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.
11
datasets available to search
ShareScore release 0.9.0
Dataset results
11 results for “Rubioideae”
Linked collectors and determiners for: Revision of Chassalia (Rubiaceae-Rubioideae-Palicoureeae) in Borneo, with 14 new species.
Natural history specimen data linked to collectors and determiners held within, "Revision of Chassalia (Rubiaceae-Rubioideae-Palicoureeae) in Borneo, with 14 new species". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/02cf5931-b18e-4d58-a6ff-9c7b1e37e68d">https://bionomia.net/dataset/02cf5931-b18e-4d58-a6ff-9c7b1e37e68d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/02cf5931-b18e-4d58-a6ff-9c7b1e37e68d">https://gbif.org/dataset/02cf5931-b18e-4d58-a6ff-9c7b1e37e68d</a>. Formatted as a Frictionless Data package.
Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)
<p class="MsoNormal"><span>Subfamily Rubioideae is the largest of the main lineages in the coffee family (Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic relationships among tribes and other major clades within this group of plants are still only partly resolved despite considerable efforts. While previous studies have mainly utilized data from the organellar genomes and nuclear ribosomal DNA, we here use a large number of low-copy nuclear genes obtained via a target capture approach to infer phylogenetic relationships within Rubioideae. We included 101 Rubioideae species representing all but two (the monogeneric tribes Foonchewieae and Aitchinsonieae) of the currently recognized tribes, and all but one non-monogeneric tribe were represented by more than one genus. Using data from the 353 genes targeted with the universal Angiosperms353 probe set we investigated the impact of data type, analytical approach, and potential paralogs on phylogenetic reconstruction. We inferred a robust phylogenetic hypothesis of Rubioideae with the vast majority (or all) nodes being highly supported across all analyses and datasets and few incongruences between the inferred topologies. The results were similar to those of previous studies but novel relationships were also identified. We found that supercontigs (coding sequence [CDS] + noncoding sequence) clearly outperformed CDS data in levels of support and gene tree congruence. The full datasets (353 genes) outperformed the datasets with potential paralogous genes removed (186 genes) in levels of support but increased gene tree incongruence slightly. The pattern of gene tree conflict at short internal branches was often consistent with high levels of incomplete lineage sorting (ILS) due to rapid speciation in the group. While concatenation- and coalescence-based trees mainly agreed, the observed phylogenetic discordance between the two approaches may be best explained by their differences in accounting for ILS. The use of target capture data greatly improved our confidence and understanding of the Rubioideae phylogeny, highlighted by the increased support for previously uncertain relationships and the increased possibility to explore sources of underlying phylogenetic discordance.</span></p>
Data from: Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae
<p>In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that, while ILS could by itself explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are with few exceptions highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.</p>
Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)
Open the record for dataset details and reuse information.
Data from: Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae
Open the record for dataset details and reuse information.
FIGURE 1. Ophiorrhiza debiana. A. Habitat. B in Ophiorrhiza debiana (Rubiaceae, Rubioideae), a new species from North-East India
FIGURE 1. Ophiorrhiza debiana. A. Habitat. B. Front view of flower. C & H. Inflorescence. D. & E. Bract adaxial and abaxial surface. F. & G. Bracteole adaxial and abaxial surface. I. Flower bud with bracteoles. J. Hypanthium. K. Split opened corolla of short styled flower. L. Short style with stigma andhypanthium. M. Split opened corolla of long styled flower. N Short style with stigma and hypanthium. (inset portion of style enlarged). (Photos by V.S. Hareesh & Alfred Joe).
Fig. 3 in Specialised metabolites as chemotaxonomic markers of Coptosapelta diffusa, supporting its delimitation as sisterhood phylogenetic relationships with Rubioideae
Fig. 3. The current most likely phylogenetic backbone of Rubiaceae based on nuclear (a), chloroplast (b) and mitochondrial (c) data sensu Rydin et al., (2017) and Wikstrom et al., 2020
Figure 1 from: Zhou S-S, Li R, Quan R-C, Shine L, Duan L-D (2020) Ophiorrhiza monsvictoriae (Rubiaceae, Rubioideae), a new species from Myanmar. In: Jin X-H, Xia N-H, Tan Y-H (Eds) Plant diversity of Southeast Asia-II. PhytoKeys 138: 219-223. https://doi.org/10.3897/phytokeys.138.38966
Figure 1 Ophiorrhiza monsvictoriae S.S.Zhou & L.D.Duan, sp. nov. A Habitat B front view of flower and Inflorescence C infructescence D opened corolla of long styled flower E corolla inside and outside F stamen and style G fruit H seed.
Figure 1 from: Pan B, Ma H-S, Wang R-J (2016) Spiradiclis pengshuiensis (Ophiorrhizeae, Rubioideae), a new species from Chongqing, China. PhytoKeys 63: 41-45. https://doi.org/10.3897/phytokeys.63.8016
Figure 1 - Spiradiclis pengshuiensis sp. nov. A habitat B habit C linear stipules D visiting insects E bracts and hypanthium F–I longitudinal section of long- (F, H) and short-styled flowers (G, I), respectively, showing the induments, relative positions and morphology of the stigmas and anthers and the developing capsules in distylous flowers J infructescence K–L transverse and longitudinal section of young capsules, respectively M mature capsule N dehiscent capsules O seeds. Photos by Ruijiang Wang.
Fig. 1 in Specialised metabolites as chemotaxonomic markers of Coptosapelta diffusa, supporting its delimitation as sisterhood phylogenetic relationships with Rubioideae
Fig. 1. The chemical structures of compounds 1–21.
Fig. 2. Selected 1H–1H in Specialised metabolites as chemotaxonomic markers of Coptosapelta diffusa, supporting its delimitation as sisterhood phylogenetic relationships with Rubioideae
Fig. 2. Selected 1H–1H COSY, HMBC and NOESY correlations for compounds 1, 3, 7 and 15–17.
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.