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650 results for “Angiosperms”
Mildew locus O facilitates colonization by arbuscular mycorrhiza in angiosperms
GEO Series GSE144199. Hordeum vulgare. 24 samples. Type: Expression profiling by high throughput sequencing.
Essential angiosperm-specific subunits of HDA19 histone deacetylase complexes in Arabidopsis
GEO Series GSE275988. Arabidopsis thaliana. 6 samples. Type: Expression profiling by high throughput sequencing.
Evolutionary trends in the floral transcriptome: insights from one of the basalmost angiosperms, the water lily Nuphar advena (Nymphaeceae)
GEO Series GSE23082. Nuphar advena. 32 samples. Type: Expression profiling by array.
Widespread natural variation of DNA methylation within angiosperms
GEO Series GSE79526. Cannabis sativa; Cucumis sativus; Prunus persica; Manihot esculenta; Panicum virgatum; Fragaria vesca; Eucalyptus grandis; Medicago truncatula; Setaria viridis; Sorghum bicolor; Vitis vinifera; Theobroma cacao; Brassica rapa; Malus domestica; Ricinus communis; Brachypodium distachyon; Lotus japonicus; Citrus x clementina; Populus trichocarpa; Erythranthe guttata; Eutrema salsugineum; Beta vulgaris; Panicum hallii. 34 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
Data from: Evolution of angiosperm pollen. 6. the Celastrales, Oxalidales, and Malpighiales (COM) clade and Zygophyllales
Analyzing pollen morphological data on a contemporary phylogenetic framework can enhance our understanding of the distribution, diversity, and evolution of palynological characters. In this paper, the sixth in a series detailing pollen morphological characters across angiosperms, we focus on the Celastrales, Oxalidales, and Malpighiales (COM) clade and Zygophyllales, together comprising ca. 20,000 species in 47 families within fabids. We first examined pollen grains from 21 species with light, scanning electron, and transmission electron microscopy, to illustrate pollen diversity within the COM clade and Zygophyllales. Second, based on a reexamination of previously published pollen data and our new observations, we optimized 21 pollen characters on a maximum likelihood (ML) tree of 169 genera in 45 families representing all four orders, using Fitch parsimony, ML, and hierarchical Bayesian inference. The pollen morphology of this group displays great diversity, particularly in size, aperture number, supratectal element shape, and tectum sculpture. Plesiomorphic states for 18 characters were inferred unambiguously under all methods for the COM clade, and over 300 character state changes were hypothesized by each analysis on lineages at different levels within the group. Changes of state were found to occur most frequently in the characters outline in polar view, pollen size, and tectum sculpture; changes of state occurred least frequently in the characters dispersal unit, symmetry, and tectum presence/absence. We identified diagnostic character states for several monophyletic clades and explored palynological evidence to shed light on some unresolved relationships. For example, the previously poorly resolved Malpighiales were found to be distinguished by a single pollen character state change (from annulus absent to present). Patterns of evolutionary change in several notable pollen characters, such as the number of pollen apertures (from three to other states) and tectum sculpture (from perforate to reticulate), were further confirmed, and their possible adaptive functions are proposed. Reflecting current interest in the relationship between pollen morphology and pollination syndrome, we conducted tests of correlated evolution between pollen morphology and pollination syndrome, with results demonstrating significant correlations between a thin exine and anemophily and, unexpectedly, between presence of supratectal elements and anemophily. Evidence for previously postulated evolutionary trends in aperture number (increasing), tectum sculpture (from perforate to reticulate), and infratectum structure (from columellate to granulate) is discussed. The relatively high frequency of state changes in presence or absence of supratectal elements may be linked to switches in pollination syndrome within this group.
Data from: Angiosperm phylogeny based on 18S/26S rDNA sequence data: constructing a large dataset using next-generation sequence data
The utility of 18S and 26S in broad phylogenetic analyses has been much maligned due in large part to the low signal in both genes. However, few analyses have employed complete 26S rDNA sequences over a broad range of taxa, and most alignments of the two genes are done de novo, without taking into account the secondary structure of the two rRNA genes. Here we mine next-generation sequence data to compile large matrices (429 taxa) of complete 18S + 26S gene sequences, and we compare both de novo alignment methods with curated alignments done by eye that take into account secondary structure and hard-to-align regions (profile alignments). The combined 18S + 26S topology is overall very similar to recently published gene trees for the angiosperms based on three or more genes. Overall support for the backbone or framework of the combined tree is low (bootstrap support below 50%). Few major clades have bootstrap support above 50%. Most well-supported clades are tip clades (families and orders sensu APG III 2009). Importantly, the 18S + 26S rDNA topology is consistent with current estimates of relationships: the basalmost angiosperms are recovered (Amborellaceae, Nymphaeales, Austrobaileyales), as are most major clades, including Mesangiospermae, eudicots (Eudicotyledoneae sensu Cantino et al. 2007), core eudicots (Gunneridae sensu Cantino et al. 2007), rosids (Rosidae sensu Cantino et al. 2007), asterids (Asteridae sensu Cantino et al. 2007), and Caryophyllales. Most clades recognized at the ordinal level (sensu APG III 2009) are also recovered. However, there are also some unusual placements in the 18S + 26S topology, but none of these receives bootstrap support above 50%. The profile and de novo alignments gave very similar topologies. 18S + 26S trees remain useful sources of data in large combined analyses. This is the first time a large data set of complete 26S gene sequences has been employed at this scale; this gene in particular proved to be useful phylogenetically. Targeted sequencing of 18S/26S rDNA is not advocated here, but given that these regions provide useful phylogenetic information and are abundant in next-generation sequencing runs, we suggest that the data be used rather than discarded.
Data from: Experimental signal dissection and method sensitivity analyses reaffirm the potential of fossils and morphology in the resolution of the relationship of angiosperms and Gnetales
The placement of angiosperms and Gnetales in seed plant phylogeny remains one of the most enigmatic problems in plant evolution, with morphological analyses (which have usually included fossils) and molecular analyses pointing to very distinct topologies. Almost all morphology-based phylogenies group angiosperms with Gnetales and certain extinct seed plant lineages, while most molecular phylogenies link Gnetales with conifers. In this study, we investigate the phylogenetic signal present in published seed plant morphological datasets. We use parsimony, Bayesian inference, and maximum likelihood approaches, combined with a number of experiments with the data, to address the morphological-molecular conflict. First, we ask whether the lack of association of Gnetales with conifers in morphological analyses is due to an absence of signal or to the presence of competing signals, and second, we compare the performance of parsimony and model-based approaches with morphological datasets. Our results imply that the grouping of Gnetales and angiosperms is largely the result of long branch attraction, consistent across a range of methodological approaches. Thus, there is a signal for the grouping of Gnetales with conifers in morphological matrices, but it was swamped by convergence between angiosperms and Gnetales, both situated on long branches. However, this effect becomes weaker in more recent analyses, as a result of addition and critical reassessment of characters. Even when a clade including angiosperms and Gnetales is still weakly supported by parsimony, model-based approaches favor a clade of Gnetales and conifers, presumably because they are more resistant to long branch attraction. Inclusion of fossil taxa weakens rather than strengthens support for a relationship of angiosperms and Gnetales. Our analyses finally reconcile morphology with molecules in favoring a relationship of Gnetales to conifers, and show that morphology may therefore be useful in reconstructing other aspects of the phylogenetic history of the seed plants.
Lists of angiosperms in the campos rupestres according to Reflora
<p>These two files contain a list of angiosperm species occurring in the <i>campos rupestres.</i></p><p>The file<i> </i><a href="https://zenodo.org/api/records/10085292/draft/files/cr_list_zenodo.xlsx/content">cr_list_zenodo.xlsx </a>contains a column with angiosperm species, a column with their corresponding scientific names, and a column with ID number as per information stored in Reflora's database.</p><p>The file <a href="https://zenodo.org/api/records/10085292/draft/files/list_syn_merged_no_underscore_noNA_unique_accepted_after_syn_analysis_only_angiosperms_zenodo.xlsx/content">list_syn_merged_no_underscore_noNA_unique_accepted_after_syn_analysis_only_angiosperms_zenodo.xlsx </a>contains a column describing the status of the species according to REFLORA, a column indicating clade (in this case angiosperms), a column with an assigned number, a column with the accepted names as per REFLORA, and a column containing merged synonyms, sourced from TROPICOS, ITIS, GBIF and REFLORA. </p><p>This file is color coded according to the following logic:</p><ul><li>Red cells indicate there was a lot of dissonance between synonyms retrieved from different databases (TROPICOS, ITIS, GBIF and REFLORA)</li><li>Pink cells indicate REFLORA didn't list the same synonyms as the other database, in which case the synonyms not listed in REFLORA were highlighted in red.</li><li>Orange cells indicate only REFLORA had synonyms for a given taxon (synonyms highlighted in green). </li><li>Green cells indicate the data between REFLORA and the other databases was matched.</li><li>Yellow, blue and salmon cells indicate that species had infraspecific taxa.</li></ul>
Figure 1 from: Roques A, Copeland RS, Soldati L, Denux O, Auger-Rozenberg M-A (2016) Megastigmus seed chalcids (Hymenoptera, Torymidae) radiated much more on Angiosperms than previously considered. I- Description of 8 new species from Kenya, with a key to the females of Eastern and Southern Africa. ZooKeys 585: 51-124. https://doi.org/10.3897/zookeys.585.7503
Figure 1 - Distribution in Kenya of the previously described African Megastigmus species.
Figure 2 from: Roques A, Copeland RS, Soldati L, Denux O, Auger-Rozenberg M-A (2016) Megastigmus seed chalcids (Hymenoptera, Torymidae) radiated much more on Angiosperms than previously considered. I- Description of 8 new species from Kenya, with a key to the females of Eastern and Southern Africa. ZooKeys 585: 51-124. https://doi.org/10.3897/zookeys.585.7503
Figure 2 - Distribution in Kenya of the new Megastigmus species identified during our study.
Figure 1 from: Alzate-Guarín F, Murillo-Serna JS (2016) Angiosperm flora on the páramos of northwestern Colombia: diversity and affinities. PhytoKeys 70: 41-52. https://doi.org/10.3897/phytokeys.70.8609
Figure 1 - Geographic location of the páramo complexes of Antioquia.
Chromosome-level genome assembly for the angiosperm Silene conica
<p>Genome annotation for <em>Silene conica</em> </p>
Data and R-scripts for the analyses of global woody angiosperm diversity
<p>This repository contains data and R scripts necessary to reproduce results shown in the paper: <br> Buntarou Kusumoto, Anne Chao, Wolf L. Eiserhardt, Jens-Christian Svenning, Takayuki Shiono, Yasuhiro Kubota. Occurrence-based diversity estimation reveals macroecological and conservation knowledge gaps for global woody plants. Science Advances (accepted)</p>
Data from: Angiosperm phylogeny based on 18S/26S rDNA sequence data: constructing a large dataset using next-generation sequence data
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Data from: Origin of angiosperms and the puzzle of the Jurassic gap
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Data from: An angiosperm-wide analysis of the correlates of gynodioecy
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Data from: Experimental signal dissection and method sensitivity analyses reaffirm the potential of fossils and morphology in the resolution of the relationship of angiosperms and Gnetales
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Data from: Evolution of angiosperm pollen. 6. the Celastrales, Oxalidales, and Malpighiales (COM) clade and Zygophyllales
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Progestogens and androgens influence root morphology of angiosperms in a brassinosteroid-independent way - C21- and C19-steroids a novel class of phytohormones?
GEO Series GSE286512. Arabidopsis thaliana. 12 samples. Type: Expression profiling by high throughput sequencing.
Oxygen-dependent proteolysis regulates the stability of angiosperm Polycomb Repressive Complex 2 subunit VERNALIZATION2
GEO Series GSE123459. Arabidopsis thaliana. 6 samples. Type: Expression profiling by high throughput sequencing.
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