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.
28
datasets available to search
ShareScore release 0.9.0
Dataset results
28 results for “Phalaenopsis”
Core collection of Taiwanese Phalaenopsis orchids
<p>This study establishes the first core collection (CC) for Taiwanese <em>Phalaenopsis </em>orchids, employing a novel approach crucial for preserving genetic diversity and key traits integral to breeding and research. The investigation encompasses 207 orchid commercial cultivars from ten nurseries, characterized by phenotypic and genotypic data from eight SSRs. To address missingness, multiple imputation was applied to mitigate potential uncertainties, ensuring analytic robustness. The weighted <em>k</em>-means clustering identified seven distinct clusters, revealing substantial genetic diversity. Utilizing the two-step 'P+G strategy' and MGD algorithms, 22 core accessions were selectively chosen, demonstrating the effectiveness of this approach in preserving genetic diversity while retaining key features. Evaluation of the CC revealed notable phenotypic and genotypic diversity, surpassing alternative methodologies. Pedigree background analysis supported the representativeness of the CC in preserving diverse genetic materials. We underscored the importance of evaluating the CC, detailing criteria and statistical analyses to ensure the quality, representativeness, and effectiveness of the selected accessions. This study contributes to orchid breeding, conservation efforts, and sustainable agricultural practices by providing a valuable and comprehensive resource. In conclusion, the research establishes a groundbreaking CC, offering insights into the genetic landscape of Taiwanese <em>Phalaenopsis</em> orchids and highlighting potential advancements in breeding commercially sought-after varieties.</p>
Core collection of Taiwanese Phalaenopsis orchids
Open the record for dataset details and reuse information.
Data from: Biogeography of the Phalaenopsis amabilis species complex inferred from nuclear and plastid DNAs
Background: Phalaenopsis is one of the important commercial orchids in the world. Members of the P. amabilis species complex represent invaluable germplasm for the breeding program. However, the phylogeny of the P. amabilis species complex is still uncertain. The Phalaenopsis amabilis species complex (Orchidaceae) consists of subspecies amabilis, moluccana, and rosenstromii of P. amabilis, as well as P. aphrodite ssp. aphrodite, P. ap. ssp. formosana, and P. sanderiana. The aims of this study were to reconstruct the phylogeny and biogeographcial patterns of the species complex using Neighbor Joining (NJ), Maxinum Parsimony (MP), Bayesian Evolutionary Analysis Sampling Trees (BEAST) and Reconstruct Ancestral State in Phylogenies (RASP) analyses based on sequences of internal transcribed spacers 1 and 2 from the nuclear ribosomal DNA and the trnH-psbA spacer from the plastid DNA. Results: A pattern of vicariance, dispersal, and vicariance + dispersal among disjunctly distributed taxa was uncovered based on RASP analysis. Although two subspecies of P. aphrodite could not be differentiated from each other in dispersal state, they were distinct from P. amabilis and P. sanderiana. Within P. amabilis, three subspecies were separated phylogenetically, in agreement with the vicariance or vicariance + dispersal scenario, with geographic subdivision along Huxley's, Wallace's and Lydekker's Lines. Molecular dating revealed such subdivisions among taxa of P. amabilis complex dating back to the late Pleistocene. Population-dynamic analyses using a Bayesian skyline plot suggested that the species complex experienced an in situ range expansion and population concentration during the late Last Glacial Maximum (LGM). Conclusions: Taxa of the P. amabilis complex with disjunct distributions were differentiated due to vicariance or vicariance + dispersal, with events likely occurring in the late Pleistocene. Demographic growth associated with the climatic oscillations in the Würm glacial period followed the species splits. Nevertheless, a subsequent population slowdown occurred in the late LGM due to extinction of regional populations. The reduction of suitable habitats resulted in geographic fragmenttation of the remaining taxa.
Supplementary material 2 from: Qin S, Wang H, Wang Y, Ma C, Li Z, Yang B, Jin X (2024) Phalaenopsis zhanhuoensis (Orchidaceae, Vandeae), a new species from Yunnan, China. PhytoKeys 237: 153-160. https://doi.org/10.3897/phytokeys.237.112270
Phylogram of Bayesian Inference (BI) based on nrDNA ITS and plastid sequences (matK, trnL, trnL-F, and atpB-rbcL)
FIGURE 1 in A new endophytic fungus, Tulasnella phuhinrongklaensis (Cantharellales, Basidiomycota) isolated from roots of the terrestrial orchid, Phalaenopsis pulcherrima
FIGURE 1. Phylogenetic tree derived from maximum likelihood analysis of combined ITS and LSU regions of rDNA genes of 44 sequences. Rhizoctonia obscura and R. solani were used as the outgroups. Numbers above branches are the bootstrap statistics percentages (left) and Bayesian posterior probabilities (right). Branches with bootstrap values ≥ 50% are shown at each branch and the bar represents 0.1 substitutions per nucleotide position. The fungal isolates from this study are in bold. T = type species.
FIGURE 2 in A new endophytic fungus, Tulasnella phuhinrongklaensis (Cantharellales, Basidiomycota) isolated from roots of the terrestrial orchid, Phalaenopsis pulcherrima
FIGURE 2. Tulasnella phuhinrongklaensis CMU-CR41 (holotype). Colony on different media after incubation at 25 °C for two weeks. A. Potato dextrose agar. B. Oat meal agar. C. Malt extract agar. D. Corn meal agar. E. Right-angled branching with septate hyphae (arrows). F. Mycelia stained with 5% DAPI showing binucleate cells (arrows). G. Branched chains of monilioid cells. Scale bars: A–D = 10 mm, E = 10 μm, F = 50 μm, G = 20 μm.
FIGURE 1. Phalaenopsis putaoensis X.H.Jin & H.A.Mung. A. Habit. B in Phalaenopsis putaoensis (Orchidaceae: Epidendroideae, Vandeae), a new species from Kachin State, Myanmar
FIGURE 1. Phalaenopsis putaoensis X.H.Jin & H.A.Mung. A. Habit. B. Lateral view of flower, showing 3-lobed. C. Dissected flower, showing dorsal sepal, lateral sepals, petals, lip, column and long pedicel. D. Front view of flower. Photographed by X.H. Jin.
Data from: Biogeography of the Phalaenopsis amabilis species complex inferred from nuclear and plastid DNAs
Open the record for dataset details and reuse information.
Data from: PbbHLH4 regulates floral monoterpene biosynthesis in Phalaenopsis orchids
Floral scent is an important factor in attracting pollinators and repelling florivores. In Phalaenopsis bellina (Orchidaceae), the major floral scent components are monoterpenoids. Previously, we have identified that expression of GERANYL DIPHOSPHATE SYNTHASE (PbGDPS) is highly correlated with monoterpene biosynthesis in Phalaenosis orchids. Here, we showed that both cis- and trans-regulation were present on the GDPS promoters, with trans-regulation playing a key role. To investigate the regulation of floral scent biosynthesis, we compared the transcriptomic data of two Phalaenopsis orchids with contrasting scent phenotypes. Eight transcription factors (TFs) with sequential elevation expressions through floral development stages in P. bellina were identified, and their transcript levels were higher in the scent orchid than the scentless one. Five of these TFs transactivated several structural genes involved in monoterpene biosynthesis pathway to various extent, including PbbHLH4, PbbHLH6, PbbZIP4, PbERF1, and PbNAC1. Ectopic transient expression of these TFs in scentless orchids revealed that terpenoid biosynthesis was all stimulated. PbbHLH4 most profoundly induced the monoterpene phenotype with a 950-fold increase of monoterpenoid production in the scentless orchid. In conclusion, the orchid floral monoterpenes biosynthesis was regulated sequentially and elaborately, and with PbbHLH4 playing a crucial role for monoterpene phenotype.
Data from: De novo transcriptome assembly databases in the butterfly orchid Phalaenopsis equestris
Orchids are renowned for their spectacular flowers and ecological adaptations. After the sequencing of the genome of the tropical epiphytic orchid Phalaenopsis equestris, we combined Illumina HiSeq2000 for RNA-Seq and Trinity for de novo assembly to characterize the transcriptomes for 11 diverse P. equestris tissues representing the root, stem, leaf, flower buds, column, lip, petal, sepal and three developmental stages of seeds. Our aims were to contribute to a better understanding of the molecular mechanisms driving the analysed tissue characteristics and to enrich the available data for P. equestris. Here, we present three databases. The first dataset is the RNA-Seq raw reads, which can be used to execute new experiments with different analysis approaches. The other two datasets allow different types of searches for candidate homologues. The second dataset includes the sets of assembled unigenes and predicted coding sequences and proteins, enabling a sequence-based search. The third dataset consists of the annotation results of the aligned unigenes versus the Nonredundant (Nr) protein database, Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG) databases with low e-values, enabling a name-based search.
Supplementary material 1 from: Qin S, Wang H, Wang Y, Ma C, Li Z, Yang B, Jin X (2024) Phalaenopsis zhanhuoensis (Orchidaceae, Vandeae), a new species from Yunnan, China. PhytoKeys 237: 153-160. https://doi.org/10.3897/phytokeys.237.112270
GenBank accession numbers for sequences used for phylogenetic analyses
Figure 2 from: Qin S, Wang H, Wang Y, Ma C, Li Z, Yang B, Jin X (2024) Phalaenopsis zhanhuoensis (Orchidaceae, Vandeae), a new species from Yunnan, China. PhytoKeys 237: 153-160. https://doi.org/10.3897/phytokeys.237.112270
Figure 2 Flowers of Phalaenopsis zhanhuoensis X.H.Jin & S.Y.Qin, sp. nov. A front view of flower (1) rear view of flower (2) B column and lip; lateral view of column and lip, appendage and lateral lobes (1), front view of lateral lobes (2), lateral view of lateral lobes and mid-lobe (3) C petal, sepal and lip, lip (1), dorsal sepal (2), petal (3.4), lateral sepals (5.6). Photographed by Xiaohua Jin.
Figure 1 from: Qin S, Wang H, Wang Y, Ma C, Li Z, Yang B, Jin X (2024) Phalaenopsis zhanhuoensis (Orchidaceae, Vandeae), a new species from Yunnan, China. PhytoKeys 237: 153-160. https://doi.org/10.3897/phytokeys.237.112270
Figure 1 Phylogram of Maximum Likelihood based on nrITS and plastid DNA markers (matK, trnL, trnL-F and atpB-rbcL). Numbers above branches indicate bootstrap percentages (BS) for ML.
Figure 3 from: Qin S, Wang H, Wang Y, Ma C, Li Z, Yang B, Jin X (2024) Phalaenopsis zhanhuoensis (Orchidaceae, Vandeae), a new species from Yunnan, China. PhytoKeys 237: 153-160. https://doi.org/10.3897/phytokeys.237.112270
Figure 3 Habitat and plants of Phalaenopsis zhanhuoensis X.H.Jin & S.Y.Qin, sp. nov. A front view B roots C lateral view. Photographed by Xiaohua Jin.
Supplementary material 1 from: Ma C-B, Wang X-L, Chen W-S, Liu Z, Jin X-H (2022) Phalaenopsis medogensis (Orchidaceae, Epidendroideae, Vandeae), a new species from Xizang, China. PhytoKeys 214: 39-46. https://doi.org/10.3897/phytokeys.214.93607
Voucher and GenBank accession numbers
Data from: De novo transcriptome assembly databases in the butterfly orchid Phalaenopsis equestris
Open the record for dataset details and reuse information.
Data from: PbbHLH4 regulates floral monoterpene biosynthesis in Phalaenopsis orchids
Open the record for dataset details and reuse information.
Transcriptional profiling on leaves overexpressing Pha13 or Pha21 in Phalaenopsis aphrodite
GEO Series GSE93248. Phalaenopsis aphrodite. 12 samples. Type: Expression profiling by array.
Sequencing-based approaches reveal low ambient temperature-responsive and tissue-specific microRNAs in Phalaenopsis orchid
GEO Series GSE27585. Phalaenopsis aphrodite subsp. formosana. 4 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Gene expression profiling of Phalaenopsis orchids
GEO Series GSE29910. Phalaenopsis aphrodite. 54 samples. Type: Expression profiling by array.
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.