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171 results for “plant identification”
Data from: Characterization of rhizome transcriptome and identification of a rhizomatous ER body in the clonal plant Cardamine leucantha
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Elk food habits using DNA metabarcoding for plant identification
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Data from: Comprehensive identification and clustering of CLV3/ESR-related (CLE) genes in plants finds groups with potentially shared function
CLV3/ESR (CLE) proteins are important signaling peptides in plants. The short CLE peptide (12–13 amino acids) is cleaved from a larger pre-propeptide and functions as an extracellular ligand. The CLE family is large and has resisted attempts at classification because the CLE domain is too short for reliable phylogenetic analysis and the pre-propeptide is too variable. We used a model-based search for CLE domains from 57 plant genomes and used the entire pre-propeptide for comprehensive clustering analysis. In total, 1628 CLE genes were identified in land plants, with none recognizable from green algae. These CLEs form 12 groups within which CLE domains are largely conserved and pre-propeptides can be aligned. Most clusters contain sequences from monocots, eudicots and Amborella trichopoda, with sequences from Picea abies, Selaginella moellendorffii and Physcomitrella patens scattered in some clusters. We easily identified previously known clusters involved in vascular differentiation and nodulation. In addition, we found a number of discrete groups whose function remains poorly characterized. Available data indicate that CLE proteins within a cluster are likely to share function, whereas those from different clusters play at least partially different roles. Our analysis provides a foundation for future evolutionary and functional studies.
Data from: Automated DNA-based plant identification for large-scale biodiversity assessment
Rapid degradation of tropical forests urges to improve our efficiency in large-scale biodiversity assessment. DNA-barcoding can assist greatly in this task, but commonly used phenetic approaches for DNA-based identifications rely on the existence of comprehensive reference databases, which are infeasible for hyperdiverse tropical ecosystems. Alternatively, phylogenetic methods are more robust to sparse taxon sampling but time-consuming, while multiple alignment of species-diagnostic, typically length-variable markers can be problematic across divergent taxa. We advocate the combination of phylogenetic and phenetic methods for taxonomic assignment of DNA-barcode sequences against incomplete reference databases such as GenBank, and we developed a pipeline to implement this approach on large-scale plant diversity projects. The pipeline workflow includes several steps: database construction and curation, query sequence clustering, sequence retrieval, distance calculation, multiple alignment and phylogenetic reconstruction. We describe the strategies used to establish these steps and the optimisation of parameters to fit the selected psbA-trnH marker. We tested the pipeline using infertile plant samples and herbivore diet sequences from the highly threatened Nicaraguan seasonally dry forest and exploiting a valuable purpose-built resource: a partial local reference database of plant psbA-trnH. The selected methodology proved efficient and reliable for high-throughput taxonomic assignment, and our results corroborate the advantage of applying 'strict' tree-based criteria to avoid false positives. The pipeline tools are distributed as the scripts suite 'BAGpipe' (pipeline for Biodiversity Assessment using GenBank data), which can be readily adjusted to the purposes of other projects and applied to sequence-based identification for any marker or taxon.
FIGURES 67–79. Neohydatothrips plynopygus, N. poeta, N in Identification and host-plant associations of Australian Sericothripinae (Thysanoptera, Thripidae)
FIGURES 67–79. Neohydatothrips plynopygus, N. poeta, N. samayunkur & Sericothrips staphylinus. (67–69) N. plynopygus, (67) Male sternites; (68) Antenna; (69) Meso & metanota. (70–72) N. poeta, (70) Head; (71) Metasternum; (72) Tergites. (73–76) N. samayunkur, (73) Female; (74) Head & pronotum; (75) Meso & metanota; (76) Sternites. (77–79) S. staphylinus, (77) Meso & metanota; (78) Tergites; (79) Larva II tergal setae.
FIGURES 37–45. Neohydatothrips barrowi & N in Identification and host-plant associations of Australian Sericothripinae (Thysanoptera, Thripidae)
FIGURES 37–45. Neohydatothrips barrowi & N. bellisi. (37–40) N. barrowi, (37) Head, ventral view; (38) Pro, meso & metanota; (39) Metasternum; (40) Sternites. (41–45) N. bellisi, (41) Female; (42) Meso & metanota; (43) Metasternum; (44) Head; (45) Forewing.
FIGURES 1–7 in Identification and host-plant associations of Australian Sericothripinae (Thysanoptera, Thripidae)
FIGURES 1–7. Hydatothrips aliceae. (1) Head & pronotum; (2) Forewing; (3) Meso & metanotum; (4) Sternites; (5) Tergites; (6) Metasternum; (7) Female.
FIGURES 27–36. Hydatothrips latisensibilis & H in Identification and host-plant associations of Australian Sericothripinae (Thysanoptera, Thripidae)
FIGURES 27–36. Hydatothrips latisensibilis & H. williamsi. (27–30) H. latisensibilis, (27) Head, pro, meso & metanota; (28) Tergites; (29) Male sternites; (30) Terminal antennal segments, ventral and lateral views. (31–36) H. williamsi, (31) Head; (32) Meso & metanota; (33) Tergites; (34) Tergites I–III; (35) Sternites; (36) Metasternum.
FIGURES 56–66. Neohydatothrips haydni & N in Identification and host-plant associations of Australian Sericothripinae (Thysanoptera, Thripidae)
FIGURES 56–66. Neohydatothrips haydni & N. katherinae. (56–62) N. haydni, (56) Head; (57) Forewing apex; (58) Tergites; (59) Pronotum; (60) Larva II tergal setae. (61) Meso & metanota; (62) Sternites. (63–66) N. katherinae, (63) Pronotum; (64) Meso & metanota; (65) Male sternites; (66) Head, ventral view.
FIGURES 8–14 in Identification and host-plant associations of Australian Sericothripinae (Thysanoptera, Thripidae)
FIGURES 8–14. Hydatothrips argenticinctus. (8) Female; (9) Head & pronotum; (10) Tergites; (11) Sternites; (12) Meso & metanotum; (13) Metasternum; (14) Forewing.
FIGURES 15–26. Hydatothrips bhattii & H in Identification and host-plant associations of Australian Sericothripinae (Thysanoptera, Thripidae)
FIGURES 15–26. Hydatothrips bhattii & H. haschemi. (15–19) H. bhattii, (15) Head; (16) Meso & metanota; (17) Sternites; (18) Metasternum; (19) Tergites. (20–26) H. haschemi, (20) Head & pronotum; (21) Pro, meso & metanota; (22) Tergites; (23) Sternites; (24) Male sternites; (25) Antenna; (26) Forewing apex.
FIGURES 46–55. Neohydatothrips diana & N in Identification and host-plant associations of Australian Sericothripinae (Thysanoptera, Thripidae)
FIGURES 46–55. Neohydatothrips diana & N. gracilipes. (46–51) N. diana, (46) Head; (47) Meso & metanota; (48) Tergites; (49) Metasternum; (50) Meso & metanota; (51) Forewing apex. (52–55) N. gracilipes, (52) Head & pronotum (53) Sternites; (54) Larva II tergal setae; (55) Meso & metanota.
FIGURES 3–16 in Description of new cicada species associated with the coffee plant and an identification key for the species of Fidicinoides (Hemiptera: Cicadidae) from Brazil
FIGURES 3–16. Illustrations of morphological structures used in the key to the Brazilian Fidicinoides. 3. Body of F. opalina. 4. Body of F. s e r i c a n s. 5. Mesonotal marking of F. pauliensis. 6. Mesonotal markings of F. picea. 7. Pronotum of F. pronoe. 8. Mesothorax of F. d i s t a n t i. 9. Pronotum of F. b r i s a. 10. Pronotum and mesonotum of F. rosabasalae. 11. Mesonotum of F. brunnea. 12. Mesonotum of F. b e s t i. 13. Pronotum and mesonotum of F. su cin al ae. 14. Timbal cover of F. saccifera. 15. Mesonotum of F. jauffretti. 16. Pronotum of F. pseudethelae.
FIGURE 1 in Description of new cicada species associated with the coffee plant and an identification key for the species of Fidicinoides (Hemiptera: Cicadidae) from Brazil
FIGURE 1. Fidicinoides sarutaiensis sp. n. A. Head and thorax (dorsal view). B. Head frontal view. C. Metathorax and abdômen (ventral view). D. Left fore femur (lateral view). E. Right fore wing. F. Right hind wing.
FIGURE 2 in Description of new cicada species associated with the coffee plant and an identification key for the species of Fidicinoides (Hemiptera: Cicadidae) from Brazil
FIGURE 2. Lateral view (left) of male Fidicinoides sarutaiensis sp. n. genitalia. Posterior view (right) of male uncus.
FIGURE. Puccinia klugkistiana on Ligustrum obtusifolium (A–F, N, O, P) and Cleistogenes hackelii (G–N). A. Plant hedges producing spermogonia and aecia in the field. B. Spermogonia on the upper leaf surface. C. Vertical section of an aecium surrounded with peridia. D. Aecia on the lower leaf surface. E. Vertical section of a spermogonium. F. Aeciospores. G. Uredinia on the leaf surface. H. Vertical section of a uredinium. I. Urediniospores. J, K. Telia on the leaf surface. L. Teliospores. M. Urediniospore observed under SEM. N. Vertical section of an uredinium observed under SEM. O. Aecium observed under SEM. P. Aeciospores with various sizes of verrucae on the surface observed under SEM. Scale bars: C = 100 μm, E, F = 20 μm, H, I = 30 μm, M = 5 μm, P = 10 μm, H, L, O = 40 μm. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Puccinia klugkistiana on Ligustrum obtusifolium (A–F, N, O, P) and Cleistogenes hackelii (G–N). A. Plant hedges producing spermogonia and aecia in the field. B. Spermogonia on the upper leaf surface. C. Vertical section of an aecium surrounded with peridia. D. Aecia on the lower leaf surface. E. Vertical section of a spermogonium. F. Aeciospores. G. Uredinia on the leaf surface. H. Vertical section of a uredinium. I. Urediniospores. J, K. Telia on the leaf surface. L. Teliospores. M. Urediniospore observed under SEM. N. Vertical section of an uredinium observed under SEM. O. Aecium observed under SEM. P. Aeciospores with various sizes of verrucae on the surface observed under SEM. Scale bars: C = 100 μm, E, F = 20 μm, H, I = 30 μm, M = 5 μm, P = 10 μm, H, L, O = 40 μm.
FIGURE. Puccinia cerinthes-agropyrina on Clematis sp. A. Plants producing spermogonia and aecia on the leaves and stems in the field. B. Spermogonia and aecia on the lower leaf surface. C. Vertical section of a spermogonium. D. Aecia on the stem. E. Aeciospores. F. Aeciospore with verrucose surface observed under SEM. G. Aecium observed under SEM. H. Vertical section of an aecium. Scale bars: C = 20 μm, E, H = 30 μm, F = 5 μm, G = 100 μm. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Puccinia cerinthes-agropyrina on Clematis sp. A. Plants producing spermogonia and aecia on the leaves and stems in the field. B. Spermogonia and aecia on the lower leaf surface. C. Vertical section of a spermogonium. D. Aecia on the stem. E. Aeciospores. F. Aeciospore with verrucose surface observed under SEM. G. Aecium observed under SEM. H. Vertical section of an aecium. Scale bars: C = 20 μm, E, H = 30 μm, F = 5 μm, G = 100 μm.
FIGURE. Puccinia miscanthi on Plantago asiatica (A–H) and Miscanthus sacchariflorus (I–Q). A. Plants producing spermogonia and aecia on the leaf surface. B. Spermogonia on the leaf surface. C. Aecia on lower leaf surface. D. Vertical section of a spermogonium. E. Aeciospores. F. Vertical section of an aecium observed under SEM. G. Aeciospores with verrucose surface observed by SEM. H. Vertical section of an aecium surrounded by peridia. I. Plants producing uredinia on the leaf surface in the field. J. Vertical section of an uredinium with paraphyses. K. Urediniospores. L. Uredinia on the leaf surface. M. Uredinium on the leaf surface observed under SEM. N. Urediniospore with echinulate surface observed under SEM. O. Telia on the leaf surface. P. Vertical section of a telium. Q. Teliospores. Scale bars: D, E, K = 20 μm, F, H, M = 100 μm, G = 5 μm, J, P, Q = 30 μm, N = 10 μm. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Puccinia miscanthi on Plantago asiatica (A–H) and Miscanthus sacchariflorus (I–Q). A. Plants producing spermogonia and aecia on the leaf surface. B. Spermogonia on the leaf surface. C. Aecia on lower leaf surface. D. Vertical section of a spermogonium. E. Aeciospores. F. Vertical section of an aecium observed under SEM. G. Aeciospores with verrucose surface observed by SEM. H. Vertical section of an aecium surrounded by peridia. I. Plants producing uredinia on the leaf surface in the field. J. Vertical section of an uredinium with paraphyses. K. Urediniospores. L. Uredinia on the leaf surface. M. Uredinium on the leaf surface observed under SEM. N. Urediniospore with echinulate surface observed under SEM. O. Telia on the leaf surface. P. Vertical section of a telium. Q. Teliospores. Scale bars: D, E, K = 20 μm, F, H, M = 100 μm, G = 5 μm, J, P, Q = 30 μm, N = 10 μm.
FIGURE. Puccinia achnatheri-sibirici on Berberis amurensis (A–H) and Stipa baicalensis (I–M). A. Plants producing spermogonia and aecia on leaf surface in the field. B. Aecia on the lower leaf surface. C. Vertical section of a spermogonium. D. Spermogonia on the upper leaf surface. E. Vertical section of an aecium surrounded with peridia. F. Aeciospores. G. Aecium observed under SEM. H. Aeciospore with verrucose surface observed under SEM. I, J. Telia on the leaf surface. K. Urediniospores. L. Teliospores. M. Vertical section of a telium. Scale bars: C, F, L, M = 20 μm, E = 50 μm, G = 100 μm, H = 5 μm. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Puccinia achnatheri-sibirici on Berberis amurensis (A–H) and Stipa baicalensis (I–M). A. Plants producing spermogonia and aecia on leaf surface in the field. B. Aecia on the lower leaf surface. C. Vertical section of a spermogonium. D. Spermogonia on the upper leaf surface. E. Vertical section of an aecium surrounded with peridia. F. Aeciospores. G. Aecium observed under SEM. H. Aeciospore with verrucose surface observed under SEM. I, J. Telia on the leaf surface. K. Urediniospores. L. Teliospores. M. Vertical section of a telium. Scale bars: C, F, L, M = 20 μm, E = 50 μm, G = 100 μm, H = 5 μm.
FIGURE. Puccinia digitaticoronata on Rhamuns sp. (A–C, F, J) and species of Poaceae (D, E, G–I, K, L). A. Vertical section of spermogonia. B. Vertical section of an aecium surrounded with peridia. C. Aeciospores. D. Plants producing uredinia on the leaf surface in the field. E. Urediniospores. F. Aecium observed under SEM. G. Uredinia on the leaf surface. H. Telia on the leaf surface. I. Vertical section of an uredinium. J. Aeciospore with verrucose surface observed under SEM. K. Teliospores. L. Vertical section of a telium. Scale bars: A, I = 40 μm, B = 60 μm, C, E, K, L= 20 μm, J, F = 80 μm. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Puccinia digitaticoronata on Rhamuns sp. (A–C, F, J) and species of Poaceae (D, E, G–I, K, L). A. Vertical section of spermogonia. B. Vertical section of an aecium surrounded with peridia. C. Aeciospores. D. Plants producing uredinia on the leaf surface in the field. E. Urediniospores. F. Aecium observed under SEM. G. Uredinia on the leaf surface. H. Telia on the leaf surface. I. Vertical section of an uredinium. J. Aeciospore with verrucose surface observed under SEM. K. Teliospores. L. Vertical section of a telium. Scale bars: A, I = 40 μm, B = 60 μm, C, E, K, L= 20 μm, J, F = 80 μm.
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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.
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.