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77 results for “gymnosperm”
Data from: Stomatal sensitivity to CO2 diverges between angiosperm and gymnosperm tree species
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Data from: Revisiting the relative growth rate hypothesis for gymnosperm and angiosperm species co‐occurrence
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Steep topography buffers threatened gymnosperm species against anthropogenic pressures in China
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Angiosperm to Gymnosperm host-plant switch entails shifts in microbiota of the Welwitschia bug, Probergrothius angolensis (Distant, 1902)
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Data from: A high frequency of allopolyploid speciation in the gymnospermous genus Ephedra and its possible association with some biological and ecological features
The origin and evolution of polyploids have been studied extensively in angiosperms and ferns but very rarely in gymnosperms. With the exception of three species of conifers, all natural polyploid species of gymnosperms belong to Ephedra, in which more than half of the species show polyploid cytotypes. Here we investigate the origin and evolution of polyploids of Ephedra distributed in the Qinghai-Tibetan Plateau (QTP) and neighboring areas. Flow cytometry (FCM) was used to measure the ploidy levels of the sampled species that are represented by multiple individuals from different populations, and then two single-copy nuclear genes (LFY and DDB2) and two chloroplast DNA fragments were used to unravel the possible origins and maternal donors of the polyploids. The results indicate that the studied polyploid species are allopolyploids, and suggest that allotetraploidy is a dominant mode of speciation in Ephedra. The high percentage of polyploids in the genus could be related to some of its biological attributes such as vegetative propagation, a relatively high rate of unreduced gamete formation, and a small genome size relative to most other gymnosperms. Significant ecological divergences between allotetraploids and their putative progenitors were detected by PCA analyses and ANOVA and Tukey's tests, with the exception of E. saxatilis. The overlap of geographical distributions and ecological niches of some diploid species could have provided opportunities for interspecific hybridization and allopolyploid speciation.
Data from: Dancing together and separate again: gymnosperms exhibit frequent changes of fundamental 5S and 35S rRNA genes (rDNA) organisation
In higher eukaryotes, the 5S rRNA genes occur in tandem units and are arranged either separately (S-type arrangement) or linked to other repeated genes, in most cases to rDNA locus encoding 18S–5.8S–26S genes (L-type arrangement). Here we used Southern blot hybridisation, PCR and sequencing approaches to analyse genomic organisation of rRNA genes in all large gymnosperm groups, including Coniferales, Ginkgoales, Gnetales and Cycadales. The data are provided for 27 species (21 genera). The 5S units linked to the 35S rDNA units occur in some but not all Gnetales, Coniferales and in Ginkgo (~30% of the species analysed), while the remaining exhibit separate organisation. The linked 5S rRNA genes may occur as single-copy insertions or as short tandems embedded in the 26S–18S rDNA intergenic spacer (IGS). The 5S transcript may be encoded by the same (Ginkgo, Ephedra) or opposite (Podocarpus) DNA strand as the 18S–5.8S–26S genes. In addition, pseudogenised 5S copies were also found in some IGS types. Both L- and S-type units have been largely homogenised across the genomes. Phylogenetic relationships based on the comparison of 5S coding sequences suggest that the 5S genes independently inserted IGS at least three times in the course of gymnosperm evolution. Frequent transpositions and rearrangements of basic units indicate relatively relaxed selection pressures imposed on genomic organisation of 5S genes in plants.
Figure 4 from: Lu Y-F, Chen Z-L, He A-G, Liu J-L, Wang P, Chen W-J, Jin X-F (2022) Torreya dapanshanica (Taxaceae), a new species of gymnosperm from Zhejiang, East China. PhytoKeys 192: 29-36. https://doi.org/10.3897/phytokeys.192.79506
Figure 4 Variation of seed shape and size of Torreya dapanshanica (A1‒A5) and T. jiulongshanensis (B1‒B8).
Figure 3 from: Lu Y-F, Chen Z-L, He A-G, Liu J-L, Wang P, Chen W-J, Jin X-F (2022) Torreya dapanshanica (Taxaceae), a new species of gymnosperm from Zhejiang, East China. PhytoKeys 192: 29-36. https://doi.org/10.3897/phytokeys.192.79506
Figure 3 Leaf apex of Torreya dapanshanica (A1‒A4) and T. jiulongshanensis (B1‒B4) A1 and B1 seed bearing individuals (adaxially) A2 and B2 seed bearing individuals (abaxially) A3 and B3 pollen cone bearing individuals (adaxially) A4 and B4 pollen cone bearing individuals (adaxially).
Figure 2 from: Lu Y-F, Chen Z-L, He A-G, Liu J-L, Wang P, Chen W-J, Jin X-F (2022) Torreya dapanshanica (Taxaceae), a new species of gymnosperm from Zhejiang, East China. PhytoKeys 192: 29-36. https://doi.org/10.3897/phytokeys.192.79506
Figure 2 Photographs of Torreya dapanshanica sp. nov. A branch with seeds B branch with pollen cones C branch with pollen cones D pollen cone showing pollen sacs E ovule (fertilized) F fertilized ovule with bracts G seeds with arils H cross section of seed (showing aril) I seeds without aril J cross section of seed (showing deeply ruminate megagametophyte).
Figure 1 from: Lu Y-F, Chen Z-L, He A-G, Liu J-L, Wang P, Chen W-J, Jin X-F (2022) Torreya dapanshanica (Taxaceae), a new species of gymnosperm from Zhejiang, East China. PhytoKeys 192: 29-36. https://doi.org/10.3897/phytokeys.192.79506
Figure 1 Torreya dapanshanica sp. nov. A branch with seeds B leaf (abaxial surface) C branch with pollen cones D microsporophyll/stamen (abaxial surface with four pollen sacs) E microsporophyll/stamen (adaxial surface) F branch with ovules G ovule (showing macrosporophyll and bracts) H seeds without aril I cross section of seed (showing deeply ruminate megagametophyte) (drawn by Xiao-Feng Jin; based on Xiao-Feng Jin 4036B, ZM).
Data from: Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms
BACKGROUND: A detailed knowledge about spatial and temporal gene expression is important for understanding both the function of genes and their evolution. For the vast majority of species, transcriptomes are still largely uncharacterized and even in those where substantial information is available it is often in the form of partially sequenced transcriptomes. With the development of next generation sequencing, a single experiment can now simultaneously identify the transcribed part of a species genome and estimate levels of gene expression. RESULTS: mRNA from actively growing needles of Norway spruce (Picea abies) was sequenced using next generation sequencing technology. In total, close to 70 million fragments with a length of 76 bp were sequenced resulting in 5 Gbp of raw data. A de novo assembly of these reads, together with publicly available expressed sequence tag (EST) data from Norway spruce, was used to create a reference transcriptome. Of the 38,419 PUTs (putative unique transcripts) longer than 150 bp in this reference assembly, 83.5% show similarity to ESTs from other spruce species and of the remaining PUTs, 3,704 show similarity to protein sequences from other plant species, leaving 4,167 PUTs with limited similarity to currently available plant proteins. By predicting coding frames and comparing not only the Norway spruce PUTs, but also PUTs from the close relatives Picea glauca and Picea sitchensis to both Pinus taeda and Taxus mairei, we obtained estimates of synonymous and non-synonymous divergence among conifer species. In addition, we detected close to 15,000 SNPs of high quality and estimated gene expression differences between samples collected under dark and light conditions. CONCLUSIONS: Our study yielded a large number of single nucleotide polymorphisms as well as estimates of gene expression on transcriptome scale. In agreement with a recent study we find that the synonymous substitution rate per year (0.6 x 10-09 and 1.1 x 10-09) is an order of magnitude smaller than values reported for angiosperm herbs. However, if one takes generation time into account, most of this difference disappears. The estimates of the dN/dS ratio (non-synonymous over synonymous divergence) reported here are in general much lower than 1 and only a few genes showed a ratio larger than 1.
Text-fig. 8. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. Structure of seed extracted from seedbearing capsule. a, b: general morphology; c–e: detailed cellular structure. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 1 mm (a, b; same scale for both figures), 100 µm (c–e). in Taimyria Gen. Nov., A New Genus Of Evolutionary Advanced Gymnosperms From Triassic Of The Taimyr Peninsula, Siberia, Russia
Text-fig. 8. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. Structure of seed extracted from seedbearing capsule. a, b: general morphology; c–e: detailed cellular structure. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 1 mm (a, b; same scale for both figures), 100 µm (c–e).
Text-fig. 3. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. a: morphology of female cone; b: position of seed-bearing discs forming parastichous lines; c: seed scar structure. Scale bar 1 cm (a, b), 100 µm (c). in Taimyria Gen. Nov., A New Genus Of Evolutionary Advanced Gymnosperms From Triassic Of The Taimyr Peninsula, Siberia, Russia
Text-fig. 3. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. a: morphology of female cone; b: position of seed-bearing discs forming parastichous lines; c: seed scar structure. Scale bar 1 cm (a, b), 100 µm (c).
Data from: Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms
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Data from: Dancing together and separate again: gymnosperms exhibit frequent changes of fundamental 5S and 35S rRNA genes (rDNA) organisation
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Data from: A high frequency of allopolyploid speciation in the gymnospermous genus Ephedra and its possible association with some biological and ecological features
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Spatiotemporal transcriptome atlas of ovule development in gymnosperms reveals co-regulatory patterns of gene expression associated with polarity establishment
GEO Series GSE287157. Pinus tabuliformis; Cycas panzhihuaensis; Gnetum montanum; Ginkgo biloba. 10 samples. Type: Other.
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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)
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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.