A5086075941- Plant Molecular Biology Research
- Genetic Mapping and Diversity in Plants and Animals
- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Plant Gene Expression Analysis
- Bioenergy crop production and management
- Plant Reproductive Biology
- Bioinformatics and Genomic Networks
- Plant Stress Responses and Tolerance
- Genetic and phenotypic traits in livestock
- Chromosomal and Genetic Variations
- Biofuel production and bioconversion
- Mycorrhizal Fungi and Plant Interactions
- Forest Ecology and Biodiversity Studies
- Gene expression and cancer classification
- Photosynthetic Processes and Mechanisms
- Plant Water Relations and Carbon Dynamics
- Evolution and Genetic Dynamics
- Plant responses to elevated CO2
- Forest ecology and management
- Plant Disease Resistance and Genetics
- Ecology and Vegetation Dynamics Studies
- Plant Pathogens and Fungal Diseases
- Plant tissue culture and regeneration
- Molecular Biology Techniques and Applications
Umeå Plant Science Centre
2016-2025
Umeå University
2016-2025
Science for Life Laboratory
2012-2025
Uppsala University
2024
University of Florence
2024
Mount Saint Vincent University
2022
Université de Picardie Jules Verne
2012
KTH Royal Institute of Technology
2012
Swedish e-Science Research Centre
2012
University of Southampton
2005-2010
Conifers have dominated forests for more than 200 million years and are of huge ecological economic importance. Here we present the draft assembly 20-gigabase genome Norway spruce (Picea abies), first available any gymnosperm. The number well-supported genes (28,354) is similar to >100 times smaller Arabidopsis thaliana, there no evidence a recent whole-genome duplication in gymnosperm lineage. Instead, large size seems result from slow steady accumulation diverse set long-terminal repeat...
An increased understanding of leaf area development is important in a number fields: food and non-food crops, for example short rotation forestry as biofuels feedstock, intricately linked to biomass productivity; paleontology shape characteristics are used reconstruct paleoclimate history. Such fields require measurement large collections leaves, with resulting conclusions being highly influenced by the accuracy phenotypic process. We have developed LAMINA (Leaf shApe deterMINAtion), new...
• Limited information on likely supply and spatial yield of bioenergy crops exists for the UK. Here, productivities are reported poplar (Populus spp.) willow (Salix grown as short-rotation coppice (SRC), using data from a large 49-site trial network. A partial least-squares regression technique was used to upscale actual field observations across England Wales. Spatial productivity then assessed under different land-use scenarios. Mean modelled yields ranged between 4.9 10.7 oven-dry tonnes...
Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer Arabidopsis data, which includes expression networks associated visualization tools. Standard features model organism database are provided, including genome browsers, gene list annotation, Blast homology searches information pages. Community annotation updating...
Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield quality improvement in these largely undomesticated species, efforts to engineer elite varieties will benefit from improved understanding transcriptional network underlying cambial growth wood formation. We generated high-spatial-resolution RNA sequencing data spanning secondary phloem, vascular cambium, wood-forming tissues Populus tremula The transcriptome...
Abstract Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly Rhododendron simsii , primary ancestor azalea cultivars. Genome analyses unveil remnants an ancient whole-genome duplication preceding radiation Ericaceae, likely contributing to genomic architecture flowering time. Small-scale gene duplications contribute expansion families involved in pigment biosynthesis....
Understanding the underlying mechanisms and links between genome evolution adaptive innovations stands as a key goal in evolutionary studies. Poplars, among world's most widely distributed cultivated trees, exhibit extensive phenotypic diversity environmental adaptability. In this study, we present genus-level super-pangenome comprising 19 Populus genomes, revealing likely pivotal role of private genes facilitating local climate adaptation. Through integration pangenomes with transcriptomes,...
Summary The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the response a full‐sib second generation (F 2 ) mapping population from cross between Populus trichocarpa (93‐968) and P. deltoides Bart (ILL‐129) known be highly divergent for vast range phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis microarray experiments demonstrate that ‘genetical genomics’ can used provide information on at species level....
• Populus has become an important model plant system. However, utilization of the increasingly extensive collection genetics and genomics data created by community is currently hindered lack a central resource, such as organism database (MOD). Such MODs offer single entry point to resources available within system, typically including tools for exploring querying those resources. As starting overcoming MOD Populus, we present Genome Integrative Explorer (PopGenIE), integrated set genome...
While several studies have investigated general properties of the genetic architecture natural variation in gene expression, few these considered natural, outbreeding populations. In parallel, systems biology has established that a feature biological networks is they are scale-free, rendering them buffered against random mutations. To date, attempted to examine relationship between selective processes acting maintain expression and associated co-expression network structure. Here we utilised...
Significance There are two main groups of land plants, flowering plants (also referred to as angiosperms) and gymnosperms. Compared with angiosperms, gymnosperms have larger genomes, often approximately 20 Gb, a higher abundance transposons other repetitive elements that silenced by DNA methylation. Here, we present whole genome single-base resolution methylation analysis the important conifer Norway spruce ( Picea abies ), providing an resource for epigenetic study this species. We show is...
The initiation of growth cessation and dormancy represent critical life-history trade-offs between survival have important fitness effects in perennial plants. Such adaptive traits often show strong local adaptation along environmental gradients but, despite their importance, the genetic architecture these remains poorly understood. We integrate whole genome re-sequencing with phenotypic data from common garden experiments to investigate genomic basis across a latitudinal gradient European...
Despite the global economic and ecological importance of forest trees, genomic basis differential adaptation speciation in tree species is still poorly understood. Populus tremula tremuloides are two most widespread Northern Hemisphere. Using whole-genome re-sequencing data 24 P. 22 individuals, we find that diverged ∼2.2-3.1 million years ago, coinciding with severing Bering land bridge onset dramatic climatic oscillations during Pleistocene. Both have experienced substantial population...
Plastid sequences are a cornerstone in plant systematic studies and key aspects of their evolution, such as uniparental inheritance absent recombination, often treated axioms. While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them require extensive sampling, abundant sequence data, detailed testing. Using advancements high-throughput sequencing, we analyzed the whole plastomes 65 accessions Picea, genus ∼35 coniferous forest tree species, test...
Abstract A central aim of evolutionary genomics is to identify the relative roles that various forces have played in generating and shaping genetic variation within among species. Here we use whole-genome resequencing data characterize compare genome-wide patterns nucleotide polymorphism, site frequency spectrum, population-scaled recombination rates three species Populus: Populus tremula, P. tremuloides, trichocarpa. We find tremuloides has highest level variation, skewed allele...
Significance We performed de novo, full-genome sequence analysis of two Populus species, North American quaking and Eurasian trembling aspen, that contain striking levels genetic variation. Our results showed positive negative selection broadly affects patterns genomic variation, but to varying degrees across coding noncoding regions. The strength rates divergence were strongly related differences in gene expression coexpression network connectivity. These highlight the importance both...
Hybridization and resulting introgression are important processes shaping the tree of life appear to be far more common than previously thought. However, how genome evolution was shaped by various genetic evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data 227 individuals from multiple widespread Populus species characterize their contemporary patterns quantify genomic signatures past introgression. We observe a high frequency confirm that...
Abstract Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, hybrid poplar widely used in forest plantations. However, distinguishing its diploid homologous chromosomes difficult, complicating advanced functional studies on specific alleles. In this study, we applied trio-binning design PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies the 2 parents of well-studied F1 “84K” (Populus alba ×...
Fast-growing hybrid poplar (Populus spp.) have potential as a short-rotation coppice crop grown for biomass energy. This work identifies traits fast growth studied in an American interspecific pedigree derived from Populus trichocarpa Torr. & A. Gray × deltoides Marsh. the United Kingdom first time. The yield after rotation was estimated to range 0.04 23.68 oven-dried t·ha 1 ·year . great suggests that genotypes this may be used understand genetic basis of high coppice, which would...