Biology subjects

Hvidsten, T. R.

Publications and source records attributed to Hvidsten, T. R..

7 recordsLinked to original sources

bioRxiv2018

From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus.

Microbial communities that degrade lignocellulosic biomass are typified by high levels of species- and strain-level complexity as well as synergistic interactions between both cellulolytic and non-cellulolytic microorganisms. Coprothermobacter proteolyticus frequently dominates thermophilic, lignocellulose-degrading communities with wide geographical distribution, which is in contrast to reports that it ferments proteinaceous substrates and is incapable of polysaccharide hydrolysis. Here we deconvolute a highly efficient cellulose-degrading consortium (SEM1b) that is co-dominated by Clostridium (Ruminiclostridium) thermocellum- and multiple heterogenic strains affiliated to C. proteolyticus. Metagenomic analysis of SEM1b recovered metagenome-assembled genomes (MAGs) for each constituent population, whilst in parallel two novel strains of C. proteolyticus were successfully isolated and sequenced. Annotation of all C. proteolyticus genotypes (two strains and one MAG) revealed their genetic acquisition of various carbohydrate-active enzymes (CAZymes), presumably derived from horizontal gene transfer (HGT) events involving C. thermocellum- or Thermotogae-affiliated populations that are historically co-located. HGT material included whole saccharolytic operons and dockerin-encoding enzymatic subunits that are synonymous with cellulosomes. Finally, temporal genome-resolved metatranscriptomic analysis of SEM1b revealed expression of C. proteolyticus CAZymes at different SEM1b life-stages as well as co-expression of CAZymes from multiple SEM1b populations, inferring deeper microbial interactions that are dedicated towards co-degradation of cellulose and hemicellulose. We show that C. proteolyticus, a ubiquitous keystone population, consists of closely related strains that have adapted via HGT to degrade both oligo- and longer polysaccharides present in decaying plants and microbial cell walls, thus explaining its dominance in thermophilic anaerobic digesters on a global scale.

microbiology↗

bioRxiv2017

Evolution of cold acclimation in temperate grasses (Pooideae)

In the past 50 million years climate cooling has triggered the expansion of temperate biomes. During this period, many extant plant lineages in temperate biomes evolved from tropical ancestors and adapted to seasonality and cool conditions. Among the Poaceae (grass family), one of the subfamilies that successfully shifted from tropical to temperate biomes is the Pooideae (temperate grasses). Subfamily Pooideae contains the most important crops cultivated in the temperate regions including wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to the need of well-adapted cultivars, extensive research has produced a large body of knowledge about the mechanisms underlying cold adaptation in cultivated Pooideae species. Especially cold acclimation, a process which increases the frost tolerance during a period of non-freezing cold, plays an important role. Because cold adaptation is largely unexplored in lineages that diverged early in the evolution of the Pooideae, little is known about the evolutionary history of cold acclimation in the Pooideae. Here we test if several species of early diverging lineages exhibit increased frost tolerance after a period of cold acclimation. We further investigate the conservation of five well-studied gene families that are known to be involved in the cold acclimation of Pooideae crop species. Our results indicate that cold acclimation exists in early diverging lineages, but that genes involved in regulation of cold acclimation are not conserved. The investigated gene families show signs of lineage-specific evolution and support the hypothesis that gene family expansion is an important mechanism in adaptive evolution.

evolutionary biology↗

bioRxiv2017

Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen

Research conductedThe phytohormone ethylene impacts secondary stem growth in plants by stimulating cambial activity, xylem development and fiber over vessel formation. Here we report the effect of ethylene on secondary cell wall formation and the molecular connection between ethylene signaling and wood formation.\n\nMethodsWe applied exogenous ethylene or its precursor 1-aminocyclopropane-1-carboxylic acid (ACC) to wild type and ethylene insensitive hybrid aspen trees (Populus tremula x tremuloides) and studied secondary cell wall anatomy, chemistry and ultrastructure. We furthermore analyzed the transcriptome (RNA Seq) after ACC application to wild type and ethylene insensitive trees.\n\nKey resultsWe demonstrate that ACC and ethylene induce gelatinous-layers (G-layers) and alter the fiber cell wall cellulose microfibril angle. G-layers are tertiary wall layers rich in cellulose, typically found in tension wood of aspen trees. A vast majority of transcripts affected by ACC are downstream of ethylene perception and include a large number of transcription factors (TFs). Motif-analyses reveal potential connections between ethylene TFs (ERFs, EIN3/EIL1) and wood formation.\n\nConclusionG-layer formation upon ethylene application suggests that the increase in ethylene biosynthesis observed during tension wood formation is important for its formation. Ethylene-regulated TFs of the ERF and EIN3/EIL1 type could transmit the ethylene signal.

plant biology↗

bioRxiv2017

Subfunctionalization versus neofunctionalization after whole-genome duplication

The question of what is the predominant evolutionary fate of genes after duplication events has been hotly debated for decades1,2. Two recently published articles in Nature (Lien et al.3) and Nature Genetics (Braasch et al.4) investigated the regulatory fate of gene duplicates after the salmonid-specific (Ss4R) and teleost specific (Ts3R) whole genome duplication (WGD) events, respectively. Both studies relied on tissue expression atlases for estimating regulatory divergence and used closely related unduplicated sister taxa (i.e. Northern pike and the spotted gar, respectively) as proxies for the ancestral expression state. Surprisingly, the two studies reach very different conclusions about the evolutionary mechanisms impacting gene expression after WGD. Braasch et al.4 concluded that the expression divergence was consistent with partitioning of tissue regulation between duplicates (subfunctionalization), while Lien et al.3 concluded that most divergence in tissue regulation were consistent with one copy maintaining ancestral tissue regulation while the other having diverged (in line with neofunctionalization). Here we show that this striking discrepancy in the conclusions of the two studies is a consequence of the data analysis approaches used, and is not related to underlying differences in the data.

evolutionary biology↗

bioRxiv2017

Comparative transcriptomics reveals lineage specific evolution of cold response in Pooideae

BackgroundUnderstanding how complex traits evolve through adaptive changes in gene regulation remains a major challenge in evolutionary biology. Over the last ~50 million years, Earth has experienced climate cooling and ancestrally tropical plants have adapted to expanding temperate environments. The grass subfamily Pooideae dominates the grass flora of the temperate regions, but the role of cold-response gene regulation in the transitioning from tropical to temperate climate remains unexplored.\n\nResultsTo establish if molecular responses to cold are conserved throughout the phylogeny, we assembled the transcriptomes of five Pooideae species spanning early to later diverging lineages, and compared short- and long-term cold responsive genes using 8633 high confidence ortholog groups with resolved gene tree topologies. We found that a majority of cold responsive genes were specific to one or two lineages, an observation that we deem incompatible with a cold adapted Pooideae ancestor. However, all five species shared short-term cold response in a small set of general stress genes as well as the ability to down-regulate the photosynthetic machinery during cold temperatures.\n\nConclusionsOur observations indicate that the different Pooideae lineages have assembled cold response programs in parallel by taking advantage of a common potential for cold adaptation.

evolutionary biology↗

bioRxiv2017

Diet And Life Stage Associated Remodeling Of Lipid Metabolism Regulation In The Duplicated Atlantic Salmon Genome

Atlantic salmon migrates from rivers to sea to feed, grow and develop gonads before returning to spawn in freshwater. These habitat shifts require great phenotypic plasticity. To address the unresolved question of how the shift in diet between fresh and saltwater affects the regulation of metabolic function, we fed salmon contrasting diets in each of the two life stages. Combining transcriptomics with comparative genomics, we found that lipid metabolism undergoes a concerted shift between fresh- and saltwater stages. Lipogenesis and lipid transport become less active in liver after transition to saltwater, while genes for lipid uptake in gut are more expressed in lipid-rich seawater environments. We assess how the whole-genome duplication that gave rise to the salmonids has impacted the evolution of lipid metabolism, and find signatures of pathway-specific selection pressure on gene duplicates, as well as a limited number of cases of increased gene dosage.

evolutionary biology↗

bioRxiv2016

High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula

Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, and efforts to engineer new, elite varieties will benefit from an improved understanding of the transcriptional network underlying cambial growth and wood formation. We generated high-spatial-resolution RNA Sequencing data spanning the secondary phloem, vascular cambium and wood forming tissues. The transcriptome comprised 28,294 expressed, previously annotated genes, 78 novel protein-coding genes and 567 long intergenic non-coding RNAs. Most paralogs originating from the Salicaceae whole genome duplication were found to have diverged expression, with the notable exception of those with high expression during secondary cell wall deposition. Co-expression network analysis revealed that the regulation of the transcriptome underlying cambial growth and wood formation comprises numerous modules forming a continuum of active processes across the tissues. The high spatial resolution enabled identification of novel roles for characterised genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and lignification. The associated web resource (AspWood, http://aspwood.popgenie.org) integrates the data within a set of interactive tools for exploring the expression profiles and co-expression network.

plant biology↗