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9 results for “Brassiceae”
Dataset for "High photosynthesis rates in Brassiceae species are mediated by leaf anatomy enabling high biochemical capacity, rapid CO2 diffusion and efficient light use"
<p>Dataset used in the paper</p> <p>Retta MA, Van Doorselaer L, Driever SM, Yin X, de Ruijter NCA, Verboven P, Nicolaï BM, Struik PC. High photosynthesis rates in Brassiceae species are mediated by leaf anatomy enabling high biochemical capacity, rapid CO<sub>2</sub> diffusion and efficient light use. New Phytol. 2024 Sep 18. doi: 10.1111/nph.20136. PMID: 39294895.</p> <p>Please cite the paper presenting this datase.</p> <h1><strong>Plant Species and Inbred Lines:</strong></h1> <ul> <li><em>Hirschfeldia incana L. (7th generation inbred line 190003 HIN-NIJ-07-B) </em></li> <li><em>Brassica nigra L. (3rd generation inbred line 210093 BNI-DG1-03-B)</em></li> <li><em>Brassica rapa L. (inbred line ‘R-o-18’)</em></li> <li><em>Arabidopsis thaliana (accession Columbia)</em></li> </ul> <h1><strong>Growth Conditions:</strong></h1> <ul> <li><em>Media:</em> Rock-wool blocks (Grodan Plantop, Roermond, Netherlands, 10×10×7.5 cm)</li> <li><em>Fertigation:</em> Nitrogen-rich nutrient solution via automated dripping system.</li> <li><em>Light Conditions:</em> 12 h day/12 h night, light intensity of 200 µmol m-2 s-1 and 1800 µmol m-2 s-1</li> <li><em>Temperature:</em> Day/Night temperatures of 23 °C and 20 °C, respectively.</li> <li><em>Relative Humidity:</em> 70%</li> </ul> <h1><strong>Codes</strong></h1> <p><strong>Species:</strong></p> <ul> <li><em>Hirschfeldia incana L. - H. incana</em></li> <li><em>Brassica nigra L. - B. nigra</em></li> <li><em>Brassica rapa L. - B. rapa</em></li> <li><em>Arabidopsis thaliana - A. thaliana</em></li> </ul> <p><strong>Light conditions:</strong></p> <ul> <li><em>High light - HL</em></li> <li><em>Low light - LL</em></li> </ul> <p><strong>Replicates:</strong></p> <ul> <li><em>Biological replicates were labeled with numbers, e.g. replicate one from high light grown Hirschfeldia incana is referred to as HiHL1</em></li> </ul> <h1><strong>Measurements</strong></h1> <h2><strong>Leaf Gas Exchange and Chlorophyll Fluorescence Measurements (GasExchangeData.zip):</strong></h2> <ul> <li>Four leaves per species per treatment.</li> <li>Conducted using a LI-6800 (LI-COR, Lincoln, NE, USA) on the mid-position of the youngest fully expanded leaf.</li> <li>The resoponse of photosynthesis to irradiance and external CO2 concentrations augumneted with multi-phase flash fluorescence were made</li> </ul> <h2><strong>Optical Properties Measurement </strong>(<strong>Absorbance & chlorophyll.zip):</strong></h2> <ul> <li><em>Leaves:</em> Four leaves per species per treatment.</li> <li>Leaf transmittance and reflectance measured using a dual channel spectrophotometer (absorptance_reflac_data_355_750.xlsx)</li> <li>Chlorophyll content measured using a spectrophotometer (Chlorophyll.xlsx).</li> </ul> <h2><strong>Stomatal Density and Size Analysis </strong>(<strong>Stomata.zip):</strong></h2> <p><strong>Sampling:</strong></p> <ul> <li><em>Leaves:</em> Four leaves per species per treatment.</li> <li><em>Plants:</em> Samples taken from three different plants.</li> <li><em>Leaf-side:</em> abaxial and adxial leaf side.</li> </ul> <p><strong>Microscopy Setup:</strong></p> <ul> <li>Stomatal imprints made using clear nail polish, imaged using a light microscope at 20x.</li> </ul> <p><strong>Data Output:</strong></p> <ul> <li><em>Imaging Results:</em> .jpg files organised under folders for species e.g. AtHL\R1 T+B.zip contains images ofimprints of top (T) and bottom (B) leaf sides from replicate plant 1 (R1) of A. thaliana grown under high light (AtHL). The images are named as for example, AT_HL_BOTTOM_R1_A_stacked_minimum.jpg, The leters A to E label various imges made from one imprint.</li> </ul> <h2><strong>Light and Electron Microscopy of Leaf Sections (</strong><strong>CellwallChloroplast.zip):</strong></h2> <p><strong>Sampling:</strong></p> <ul> <li><em>Leaves:</em> Four leaves per species per treatment.</li> <li><em>Plants:</em> Samples taken from four different plants.</li> </ul> <p><strong>Sample preparation</strong></p> <ul> <li>Leaf samples fixed, dehydrated, embedded in Araldite, and sectioned for imaging.</li> <li>1 µm think sections were made for light microscopy</li> <li>Sections of 70 nm were double stained for TEM</li> </ul> <p><strong>Microscopy Setup:</strong></p> <ul> <li>Mesophyll cells imaged at 400x and 700x to measure chloroplast coverage.</li> <li>Electron microscopy performed with Zeiss EM900 electron microscope.</li> </ul> <h2><strong>Mesophyll Chlorophyll (ConfocalData.zip):</strong></h2> <p><strong>Sampling:</strong></p> <ul> <li><em>Leaves:</em> Three leaves per species per treatment.</li> <li><em>Plants:</em> Samples taken from three different plants.</li> <li><em>Thickness:</em> 200 ± 10 µm sections prepared using a sliding microtome</li> </ul> <p><strong>Microscopy Setup:</strong></p> <ul> <li><em>Microscope:</em> Leica DM8 inverted scope equipped with a Stellaris 5 confocal microscope (Leica Microsystems, Wetzlar, Germany).</li> <li><em>Excitation:</em> 490 nm excitation laser line</li> <li><em>Fluorescence Recording:</em> Chlorophyll autofluorescence recorded in a spectral range of 660−700 nm.</li> <li><em>Objective:</em> Leica objective ×10/0.4 NA.</li> <li><em>Z-Stacks:</em> 85–112 µm depth, two random positions per sample</li> </ul> <p><strong>Data Output:</strong></p> <ul> <li><em>Imaging Results:</em> Z-stacks of chlorophyll autofluorescence in mesophyll cells.</li> <li><em>Spectral Information:</em> Chlorophyll autofluorescence recorded in the 660−700 nm range.</li> </ul> <p><strong>Analysis:</strong></p> <ul> <li><em>Software:</em> The confocal files are in .lif format and can be viewed using Leica application suite (LASx), ImageJ</li> </ul>
A new tree-based methodological framework to infer the evolutionary history of Mesopolyploid lineages: An application to the Brassiceae tribe (Brassicaceae)
<p>Whole genome duplication events are notably widespread in plants and this poses particular challenges for phylogenetic inference in allopolyploid lineages, i.e. lineages that result from the merging of two or more diverged genomes after interspecific hybridization. The nuclear genomes resulting from allopolyploidization contain homologous gene copies from different evolutionary origins called homoeologs, whose orthologs must be sorted out in order to reconstruct the evolutionary history of polyploid clades. In this study, we propose a methodological approach to resolve the phylogeny of allopolyploid clades focusing on mesopolyploid genomes, which experienced some level of genome reshuffling and gene fractionation across their subgenomes. To illustrate our methodological framework, we applied it to a clade belonging to the model Brassicaceae plant family, the Brassiceae tribe, that experienced a mesohexaploidy event. The dataset analysed consists of both publically available genomic sequences and new transcriptomic data according to taxa. The present methodology requires a well-annotated reference genome, for which the identification of the parental subgenome fragments has been performed (e.g. Brassica rapa and Brassica oleracea). Focusing on fully retained genes (i.e., genes for which all homoeologous gene copies inherited from the parental lineages are still present in the reference genome), the method constructs multilabelled gene trees that allow subsequent assignment of each gene copy to its diploid parental lineage. Once the orthologous copies are identified, genes from the same parental origin are concatenated and tree-building methods are used to reconstruct the species tree. This method allows resolving the phylogenetic relationships (i) among extant species within a mesopolyploid clade, (ii) among the parental lineages of a mesopolyploid lineage, and (iii) between the parental lineages and closely related extant species. We report here the first well-resolved nuclear-based phylogeny of the Brassiceae tribe.</p>
A new tree-based methodological framework to infer the evolutionary history of Mesopolyploid lineages: An application to the Brassiceae tribe (Brassicaceae)
Open the record for dataset details and reuse information.
Supplementary material 3 from: Koch MA, Lemmel C (2019) Zahora, a new monotypic genus from tribe Brassiceae (Brassicaceae) endemic to the Moroccan Sahara. PhytoKeys 135: 119-131. https://doi.org/10.3897/phytokeys.135.46946
: Data type: not applicable (phylogenetic reconstruction).
Figure 3 from: Koch MA, Lemmel C (2019) Zahora, a new monotypic genus from tribe Brassiceae (Brassicaceae) endemic to the Moroccan Sahara. PhytoKeys 135: 119-131. https://doi.org/10.3897/phytokeys.135.46946
Figure 3 BEAST analysis of tribe Brassiceae based on ITS DNA sequence data (Suppl. material 2). The new genus Zahora is highlighted, and its respective stem group node is indicated (red dot). Divergence times are given as Mya (million years ago). Agronomically important species, Brassica oleracea and Raphanus sativus, are indicated and shown with their respective clades. Brassica nigra and B. carinata are also indicated with an asterisk (orange).
Supplementary material 2 from: Koch MA, Lemmel C (2019) Zahora, a new monotypic genus from tribe Brassiceae (Brassicaceae) endemic to the Moroccan Sahara. PhytoKeys 135: 119-131. https://doi.org/10.3897/phytokeys.135.46946
: Data type: DNA sequence data.
Supplementary material 1 from: Koch MA, Lemmel C (2019) Zahora, a new monotypic genus from tribe Brassiceae (Brassicaceae) endemic to the Moroccan Sahara. PhytoKeys 135: 119-131. https://doi.org/10.3897/phytokeys.135.46946
: Data type: DNA sequence data.
Figure 1 from: Koch MA, Lemmel C (2019) Zahora, a new monotypic genus from tribe Brassiceae (Brassicaceae) endemic to the Moroccan Sahara. PhytoKeys 135: 119-131. https://doi.org/10.3897/phytokeys.135.46946
Figure 1 Zahora ait-atta in its natural environment. Border region with Algeria. Near Errachidia. Oued Bou-Ibourine – type locality a sandy habitat b flowering plant c rosette during winter d lyrate leaf from lower part of the plant e rosette starts building the inflorescence f ripening heteroarthrocarpic fruits g flowers and detailed view on sepals h siliques releasing seeds from dehiscent distal part of fruit. Images taken by C. Lemmel and Z. Attioui.
Figure 2 from: Koch MA, Lemmel C (2019) Zahora, a new monotypic genus from tribe Brassiceae (Brassicaceae) endemic to the Moroccan Sahara. PhytoKeys 135: 119-131. https://doi.org/10.3897/phytokeys.135.46946
Figure 2 Distribution of known localities (red dots) of Zahora ait-atta documented from 2015 to 2019 (satellite map was taken from image metadata Copernicus/Landsat).
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