Project description:The complete chloroplast genome sequence of <i>Populus tremuloides</i> was characterized from Illumina pair-end sequencing. The chloroplast genome of <i>P. tremuloides</i> was 155,816 bp in length, containing a large single-copy region (LSC) of 85,804 bp, a small single-copy region (SSC) of 16,489 bp, and two inverted repeat (IR) regions of 26,962 bp. The overall GC content is 36.71%, while the correponding values of the LSC, SSC, and IR regions are 64.9%, 69.2%, and 60.3%, respectively. The genome contains 167 complete genes, including 86 protein-coding genes (77 protein-coding gene species), 73 tRNA genes (29 tRNA species) and 8 rRNA genes(4 rRNA species). The Neighbour-joining phylogenetic analysis showed that <i>P. tremuloides</i> and <i>Populus tremula</i> clustered together as sisters to other <i>Populus</i> species.
Project description:Gene expression response of Populus cell cultures subjected to methyl jasmonate feeding was analyzed using the Affymetrix poplar genome microarrays. Experiment Overall Design: Populus tremuloides suspension cells wereÂ treated with methyl jasmonate (MJ) in DMSO orÂ with DMSO alone (C).Â Cells were harvested after 48 hours.Â Two biological replicates were obtained for each condition.
Project description:Aim of the project: Genome wide gene expression profiles across the cambial zone are analyzed in 35um resolution from wild type hybrid aspen (Populus tremula x tremuloides) and two independent LMX5::AtIPT7 over expressor transgenic Populus tree lines.
Project description:Aim of the project: Genome wide gene expression analysis for cytokinin (100nM 2ip, 20nM NaPi buffer) fast (1h) response genes from 3 months old Hybrid aspen(Populus tremula x tremuloides)apical part (30 cm from tip; diameter:4-5mm) of stem. Stems of two individuals (trees 15 and 16) was cut into 50-100um thick (free hand)cross sections randomly selected stem discs are set to two pools: cytokinin treatment and control treatment. Samples are collected noon time (11:00-11:30). Cytokinin treatment: stem discs (several hundred) are submerged with 100nM 2ip, 20nM NaPi buffer, with modest shaking for 60 min +/- 2 min (time to collect about 30mg stem discs (several dozens) for RNA sample. Control treatment: identical to cytokinin treatment, only without 100nM 2ip.
Project description:Gene expression response of Populus cell cultures subjected to methyl jasmonate feeding was analyzed using the Affymetrix poplar genome microarrays. Keywords: Stress response Overall design: Populus tremuloides suspension cells were treated with methyl jasmonate (MJ) in DMSO or with DMSO alone (C). Cells were harvested after 48 hours. Two biological replicates were obtained for each condition.
Project description:The expression of stress-related genes induced by feeding of chestnut moth larvae (Conistra vaccinii L.) was studied with Vitreoscilla hemoglobin-expressing (VHb) and non-transgenic hybrid aspen lines (Populus tremula x P. tremuloides). Besides the herbivore-injured leaves (L1), cDNA microarray analyses were conducted using uninjured leaves of hybrid aspen lines positioned above (A) and below (B) the herbivory exposed leaves. Two-condition experiment, control vs. herbivory exposure. Two hybrid aspen lines: non-transgenic V617 and VHb expressing V617 /45. Of each plant, three leaf types were analysed: the injured/uninjured leaf (L1) and nonorthostichous leaf positioned above (A) and below (B). Biological replicates: 3. On each array, two samples representing L1, A or B leaf type of control and herbivory treatment of either V617 or V617/45 line. line V617: wt_A_rep1-3, wt_B_rep1-3, wt_L1_rep1-3 line V617/45: VHb_A_rep1-3, VHb_B_rep1-3, VHb_L1_rep1-3 leaf type A: wt_A_rep1-3, VHb_A_rep1-3 leaf type B: wt_B_rep1-3, VHb_B_rep1-4 leaf type L1: wt_L1_rep1-3, VHb_L1_rep1-5
Project description:Quaking aspens (Populus tremuloides Michx.) are found in diverse habitats throughout North America. While the biogeography of aspens' distribution has been documented, the drivers of the phenotypic diversity of aspen are still being explored. In our study, we examined differences in climate between northern and southwestern populations of aspen, finding large-scale differences between the populations. Our results suggest that northern and southwestern populations live in distinct climates and support the inclusion of genetic and phenotypic data with species distribution modeling for predicting aspens' distribution.
Project description:The majority of trees live in association with symbiotic fungi, which facilitate their access to soil nutrients. The ectomycorrhizal symbiosis represents a complex biological system involving multifaceted interactions between the two partners. The establishment of the symbiosis depends on various conditions (e.g. climate), but also on the genetic traits of the partners. To evaluate the impact of the genetic predisposition on the development and functioning of ectomycorrhizas, we compared the transcriptome of roots from Populus trichocarpa and Populus deltoides colonized with Laccaria bicolor. The Populus whole-genome expression array version 2.0 (S. DiFazio, A. Brunner, P. Dharmawardhana, and K. Munn, unpublished data) manufactured by NimbleGen Systems Limited (Madison, WI) contains in duplicates three independent, non-identical, 60-mer probes per whole gene model plus control probes and labeling controls. Included in the microarray are 65,965 probe sets corresponding to 55,970 gene models predicted on the P.trichocarpa genome sequence version 1.0 and 9,995 aspen cDNA sequences (Populus tremula, Populus tremuloides, and P. tremula x P. tremuloides). NimbleGen whole genome microarray analyses were performed in triplicate as per manufacturer's instructions. We carried out six hybridizations (NimbleGen) with samples derived from Populus trichocarpa and Populus deltoides mycorrhizal root tips. Three samples (biological replicates) originated from Populus trichocarpa (GSM648401, GSM648403, GSM648405) and three biological replicates from Populus deltoides (GSM648408, GSM648411, GSM648414). cDNA was synthesized using CLONTECH Super Smart cDNA Synthesis kit containing an amplification step on the cDNA level. All samples were labeled with Cy3.
Project description:<h4>Aim</h4>We assessed the vulnerability of an isolated, relictual Pleistocene hybrid aspen population of conservation interest (<i>Populus x. smithii</i>) and the nearest populations of its parent species (<i>Populus grandidentata</i> and <i>Populus tremuloides</i>) to springtime post-bud break freezing and growing season drought stress. Response to these stressors in the three taxa was compared in terms of avoidance and tolerance.<h4>Location</h4>North American Midwest; USA.<h4>Methods</h4>Unique genets from the hybrid Niobrara River population and from the two parental populations were propagated in a common garden from rhizome cuttings. We tracked their phenology before and after bud break and measured their vulnerability to freezing (stem electrolyte leakage and leaf chlorophyll fluorescence) and to drought (stem hydraulic conductance, leaf osmotic potential, stomatal pore index, and gas exchange).<h4>Results</h4><i>Populus grandidentata</i> was slower to leaf out, showed lower vulnerability to stem freezing and drought-induced cavitation, but exhibited a lower capacity to tolerate drought stress through leaf resistance traits compared to <i>P. tremuloides</i>. Hybrids were similar to <i>P. grandidentata</i> in their overwintering strategy, exhibiting later bud break, and in their higher resistance to stem freezing damage, but they were more similar to <i>P. tremuloides</i> in their higher vulnerability to drought-induced cavitation. The hybrids shared various leaf-level gas exchange traits with both parents. All aspens showed limited loss of leaf photosynthetic function following moderate freezing.<h4>Main conclusions</h4>The Niobrara River hybrid population is vulnerable to drought due to its combination of inherited drought avoidance and tolerance traits. As climate changes, <i>P. x smithii</i> will likely suffer from increased drought stress, while being unaffected by frost during warmer springs. The two parental species contrast in their survival mechanisms in response to climatic stress, with <i>P. tremuloides</i> tending toward freezing tolerance but drought avoidance and <i>P. grandidentata</i> tending toward freezing avoidance and drought tolerance.
Project description:<i>Populus tremuloides</i> is the widest-ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome-wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, ploidy levels, admixture, and Pleistocene range dynamics of <i>P. tremuloides</i>, and tested several historical biogeographical hypotheses. We found three genetic lineages located mainly in coastal-Cascades (cluster 1), east-slope Cascades-Sierra Nevadas-Northern Rockies (cluster 2), and U.S. Rocky Mountains through southern Canadian (cluster 3) regions of the <i>P. tremuloides</i> range, with tree graph relationships of the form ((cluster 1, cluster 2), cluster 3). Populations consisted mainly of diploids (86%) but also small numbers of triploids (12%) and tetraploids (1%), and ploidy did not adversely affect our genetic inferences. The main vector of admixture was from cluster 3 into cluster 2, with the admixture zone trending northwest through the Rocky Mountains along a recognized phenotypic cline (Utah to Idaho). Clusters 1 and 2 provided strong support for the "stable-edge hypothesis" that unglaciated southwestern populations persisted in situ since the last glaciation. By contrast, despite a lack of clinal genetic variation, cluster 3 exhibited "trailing-edge" dynamics from niche suitability predictions signifying complete northward postglacial expansion. Results were also consistent with the "inland dispersal hypothesis" predicting postglacial assembly of Pacific Northwestern forest ecosystems, but rejected the hypothesis that Pacific-coastal populations were colonized during outburst flooding from glacial Lake Missoula. Overall, congruent patterns between our phylogeographic and ecological niche modeling results and fossil pollen data demonstrate complex mixtures of stable-edge, refugial locations, and postglacial expansion within <i>P. tremuloides</i>. These findings confirm and refine previous genetic studies, while strongly supporting a distinct Pacific-coastal genetic lineage of quaking aspen.