphylla, Pittosporum tennuifolium, Rubus sp.,?Hebe (Shelter-50). E. Coprolite-16, containing Sophora microphylla, Hebe?cupressoides (Shelter-102). F. Coprolite-62, containing Sophora microphylla (Shelter-70). G. Coprolite-14, containing Hebe cupressoides, Sophora microphylla, Rubus sp., Pittosporum tennuifolium (Shi.e. elter-102). H. Coprolite-60, containing Sophora microphylla (Shelter-103).
FIGURE 22 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 22. Pseudopanax leaf (reflected light) and cuticle morphology (transmitted light microscopy). A. Intact Pseudopanax ferox leaf (LX3111, Shelter-37, scale bar equals 10 mm). B. Pseudopanax ferox stomatal complexes on abaxial surface (LX2711, Shelter-1, scale bar equals 100 μm). C. Pseudopanax ferox (LX5490, Coprolite-15, scale bar equals 100 μm). D. Pseudopanax crassifolious, abaxial surface showing much larger and more irregular epidermal cells (modern reference material, OPH5338, scale bar equals 100 μm). E. Pseudopanax crassifolious, abaxial surface also showing much larger and more irregular epidermal cells (modern reference material, OPH9835, scale bar equals 100 μm).
FIGURE 21 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 21. Pittosporum tenuifolium cuticle morphology (Transmitted light microscopy). A. Paracytic stomatal complexes on adaxial surface with a relatively sharply bounded trichome base at lower left (LX2576, Shelter-63, scale bar equals 40 μm). B. Paracytic stomatal complexes on abaxial surface with a more typical indistinctly bounded trichome base at upper right (LX2455, Shelter-111, scale bar equals 40 μm).
FIGURE 20 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 20. Olearia sp. cuticle morphology (Transmitted light microscopy). A. Abaxial surface showing a dense mass of trichome bases obscuring most stomatal complexes (LX2495, Coprolite-13, scale bar equals 40 μm). B. Non-stomatal (adaxial) surface showing a trichome attachment scar extending over several epidermal cells (LX3147, Shelter-12, scale bar equals 40 μm).
FIGURE 13 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 13. Loranthaceae (Korthalsella and Illiostylus) cuticle morphology (Transmitted light microscopy). A. Korthalsella sp., showing generally aligned stomatal complexes (LX2450, Shelter-82, scale bar equals 100 μm). B. Korthalsella sp., detail showing a single stomatal complex (LX2450, Shelter-82, scale bar equals 40 μm). C. Korthalsella sp., showing stomatal orientation perpendicular to epidermal cell rows (LX3371, Coprolite-79, scale bar equals 100 μm). D. Korthalsella sp., detail of stomatal complex (LX3371, Coprolite-79, scale bar equals 40 μm). E. Korthalsella salicornioides for comparison (Herbarium specimen, OPH9239, scale bar equals 100 μm). F. Korthalsella salicornioides for comparison (Herbarium specimen, OPH9239, scale bar equals 40 μm). G. Illiostylus micranthus for comparison (Herbarium specimen, OPH8301, scale bar equals 100 μm). H. Illiostylus micranthus for comparison (Herbarium specimen, OPH8301, scale bar equals 100 μm).
FIGURE 17 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 17. Coprosma propinqua (both LX3272, Shelter-62, scale bars equals 40 μm). A. Four stomatal complexes on abaxial surface with prominent fine ridges perpendicular to the stomatal pore. B. Zone of simple trichomes.
FIGURE 12. Kunzea ericoides. A in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 12. Kunzea ericoides. A. Abaxial surface, showing lid cell to left and stomatal complexes to right (LX3256, Shelter-62, scale bar equals 40 μm). B. Single lid cell (LX3253, Shelter-62, scale bar equals 40 μm).
FIGURE 8 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 8. Carmichaelia sp. cuticle morphology (Transmitted light microscopy). A. Showing transversely oriented stomatal complexes along the stem (long-axis of the stem is left-right) (LX2570, Shelter-46, scale bar equals 100 μm). B. Also with transversely oriented stomatal complexes, but including trichome attachment (arrowed, SL6583, LX2478, Coprolite-11, scale bar equals 100 μm).
FIGURE 5 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 5. Examples of shelters the Cromwell Region. A. Shelter-29. Note relict Sophora microphylla tree (c. 350 mm diameter) outside. B. Shelter-71 (arrowed). This picture encapsulates the typical rocky and treeless environment of the Gorges today – and how the record of the rock shelters represents tiny windows into the very different vegetation of the past. C. Shelter-58, view from within the shelter, out over Lake Dunstan in the Cromwell Gorge. D. Shelter-69 (arrowed) above the vehicle track. E. Shelter-31. Vehicle track in the background. F. Shelter-43 (arrowed). Longest icicles are about 400 mm. G. Shelter-83. Trowel (260 mm) for scale. H. Shelter-83, internal view to show 'piedmont' of remaining sediment. Grey and brown mid-late Holocene material is overlain by a post-European cap of light material with rabbit and sheep coprolites. Trowel (260 mm) for scale.
FIGURE 16 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 16. Myrsine divaricata cuticle morphology (Transmitted light microscopy). A. Margin of a leaf showing dark glandular structures, situated just inside the margin, and veins, projecting from below (LX2515, Shelter-103, scale bar equals 1 mm). B. Typical abaxial surface cuticle showing scattered stomatal complexes and the stem of a peltate trichome (the cap has detached) at right (LX2557, Shelter-50, scale bar equals 100 μm). C. Detail showing an intact peltate trichome at left and two stomatal complexes at right. Note the highly sinuous margins of the epidermal and subsidiary cells (LX2789, Coprolite-21, scale bar equals 40 μm). D. Typical non-stomatal (adaxial) surface showing the distinctive ridged ornamentation and obscured outlines of the epidermal cells (LX2811 Shelter-96, scale bar equals 40 μm).
FIGURE 7 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 7. Poaceae cuticle morphology (Transmitted light microscopy). A. Showing characteristic long and short epidermal cells, and an (arrowed) stomatal complex (LX2529, Shelter-102, scale bar equals 100 μm). B. Detail, including a stomatal complex (LX2533, Shelter-80, scale bar equals 40 μm). C. A zone of long and short epidermal cells above, and a zone of epidermal cells with trichomes below (LX3184, Shelter-10, scale bar equals 100 μm). D. Two zone of long and short epidermal cells with a zone of purely long cells between (LX3224, Shelter-108, scale bar equals 100 μm).
FIGURE 4 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 4. The Roxburgh Region, showing shelter locations (blue dots) centered on the Roxburgh Gorge. Groups of closely spaced shelters are surrounded by an ellipse. Lines indicate the 'sectors'.
FIGURE 1 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 1. General location, indicating Central Otago in New Zealand and the three 'regions' that were studied.
FIGURE 3 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 3. The Cromwell Region, showing shelter locations (blue dots) to the east of Lake Dunstan and within the Cromwell Gorge. Groups of closely spaced shelters are surrounded by an ellipse. Groups of closely spaced shelters are surrounded by an ellipse. Lines indicate the 'sectors'.
FIGURE 6 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 6. Examples of the dried vegetation zone in Cromwell Region shelters. A. Shelter-41. Surface view of an extracted mass of chewed twigs and leaf fragments. Ballpoint pen (140 mm) for scale. B. Shelter-40. Cross section showing a brown zone of dry vegetation (arrowed) below a grey zone of lithic rubble and capped by a zone within which sheep and rabbit coprolites are prominent. Ballpoint pen (140 mm) for scale. C. Shelter-46. Lens of twigs and leaf material below ballpoint pen (140 mm) and trowel, exposed in the face of a relict 'piedmont' of sediment. D. Shelter-71. A relatively thick brown, vegetation-rich zone adjacent trowel, capped by a pale lithic rubble. This is a close up of the floor of the shelter in Figure 5B. Trowel (260 mm) for scale. E. Shelter-78. Cross-section of an extracted lump of fine twigs and leaf material. Hand for scale. F. Shelter-28. Cross section of a sand-rich zone of dry vegetation and moa feathers. Rock hammer (handle 35 mm wide) for scale. G. Shelter-83. Surface view of extracted block of silt-rich sediment, with dried leaves on the partings. Ballpoint pen (140 mm) for scale. H. Shelter-88. Small relict 'piedmont' of sediment to left of trowel (260 mm), with brown zone of dry vegetation (arrowed).
FIGURE 11. Melicytus alpinus. A in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 11. Melicytus alpinus. A. Abaxial surface, showing typical range of stomatal complexes and orientation (LX5560, Shelter-6, scale bar equals 100 μm). B. Detail of stomatal complexes showing the prominent outer stomatal ledges and thickened polar T-pieces (LX5338, Coprolite-106, scale bar equals 40 μm).
FIGURE 15 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 15. Malvaceae (Plagianthus sp. or Hoheria sp.) abaxial surface cuticle morphology (Transmitted light microscopy). A. Stellate trichome at upper right (LX2520, Shelter-103, scale bar equals 40 μm. B. Stellate trichome at upper right, group of stomatal complexes at lower left (LX2951, Shelter-33, scale bar equals 40 μm). C. 'balloon' trichome (LX2520, Shelter-103, scale bar equals 40 μm). D. two-armed trichome (LX2520, Shelter-103, scale bar equals 40 μm).
FIGURE 14 in A vanished ecosystem: Sophora microphylla (Kōwhai) dominated forest recorded in mid-late Holocene rock shelters in Central Otago, New Zealand
FIGURE 14. Muehlenbeckia sp. A. Abaxial surface with stomatal complexes below and peltate trichome with divided base above (LX2891, Shelter-95, scale bar equals 40 μm). B. Three stomatal complexes among fine surface ridging and peltate trichome with divided base at lower left (LX3100, Coprolite-36, scale bar equals 40 μm).
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.
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.