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260 results for “Nicotiana”
Nicotiana benthamiana as a model organism for plant biology study
<p><em>Nicotiana benthamiana</em> is an amenable model organism for plant biology study. Several functional genomics tools, including viral vectors, RNAi, ethylmethanesulfonate (EMS) mutagenesis, CRISPR-mediated genome editing, and agroinfiltration, are available in the <em>N. benthamiana</em> experimental system. These tools can be applied to research in genomics, biochemistry, metabolomics, cell biology and pathology as well as other topics in plant biology.</p> <p>*This is an updated graphical abstract for commnetary article "Dude, where is my mutant? <em>Nicotiana benthamiana</em> meets forward genetics" (Derevnina et al., 2019, New Phytologist 221(2):607-610).</p>
Herbarium specimen image of Nicotiana macgillivrayi Seem., part of the collection of Natural History Museum London
Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published.<br><br>Content of this deposition:<br><br>- A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values.<br>- A JPEG image file of the scanned herbarium sheet.<br>- A lossless TIFF image from which the JPEG image has been derived.
Nicotiana tomentosiformis genome assembly and annotation
<p><em>De novo</em> genome assembly and annotation of <em>Nicotiana tomentosiformis</em>.</p> <p>The following files are available:</p> <ul> <li>ntom.fa.gz: reference genome sequence in fasta format</li> <li>ntom.gff3.gz: gene annotation in GFF3 format</li> <li>ntom.gtf.gz: gene annotation in GTF format</li> <li>ntom.tx.fa.gz: transcript sequences in fasta format</li> <li>ntom.cds.fa.gz: coding sequences in fasta format</li> <li>ntom.prot.fa.gz: protein sequences in fasta format</li> <li>ntom.tsv.gz: gene functional annotation in TSV format</li> <li>ntom.rt.fa.gz: retrotransposon sequences in fasta format</li> <li>ntom.rt.gff3.gz: retrotransposon annotation on GFF3 format</li> <li>ntom.rt.tsv.gz: retrotransposon annotation in TSV format</li> <li>ntom.chr_to_id.tsv.gz: mapping of sequence names to ids in TSV format</li> </ul>
Nicotiana tabacum genome assembly and annotation
<p><em>De novo</em> genome assembly and annotation of <em>Nicotiana tabacum</em>.</p> <p>The following files are available:</p> <ul> <li>ntab.fa.gz: reference genome sequence in fasta format</li> <li>ntab.gff3.gz: gene annotation in GFF3 format</li> <li>ntab.gtf.gz: gene annotation in GTF format</li> <li>ntab.tx.fa.gz: transcript sequences in fasta format</li> <li>ntab.cds.fa.gz: coding sequences in fasta format</li> <li>ntab.prot.fa.gz: protein sequences in fasta format</li> <li>ntab.tsv.gz: gene functional annotation in TSV format</li> <li>ntab.rt.fa.gz: retrotransposon sequences in fasta format</li> <li>ntab.rt.gff3.gz: retrotransposon annotation on GFF3 format</li> <li>ntab.rt.tsv.gz: retrotransposon annotation in TSV format</li> <li>ntab.chr_to_id.tsv.gz: mapping of sequence names to ids in TSV format</li> </ul>
Nicotiana sylvestris genome assembly and annotation
<p><em>De novo</em> genome assembly and annotation of <em>Nicotiana sylvestris</em>.</p> <p>The following files are available:</p> <ul> <li>nsyl.fa.gz: reference genome sequence in fasta format</li> <li>nsyl.gff3.gz: gene annotation in GFF3 format</li> <li>nsyl.gtf.gz: gene annotation in GTF format</li> <li>nsyl.tx.fa.gz: transcript sequences in fasta format</li> <li>nsyl.cds.fa.gz: coding sequences in fasta format</li> <li>nsyl.prot.fa.gz: protein sequences in fasta format</li> <li>nsyl.tsv.gz: gene functional annotation in TSV format</li> <li>nsyl.rt.fa.gz: retrotransposon sequences in fasta format</li> <li>nsyl.rt.gff3.gz: retrotransposon annotation on GFF3 format</li> <li>nsyl.rt.tsv.gz: retrotransposon annotation in TSV format</li> <li>nsyl.chr_to_id.tsv.gz: mapping of sequence names to ids in TSV format</li> </ul>
Figure 9 in Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus
Figure 9. ELISA plate readings (O.D at 405nm) of leaf samples of transgenic lines (T1-T8) and control plants after 15 dpi.
Figure 7 in Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus
Figure 7. PCR Products of the hpt gene from T0 transgenic plants. Lane 1-9 are transgenic. Lane 10, +ve control. Lane 11, control (untransformed) plant.
Figure 6. DNA bands from T0 in Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus
Figure 6. DNA bands from T0 transgenic and Agro-infilterated plants. Lane 1-10, transgenic plants. Lane 11-13, agro-infilterated plants.
Figure 3 in Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus
Figure 3. Symptoms development on propagative host plants after mechanical inoculation with ChiVMV isolate ATIPK. (a) N. tabacum showing mosaic, mottling and vein clearing (b) C. annum (cv. Loungi) displays the symptoms of mottling, mosaic, leaf deformation and vein clearing.
Figure 2 in Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus
Figure 2. Symptoms of ChiVMV on chilli leaves collected from Islamabad. (a) Shows mottling and severe vein clearing and distortion. (b) Shows reduced leaf size with mottling and distortion.
How to start a LINE: 5' switching rejuvenates LINE retrotransposons in tobacco and related Nicotiana species
<p>Here we provide supplementary data for our study of Retrotransosable Elements (RTE) in tobacco and other Nightshades.</p> <p> </p> <p>In contrast to their conserved mammalian counterparts, plant long interspersed nuclear elements (LINEs) are highly variable, splitting into many low-copy families. Curiously, LINE families from the RTE clade retain a stronger sequence conservation and hence reach higher copy numbers. The cause of this RTE-typical property is not yet understood, but would help clarifying why some transposable elements are removed quickly whereas others persist in plant genomes. Here, we bring forward the first detailed study of RTE LINE structure, diversity and evolution in plants. For this, we argue that the Nightshade family is the ideal taxon to follow the evolutionary trajectories of RTE LINEs, given their high abundance, recent activity and partnership to non-autonomous elements.</p> <p>Using bioinformatic, cytogenetic and molecular approaches, we detect 4029 full-length RTE LINEs across the <em>Solanaceae</em>. We finely characterize and manually curate a core group of 458 full-length LINEs in allotetraploid tobacco, show amplification after polyploidization, and trace hybridization events by RTE LINE composition of parental genomes. Finally, we reveal the role of the untranslated regions (UTRs) as causes for the unique RTE LINE amplification and evolution pattern in plants: On one hand, we detect a highly conserved motif at the 3’ UTR, suggesting strong selective constraints acting on the RTE terminus. On the other hand, we observed successive rounds of 5’ UTR cycling, constantly rejuvenating the promoter sequences. This interplay between exchangeable promoters and conserved LINE bodies and 3’ UTR likely allows RTE LINEs to persist and thrive in plant genomes.</p> <p> </p> <p>This dataset contains the nHMMs and their underlying alignments that were used for RTE detection (S1 - S4). In addition, we provide the final multiple nucleotide alignment of 458 full length SolRTE LINEs (S5) and an alignment and an annotated list of 19 representative SolRTE LINEs of tobacco (S6 - S7). Sequence names include information on the analysed genome assembly of <em>Nicotiana tabacum </em><em>Cultivar ‘TN90’</em> (GCA_000715135.1; Sierro <em>et al</em>. 2014): scaffold position (scaffold identifier; start and stop position), and sequence orientation (forward = plus; reverse = minus). Sequences of the probes used for Fluorescent <em>in situ</em> hybridisation (FISH) were provided as S8.</p>
Nicotiana tabacum L. (BR0000010152720)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Nicotiana sp. (BR0000012297986)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Nicotiana tabacum L. (BR0000010152690)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Nicotiana tabacum L. (BR0000010152782)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Nicotiana tabacum L. (BR0000012544912)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Nicotiana tabacum L. (BR0000010152935)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Nicotiana tabacum L. (BR0000010152904)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Nicotiana tabacum L. (BR0000010884089)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Nicotiana tabacum L. (BR0000012074563)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.