Ten North-American tree and shrub species
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA422818 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6386674.fastq.gz | Fastqsanger.gz |
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Project description:Shrub willow (Salix spp.), a short rotation woody biomass crop, has superior properties as a perennial energy crop for the Northeast and Midwest US. However, the insect pest potato leafhopper Empoasca fabae (Harris) (PLH) can cause serious damage and reduce yield of susceptible genotypes. Currently, the willow cultivars in use display varying levels of susceptibility under PLH infestation. However, genes and markers for resistance to PLH are not yet available for marker-assisted selection in breeding. In this study, transcriptome differences between a resistant genotype 94006 (S. purpurea) and a susceptible cultivar ‘Jorr’ (S. viminalis), and their hybrid progeny were determined. Over 600 million RNA-Seq reads were generated and mapped to the Salix purpurea reference transcriptome. Gene expression analyses revealed the unique defense mechanism in resistant genotype 94006 that involves PLH-induced secondary cell wall modification. In the susceptible genotypes, genes involved in programed cell death were highly expressed, explaining the necrosis symptoms after potato leafhopper feeding. Overall, the discovery of resistance genes and defense mechanisms provides new resources for shrub willow breeding and research in the future.
2020-01-15 | GSE143616 | GEO
Project description:BACKGROUND:While our understanding of the genetic basis of convergent evolution has improved there are still many uncertainties. Here we investigate the repeated evolution of dark colouration (melanism) in eastern fox squirrels (Sciurus niger; hereafter "fox squirrels") and eastern gray squirrels (S. carolinensis; hereafter "gray squirrels"). RESULTS:We show that convergent evolution of melanism has arisen by independent genetic mechanisms in two populations of the fox squirrel. In a western population, melanism is associated with a 24?bp deletion in the melanocortin-1-receptor gene (MC1R?24 allele), whereas in a south-eastern population, melanism is associated with a point substitution in the agouti signalling protein gene causing a Gly121Cys mutation. The MC1R?24 allele is also associated with melanism in gray squirrels, and, remarkably, all the MC1R?24 haplotypes are identical in the two species. Evolutionary analyses show that the MC1R?24 haplotype is more closely related to other MC1R haplotypes in the fox squirrel than in the gray squirrel. Modelling supports the possibility of gene flow between the two species. CONCLUSIONS:The presence of the MC1R?24 allele and melanism in gray squirrels is likely due to introgression from fox squirrels, although we cannot completely rule out alternative hypotheses including introgression from gray squirrels to fox squirrels, or an ancestral polymorphism. Convergent melanism in these two species of tree squirrels has evolved by at least two and probably three different evolutionary routes.
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Project description:North American tree species, subspecies and genetic varieties have primarily evolved in a landscape of extensive continental ice and restricted temperate climate environments. Here, we reconstruct the refugial history of western North American trees since the last glacial maximum using species distribution models, validated against 3571 palaeoecological records. We investigate how modern subspecies structure and genetic diversity corresponds to modelled glacial refugia, based on a meta-analysis of allelic richness and expected heterozygosity for 473 populations of 22 tree species. We find that species with strong genetic differentiation into subspecies had widespread and large glacial refugia, whereas species with restricted refugia show no differentiation among populations and little genetic diversity, despite being common over a wide range of environments today. In addition, a strong relationship between allelic richness and the size of modelled glacial refugia (r(2) = 0.55) suggest that population bottlenecks during glacial periods had a pronounced effect on the presence of rare alleles.
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Project description:Estimates of airborne pollen concentrations at the urban scale would be useful for epidemiologists, land managers, and allergy sufferers. Mechanistic models could be well suited for this task, but their development will require data on pollen production across cities, including estimates of pollen production by individual trees. In this study, we developed predictive models for pollen production as a function of trunk size, canopy area, and height, which are commonly recorded in tree surveys or readily extracted from remote sensing data. Pollen production was estimated by measuring the number of flowers per tree, the number of anthers per flower, and the number of pollen grains per anther. Variability at each morphological scale was assessed using bootstrapping. Pollen production was estimated for the following species: Acer negundo, Acer platanoides, Acer rubrum, Acer saccharinum, Betula papyrifera, Gleditsia triacanthos, Juglans nigra, Morus alba, Platanus x acerfolia, Populus deltoides, Quercus palustris, Quercus rubra, and Ulmus americana. Basal area predicted pollen production with a mean R2 of 0.72 (range: 0.41 - 0.99), whereas canopy area predicted pollen production with a mean R2 of 0.76 (range: 0.50 - 0.99). These equations are applied to two tree datasets to estimate total municipal pollen production and the spatial distribution of street tree pollen production for the focal species. We present some of the first individual-tree based estimates of pollen production at the municipal scale; the observed spatial heterogeneity in pollen production is substantial and can feasibly be included in mechanistic models of airborne pollen at fine spatial scales.
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Project description:The availability of a reference genome assembly for Atlantic salmon, Salmo salar, SNP genotyping platforms and low cost sequencing is enhancing the understanding of both life history and production-related traits in this important commercial species. We collected and analysed transcriptomes from selected tissues of Atlantic salmon to inform future functional and comparative genomics studies. Messenger RNA (mRNA) was isolated from brain, pituitary, ovary and liver before Illumina sequencing produced a total of 640 million 150-bp paired-end reads. Following read mapping, feature counting and normalization, cluster analysis identified genes highly expressed in a tissue-specific manner. Functional profiling identified gene clusters describing the unique functions of each tissue. Moreover, highly-expressed transcription factors present in each tissue-specific gene cluster were identified. The data and analysis presented are relevant to the emerging Functional Annotation of All Salmonid Genomes (FAASG) initiative that is seeking to develop a detailed understanding of both salmonid evolution and the genomic elements that drive gene expression and regulation.
2018-08-22 | GSE114247 | GEO
Project description:Boreal forests are experiencing dramatic climate change, having warmed 1.0°-1.9°C over the last century. Yet forest regeneration practices are often still dictated by a fixed seed zone framework, in which seeds are both harvested from and planted into predefined areas. Our goal was to determine whether seedlings sourced from southern seed zones in Minnesota USA are already better adapted to northerly seed zones because of climate change. Bur oak (Quercus macrocarpa) and northern red oak (Quercus rubra) seedlings from two seed zones (i.e., tree ecotypes) were planted into 16 sites in two northern seed zones and measured for 3 yr. Our hypotheses were threefold: (1) tree species with more southern geographic distributions would thrive in northern forests where climate has already warmed substantially, (2) southern ecotypes of these species would have higher survival and growth than the northern ecotype in northern environments, and (3) natural selection would favor seedlings that expressed phenotypic and phenological traits characteristic of trees sourced from the more southern seed zone. For both species, survival was high (>93%), and southern ecotypes expressed traits consistent with our climate adaptation hypotheses. Ecotypic differences were especially evident for red oak; the southern ecotype had had higher survival, lower specific leaf area (SLA), faster height and diameter growth, and extended leaf phenology relative to the northern ecotype. Bur oak results were weaker, but the southern ecotype also had earlier budburst and lower SLA than the northern ecotype. Models based on the fixed seed zones failed to explain seedling performance as well as those with continuous predictors (e.g., climate and geographical position), suggesting that plant adaptations within current seed zone delineations do align with changing climate conditions. Adding support for this conclusion, natural selection favored traits expressed by the more southern tree ecotypes. Collectively, these results suggest that state seed sourcing guidelines should be reexamined to permit plantings across seed zones, a form of assisted migration. More extensive experiments (i.e., provenance trails) are necessary to make species-specific seed transfer guidelines that account for climate trends while also considering the precise geographic origin of seed sources.
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Project description:Tree provenance trials consist of a variety of seed sources (or provenances) planted at several test sites across the range of a species. The resulting plantations are typically measured periodically to investigate provenance performance in relation to abiotic conditions, particularly climate. These trials are expensive and time consuming to establish, but are an important resource for seed transfer systems, which aim to match planting sites with well-adapted (climatically suitable) seed sources. Provenance trial measurements may be underutilized because the data are scattered across publications, conference proceedings, and university theses. Here we document an effort to collect available provenance trial measurements and associated climate data for seven eastern North American tree species (Pinus strobus, Pinus banksiana, Picea glauca, Picea mariana, Quercus rubra, Larix laricina, Betula alleghaniensis). The resulting datasets included a total of 773 provenances and 62 test sites, with 65 historical climate variables appended to each location. We hope this data will support forest managers in making seed transfer decisions, particularly in an era of rapid climate change.
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Project description:BackgroundAs it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets of taxa, species trees are frequently being inferred from multilocus data. However, the behavior of many methods for performing this inference has remained largely unexplored. Some methods have been proven to be consistent given certain evolutionary models, whereas others rely on criteria that, although appropriate for many parameter values, have peculiar zones of the parameter space in which they fail to converge on the correct estimate as data sets increase in size.ResultsHere, using North American pines, we empirically evaluate the behavior of 24 strategies for species tree inference using three alternative outgroups (72 strategies total). The data consist of 120 individuals sampled in eight ingroup species from subsection Strobus and three outgroup species from subsection Gerardianae, spanning ?47 kilobases of sequence at 121 loci. Each "strategy" for inferring species trees consists of three features: a species tree construction method, a gene tree inference method, and a choice of outgroup. We use multivariate analysis techniques such as principal components analysis and hierarchical clustering to identify tree characteristics that are robustly observed across strategies, as well as to identify groups of strategies that produce trees with similar features. We find that strategies that construct species trees using only topological information cluster together and that strategies that use additional non-topological information (e.g., branch lengths) also cluster together. Strategies that utilize more than one individual within a species to infer gene trees tend to produce estimates of species trees that contain clades present in trees estimated by other strategies. Strategies that use the minimize-deep-coalescences criterion to construct species trees tend to produce species tree estimates that contain clades that are not present in trees estimated by the Concatenation, RTC, SMRT, STAR, and STEAC methods, and that in general are more balanced than those inferred by these other strategies.ConclusionsWhen constructing a species tree from a multilocus set of sequences, our observations provide a basis for interpreting differences in species tree estimates obtained via different approaches that have a two-stage structure in common, one step for gene tree estimation and a second step for species tree estimation. The methods explored here employ a number of distinct features of the data, and our analysis suggests that recovery of the same results from multiple methods that tend to differ in their patterns of inference can be a valuable tool for obtaining reliable estimates.
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