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30 results for “chloroplast gene”
Dataset for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."
<p>Plasmid sequences for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."</p>
Concatenated data matrix of DNA sequences from two nuclear and four chloroplast gene regions
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A Pleistocene legacy of gene pools, ecodemes and admixtures of Stuckenia pectinata (L.) Börner as evidenced from microsatellites, complete chloroplast genomes and ribosomal RNA cistron (Europe, Africa)
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Data from: Gene flow among wild and domesticated almond species: insights from chloroplast and nuclear markers
Hybridization has played a central role in the evolutionary history of domesticated plants. Notably, several breeding programs relying on gene introgression from the wild compartment have been performed in fruit tree species within the genus Prunus but few studies investigated spontaneous gene flow among wild and domesticated Prunus species. Consequently, a comprehensive understanding of genetic relationships and levels of gene flow between domesticated and wild Prunus species is needed. Combining nuclear and chloroplastic microsatellites, we investigated the gene flow and hybridization among two key almond tree species, the cultivated Prunus dulcis and one of the most widespread wild relative Prunus orientalis in the Fertile Crescent. We detected high genetic diversity levels in both species along with substantial and symmetric gene flow between the domesticated P. dulcis and the wild P. orientalis. These results were discussed in light of the cultivated species diversity, by outlining the frequent spontaneous genetic contributions of wild species to the domesticated compartment. In addition, crop-to-wild gene flow suggests that ad hoc transgene containment strategies would be required if genetically modified cultivars were introduced in the northwestern Mediterranean.
Biased gene introgression and adaptation in face of chloroplast capture in Aquilegia
<p><span>Chloroplast capture</span><span>, a phenomenon that can occur through interspecific hybridization and introgression, has been frequently suggested as an explanation for cytonuclear discordance in plants. In theory, the captured donor chloroplasts may not cooperate with the recipient nuclear genome, especially chloroplast-targeted nuclear genes. However, relatively few studies have documented the mechanisms of cytonuclear coevolution and its potential species differentiation and possible functional differences in the face of chloroplast capture. To explore this crucial question, we chose the <em>Aquilegia</em> genus, which is known for having minimal sterility among the species, and we inferred that <em>A</em>. <em>amurensis</em> captured the plastome of <em>A</em>. <em>parviflora</em> based on cytonuclear discordance and gene flow between these two species. We focused on the introgression region and its differentiation with closely related species, especially its composition in a chloroplast capture scenario. We found that nuclear genes encoding cytonuclear enzyme complexes or organelle localized (CECs) were significantly enriched in the introgression regions, indicating that the CEC genes of chloroplast donor species were selectively retained and displaced the original CEC genes in chloroplast receptor species due to cytonuclear interactions during introgression. Notably, the intrinsic factor of cytonuclear compatibility may have a higher degree of evolutionary distance for the introgressed CEC genes between <em>A</em>. <em>amurensis</em> and <em>A</em>. <em>parviflora</em>. Introgression from <em>A</em>. <em>parviflora</em> promotes the differentiation of <em>A</em>. <em>amurensis</em> and <em>A</em>. <em>japonica</em>. Furthermore, we found that one of the overrepresented gene ontology terms in these introgressed genes was terpene synthase activity (GO: 0010333) in which more than one-third of the genes were CEC genes, showing that <em>A</em>. <em>amurensis</em> had similar release patterns for terpenes in flowers of <em>A</em>. <em>parviflora</em> when compared with <em>A</em>. <em>japonica</em>.</span> <span>Altogether, this study helps to clarify the mechanisms of cytonuclear coevolution, species differentiation and functional differences in face of chloroplast capture and highlights a critical role of chloroplast capture in adaptation.</span></p>
Data from: Gene flow among wild and domesticated almond species: insights from chloroplast and nuclear markers
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Biased gene introgression and adaptation in face of chloroplast capture in Aquilegia amurensis
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Data from: Congruent deep relationships in the grape family (Vitaceae) based on sequences of chloroplast genomes and mitochondrial genes via genome skimming
Vitaceae is well-known for having one of the most economically important fruits, i.e., the grape (Vitis vinifera). The deep phylogeny of the grape family was not resolved until a recent phylogenomic analysis of 417 nuclear genes from transcriptome data. However, it has been reported extensively that topologies based on nuclear and organellar genes may be incongruent due to differences in their evolutionary histories. Therefore, it is important to reconstruct a backbone phylogeny of the grape family using plastomes and mitochondrial genes. In this study, next-generation sequencing data sets of 27 species were obtained using genome skimming with total DNAs from silica-gel preserved tissue samples on an Illumina HiSeq 2500 instrument. Plastomes were assembled using the combination of de novo and reference genome (of V. vinifera) methods. Sixteen mitochondrial genes were also obtained via genome skimming using the reference genome of V. vinifera. Extensive phylogenetic analyses were performed using maximum likelihood and Bayesian methods. The topology based on either plastome data or mitochondrial genes is congruent with the one using hundreds of nuclear genes, indicating that the grape family did not exhibit significant reticulation at the deep level. The results showcase the power of genome skimming in capturing extensive phylogenetic data: especially from chloroplast and mitochondrial DNAs.
Data from: Whole chloroplast genome and gene locus phylogenies reveal the taxonomic placement and relationship of Tripidium (Panicoideae: Andropogoneae) to sugarcane
Background: For over 50 years, attempts have been made to introgress agronomically useful traits from Erianthus sect. Ripidium (Tripidium) species into sugarcane based on both genera being part of the 'Saccharum Complex', an interbreeding group of species believed to be involved in the origins of sugarcane. However, recent low copy number gene studies indicate that Tripidium and Saccharum are more divergent than previously thought. The extent of genus Tripidium has not been fully explored and many species that should be included in Tripidium are still classified as Saccharum. Moreover, Tripidium is currently defined as incertae sedis within the Andropogoneae, though it has been suggested that members of this genus are related to the Germainiinae. Results: Eight newly-sequenced chloroplasts from potential Tripidium species were combined in a phylogenetic study with 46 members of the Panicoideae, including seven Saccharum accessions, two Miscanthidium and three Miscanthus species. A robust chloroplast phylogeny was generated and comparison with a gene locus phylogeny clearly places a monophyletic Tripidium clade outside the bounds of the Saccharinae. A key to the currently identified Tripidium species is presented. Conclusion: For the first time, we have undertaken a large-scale whole plastid study of eight newly assembled Tripidium accessions and a gene locus study of five Tripidium accessions. Our findings show that Tripidium and Saccharum are eight million years divergent, last sharing a common ancestor 12 million years ago. We demonstrate that four species should be removed from Saccharum/Erianthus and included in genus Tripidium. In a genome context, we show that Tripidium evolved from a common ancestor with and extended Germainiinae clade formed from Germainia, Eriochrysis, Apocopis, Pogonatherum and Imperata. We re-define the 'Saccharum complex' to a group of genera that can interbreed in the wild and extend the Saccharinae to include Sarga along with Sorghastrum, Microstegium vimineum and Polytrias (but excluding Sorghum). Monophyly of genus Tripidium is confirmed and the genus is expanded to include Tripidium arundinaceum, Tripidium procerum, Tripidium kanashiroi and Tripidium rufipilum. As a consequence, these species are excluded from genus Saccharum. Moreover, we demonstrate that genus Tripidium is distinct from the Germainiinae.
Chloroplast DNA barcoding genes matK and psbA-trnH are not suitable for species identification and phylogenetic analyses in closely related pines
<p>Multispecies alignment of <em>matK</em> sequences used in the study in fasta format.</p> <p>Multispecies alignment of <em>trnH-psbA </em>sequences used in the study in fasta format.</p> <p>Multispecies alignment of <em>rbcL</em> sequences used in the study in fasta format.</p> <p> </p>
Data from: Whole chloroplast genome and gene locus phylogenies reveal the taxonomic placement and relationship of Tripidium (Panicoideae: Andropogoneae) to sugarcane
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Data from: Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling
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Data from: Congruent deep relationships in the grape family (Vitaceae) based on sequences of chloroplast genomes and mitochondrial genes via genome skimming
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Gene expression in response to chloroplastic H2O2: IS-GUS-2-17 vs. IS-tAPX-19-23 under estrogen treatment
GEO Series GSE35526. Arabidopsis thaliana. 4 samples. Type: Expression profiling by array.
The comparison for the transcript levels of chloroplast-encoded genes between wild type (Col-0) and pbf8 mutants
GEO Series GSE239827. Arabidopsis thaliana. 4 samples. Type: Expression profiling by high throughput sequencing.
HOT3/eIF5B1 confers Kozak motif-dependent translational control of photosynthesis-associated nuclear genes for chloroplast biogenesis
GEO Series GSE212857. Arabidopsis thaliana. 24 samples. Type: Expression profiling by high throughput sequencing; Other.
The Bayesian trees of the nuclear gene DMC1 and the chloroplast gene rps16 sequences
<p>Some plants with low fertility are morphologically intermediate between <i>Roegneria stricta</i><i> </i>and<i> Roegneria</i> <i>turczaninovii</i>, and were suspected to be natural hybrids between these species. In this study, karyotype analysis showed that natural hybrids and its putative parents were tetraploids (2n = 4x = 28). Meiotic pairing in natural hybrids is more irregular than its putative parents. Results of genomic <i>in situ</i> hybridization and fluorescence <i>in situ</i> hybridization indicate that natural hybrids contain the same genome as its putative parents. The nuclear gene DNA meiotic recombinase 1 (<i>DMC</i>1) and the chloroplast gene <i>rps</i>16 of natural hybrids and its putative parents were analyzed for evidence of hybridization. The results from molecular data supported by morphology and cytology demonstrated that the plants represent natural hybrids between <i>R. stricta</i><i> </i>and<i> R.</i> <i>turczaninovii</i>. The study is important understanding species evolution in the genus since it demonstrates for the first time the existence of populations of natural homoploid hybrids in <i>Roegneria. </i>The study also reports for the first time that the composition of the genomic formula of <i>R.</i> <i>turczaninovii </i>is <b>StY</b>, confirming that the current taxonomic status is correct.</p> <p> </p>
The Bayesian trees of the nuclear gene DMC1 and the chloroplast gene rps16 sequences
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PSI photoinhibition alters iron homeostasis in chloroplasts and initiates retrograde signaling regulating nuclear gene expression
GEO Series GSE242125. Arabidopsis thaliana. 32 samples. Type: Expression profiling by high throughput sequencing.
Chloroplast nucleoid is organized by membrane association of transcribed genes
GEO Series GSE228230. Arabidopsis thaliana. 148 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; 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)
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.