Find research datasets worth reusing

openOpenDec 2003View details →

Soil Water (Lysimeter) Chemistry for Mature Balsam Poplar and White Spruce for BCEF

This dataset includes soil water samples (lysimeter samples) collected from mature balsam poplar (BP1, BP2 and BP3) and white spruce (FP4A, FP4B, FP4C) stands during 2000 and 2001. Five Lysimeter were installed at 12 cm and four at the 40 cm in each stand type. Water from the Tanana River and small, non-silt, streams on the eastern portion of the floodplain were collected during many sampling periods.

Balsam Poplar NPP: Tree density and basal area by diameter sizeclass in upland and flooplain mid- and late-successional stands: 1989-2008

This data set is derived from BNZ LTER inventory plots. Stand density and basal area are listed by diameter size class of live balsam poplar trees for each replicate stand within mid- and late-successional upland and floodplain landscapes by year from 1989-2008.

Balsam Poplar NPP: average NPP per tree by diameter sizeclass for 4 time periods between 1993 and 2008

This data set is derived from BNZ LTER inventory plots, where DBH of all trees is measured every 3 to 4 years, and increment changes in AG biomass are derived from allometric equations. Data included in this file were obtained from 1993, 1997, 2000, 2004 and 2008 inventories, generating 4 growth increments between 1997 and 2008. Data are reported by diameter sizeclass (10 cm increments), and include NPP increments (averaged across all trees within each landscape and successional stage) for which adequate numbers of trees (typically >5) were present to obtain useful measurements (see N in data file).

Balsam poplar NPP per tree calculated from dendrometer bands annually from 1994 to 2008

This data set is derived from BNZ LTER inventory plots, where band dendrometers are in place on trees within each diameter size class (typically 10 trees per 10 cm increment diameter size class). Dendrometer bands are read in the fall each year. Biomass is calculated from allometric equations, from which annual biomass increments are derived. Data are reported as the average annual growth per tree across all trees within a given landscape and successional stage and reported as kg biomass/tree/year.

Balsam poplar tree diameter vs age in mid-successional and late-successional long-term Bonanza Creek LTER inventory plots

This data lists age and diameter for balsam poplar trees of varying diameters growing in mid and late successional long-term BNZ LTER inventory plots in floodplain and upland landscapes.

opencc-by-4.0Oct 2023View details →

TLS Z+F Imager 5010 point clouds of hybrid poplar trees from short-rotation crops after 5, 6, and 7 growing seasons

The point clouds are obtained from hybrid poplar crops installed in NE Romania, managed in short rotation (SRWCs) between 5, 6, and 7 growing seasons. The crops were planted every spring, outside the growing season, at a depth of 0.6 m in the ground with two clones: AF8 and Pannonia. Rods (2-meter-long cuttings) were used as planting material at a density of 1667 trees per ha (3 x 2 m). The scanning of the sample areas (3 x 10 trees for each variant, about 6 x 10 m) was outside the growing seasons.The 3D model was obtained using the Z+F Imager 5010 (Zoller and Fröhlich, Wangen, Germany), phase-shift type, providing a distance estimation accuracy of ±1 mm at 25 m and a nominal range of 187 m, and the tree individualization was done in CloudCompare v.2.12 (public license). A total of six station points and eight fixed targets or remarks (200 mm spheres) for co-registration were adopted for scanning. Trees included in the survey (without leaves) were marked with a ring of adhesive tape (black with yellow, 50 mm wide) at 1.4 m height on the tree spindle to adjust the results for calibration. Individually segmented trees can be sent on request, the database has a limit of 100 files. They can be converted into different formats via the CloudCompare application.File code: clone type _ number of growing seasons _ plot number

opencc-by-4.0Dec 2022View details →

Data from "Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar"

Data from : 'Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar' An Vanden Broeck*, Tim Meese*, Pieter Verschelde, Karen Cox, Berthold Heinze, Dieter Deforce, Ellen De Meester and Filip Van Nieuwerburgh   Related publication: Vanden Broeck, A.*, Meese, T.*, Verschelde, P. et al. Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar. BMC Biol 22, 30 (2024). https://doi.org/10.1186/s12915-024-01816-1 <ul> <li>* These authors contributed equally.</li> </ul> -------------------------------------------------- Background: Despite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar (Populus nigra cv. 'Italica' Duroi) offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome. Results: We present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH-context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe any biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the vegetative offspring's' phenotype. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment. Conclusions: Genome-wide cytosine methylation patterns in symmetrical GC-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in GC-context can be used as bio-markers to infer a common ancestor and thus to investigate the environmental history of a specific Lombardy poplar on short time-scales. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world.   ADDITIONAL FILES Additional file 1. CSV-file with information on the Lombardy poplar trees samples used for whole genome bisulfite sequencing (WGBS) in the two methylome experiments (metadata). The raw fastq datafiles obtained by whole genome bisulfite sequencing (WGBS) are available at the <a href="https://www.ncbi.nlm.nih.gov/geo/">Gene Expression Omnibus (GEO) database</a> (submission  GSE225596). Additional file 2. CSV-file with mapping statistics, bisulfite conversion rates and percentages of cytosine methylation for each DNA-sample analyzed by whole genome bisulfite sequencing (WGBS). (processed data). Additional file 3. CSV-file with the total list of GO terms that were enriched in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (processed data). Additional file 4. POWERPOINT-file. Heatmaps with GO terms over-represented in promoters containing DMRs in CpG-context per between-group pairwise comparison. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively). A. HUN4 versus ITS3; B. HUN4 versus UKD2, C; ITS3 versus SPC1; D. HUN4 versus SCP1,  E. SPC1 versus UKD2 Additional file 5. CSV-file with the raw data of the bud set observations in the common garden experiment (raw data). Additional file 6. HTML-file with the R source codes to reproduce the results of the bud set analysis (code, R script). Additional file 7. A text-file representing the Snakefile (i.e. a readable Python-based workflow) including the different steps and rules of the bioinformatics of the WGBS data analyses (code, Snakefile). Additional file 8. RMD-file with the code to reproduce the analyses to identify differential methylated predefined regions (code, R script). Additional file 9. R-script with the code to reproduce the clustering and visualizing of the GO enrichment results (code, R script). Supporting files 1. Zip-folder with: i) excel-files listing the genes in DMRs, and ii) PNG-files with the ‘Biological Coefficient of Variation (BCV)’-plots between any of the six pairwise comparisons of Lombardy poplars grouped per ortet and identified with Bioconductor package edgeR. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (processed data). Supporting files 2. Zip-folder with PNG-files representing heatmaps and excel-files with clustered GO terms significant over-represented in promoters and gene regions located in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively. The files were obtained with the Bioconductor package simplifyEnrichment (processed data). --------------------------------------------------------- Version 3: <ul> <li>Renaming of file names according to the publisher's guidelines</li> <li>Additional file 2 includes also bisulfite conversion rates per sample</li> </ul>

Figs 17–24 in Aphid-Parasitoid (Hymenoptera, Braconidae, Aphidiinae) Associations On Willows And Poplars In Iran

Figs 17–24. Lateral aspect of genitalia (+): 17 = Ephedrus helleni, 18 = E. chaitophori, 19 = Lysiphlebus confusus, 20 = Adialytus salicaphis, 21 = Euaphidius cingulatus, 22 = Aphidius salicis, 23 = Binodoxys brevicornis, 24 = B. heraclei

Figs 25–30 in Aphid-Parasitoid (Hymenoptera, Braconidae, Aphidiinae) Associations On Willows And Poplars In Iran

Figs 25–30. Dorsal aspect of petiol (+): 25 = Lysiphlebus confusus, 26 = Adialytus salicaphis, 27 = Euaphidius cingulatus, 28 = Aphidius salicis, 29 = Binodoxys brevicornis, 30 = B. heraclei

Figs 9–16 in Aphid-Parasitoid (Hymenoptera, Braconidae, Aphidiinae) Associations On Willows And Poplars In Iran

Figs 9–16. Dorsal aspect of propodeum (+): 9 = Ephedrus helleni, 10 = E. chaitophori, 11 = Lysiphlebus confusus, 12 = Adialytus salicaphis, 13 = Euaphidius cingulatus, 14 = Aphidius salicis, 15 = Bino-

Figs 1–8 in Aphid-Parasitoid (Hymenoptera, Braconidae, Aphidiinae) Associations On Willows And Poplars In Iran

Figs 1–8. Forewing (+): 1 = Ephedrus helleni, 2 = E. chaitophori, 3 = Lysiphlebus confusus, 4 = Adialytus salicaphis, 5 = Euaphidius cingulatus, 6 = Aphidius salicis, 7 = Binodoxys brevicornis, 8 = B.

Experimental surface tensions of aqueous poplar and ragweed pollenkitts reported in the study "Cloud condensation nuclei activity of six pollenkitts and the influence of their surface activity" by Prisle et al. (2019)

Surface tensions measured with a ramé-hart goniometer (Model 250) for aqueous solutions of varying concentrations comprising poplar and ragweed pollenkitts and their mixtures with ammonium sulfate

Fig. 4. Populus primaveralepensis A in Populus primaveralepensis sp. nov. (Salicaceae, Malpighiales), a new species of white poplar from the Bosque La Primavera Biosphere Reserve in western Mexico

Fig. 4. Populus primaveralepensis A.Vázquez, Muñiz-Castro & Zuno sp. nov., female individual, Vázquez-García et al. 10106c leg., IBUG. A. Inflorescence at anthesis. B. Inflorescence past anthesis. C. Developing infrutescence. D. Trunk. E. Branch with leaves and dehiscing capsules, showing the whitish pappus of seeds. Photographs: A. Vázquez.

Fig. 5. Maps. A in Populus primaveralepensis sp. nov. (Salicaceae, Malpighiales), a new species of white poplar from the Bosque La Primavera Biosphere Reserve in western Mexico

Fig. 5. Maps. A. Distribution of P. primaveralepensis A.Vázquez, Muñiz-Castro & Zuno sp. nov. and related species of Populus L. in western Mexico. B. Distribution of the species of Populus in Jalisco with a close up for P. luziarum A.Vázquez, Muñiz-Castro & Padilla-Lepe and P. primaveralepensis sp. nov.

Fig. 1. Populus primaveralepensis A in Populus primaveralepensis sp. nov. (Salicaceae, Malpighiales), a new species of white poplar from the Bosque La Primavera Biosphere Reserve in western Mexico

Fig. 1. Populus primaveralepensis A.Vázquez, Muñiz-Castro & Zuno sp. nov. A–E, I–K. Vázquez-García et al. 10106c leg., IBUG. F–H. Vázquez-García et al. 10106b leg., IBUG. A. Variability of leaves. B. Leaf bud. C. Branch with female inflorescence. D–E. Early and late state of inflorescence. F–G. Late and early male inflorescence. H. Male flower. I. Infrutescence with pappus. J. Capsule complete and in half, with pappus. K. Developing gynoecium. Illustrations: E. E. Vázquez-Verdejo.

Fig. 3. Populus primaveralepensis A in Populus primaveralepensis sp. nov. (Salicaceae, Malpighiales), a new species of white poplar from the Bosque La Primavera Biosphere Reserve in western Mexico

Fig. 3. Populus primaveralepensis A.Vázquez, Muñiz-Castro & Zuno sp. nov., male individual, Vázquez-García et al. 10106b leg., IBUG. A–B. Two views of same branch with inflorescence past anthesis. C. Inflorescence at anthesis. D. Branch showing leaf variability and venation. Photographs: A. Vázquez.