A Numerical Model Supports the Evolutionary Advantage of Recombination Plasticity in Shifting Environments

AbstractNumerous empirical studies have witnessed an increase in meiotic recombination rate in response to physiological stress imposed by unfavorable environmental conditions. Thus, inherited plasticity in recombination rate is hypothesized to be evolutionarily advantageous in changing environments. Previous theoretical models proceeded from the assumption that organisms increase their recombination rate when the environment becomes more stressful and demonstrated the evolutionary advantage of such a form of plasticity. Here, we numerically explore a complementary scenario-when the plastic increase in recombination rate is triggered by the environmental shifts. Specifically, we assume increased recombination in individuals developing in a different environment than their parents and, optionally, also in offspring of such individuals. We show that such shift-inducible recombination is always superior when the optimal constant recombination implies an intermediate rate. Moreover, under certain conditions, plastic recombination may also appear beneficial when the optimal constant recombination is either zero or free. The advantage of plastic recombination was better predicted by the range of the population's mean fitness over the period of environmental fluctuations, compared with the geometric mean fitness. These results hold for both panmixia and partial selfing, with faster dynamics of recombination modifier alleles under selfing. We think that recombination plasticity can be acquired under the control of environmentally responsive mechanisms, such as chromatin epigenetics remodeling.

IL-6 levels dominate the serum cytokine signature of severe epidermolysis bullosa: A prospective cohort study

BACKGROUND

Systemic inflammation is considered a major player in the pathogenesis of epidermolysis bullosa (EB), but its pattern has only been described in small heterogeneous cohorts. There is controversy if and how systemic inflammation should be therapeutically targeted.

METHODS

We examined serum proinflammatory, anti-inflammatory, and itch related cytokines in a paediatric cohort of 29 patients with junctional and dystrophic EB. The cytokine that emerged as the most relevant was measured in a validation cohort of 42 patients during follow-up visits over 2 years.

RESULTS

IL-6 showed the most consistent and highest aberration dominating systemic inflammation. IL-6 correlated with wound body surface area (BSA) in both, finding and validation cohorts. Patients with less than 3% wound BSA had normal IL-6, while IL-6 levels significantly increased at more than 5% and 10% of wound BSA. TGF-β was only marginally elevated in patients with severe recessive dystrophic EB, while TNF-α, IFN-γ and IL-1β varied inconsistently. Patients reporting itch showed elevations in type 2 immunity (IgE, TSLP, IL4 and/or IL-31, respectively).

CONCLUSIONS

Our data suggest a dominant skin barrier and wound healing inflammatory pattern in junctional and dystrophic EB that depends on the wound area and not on the EB type. In EB, itch mediators may be similar to other pruritic disorders.

Modeling the evolution of recombination plasticity: A prospective review

Meiotic recombination is one of the main sources of genetic variation, a fundamental factor in the evolutionary adaptation of sexual eukaryotes. Yet, the role of variation in recombination rate and other recombination features remains underexplored. In this review, we focus on the sensitivity of recombination rates to different extrinsic and intrinsic factors. We briefly present the empirical evidence for recombination plasticity in response to environmental perturbations and/or poor genetic background and discuss theoretical models developed to explain how such plasticity could have evolved and how it can affect important population characteristics. We highlight a gap between the evidence, which comes mostly from experiments with diploids, and theory, which typically assumes haploid selection. Finally, we formulate open questions whose solving would help to outline conditions favoring recombination plasticity. This will contribute to answering the long-standing question of why sexual recombination exists despite its costs, since plastic recombination may be evolutionary advantageous even in selection regimes rejecting any non-zero constant recombination.

The genomics of linkage drag in inbred lines of sunflower

Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases. However, introgressions from wild relatives might have deleterious effects on desirable traits, including yield, due to linkage drag. Here, we analyzed the genomic and phenotypic impacts of wild introgressions in inbred lines of cultivated sunflower to estimate the impacts of linkage drag. First, we generated reference sequences for seven cultivated and one wild sunflower genotype, as well as improved assemblies for two additional cultivars. Next, relying on previously generated sequences from wild donor species, we identified introgressions in the cultivated reference sequences, as well as the sequence and structural variants they contain. We then used a ridge-regression best linear unbiased prediction (BLUP) model to test the effects of the introgressions on phenotypic traits in the cultivated sunflower association mapping population. We found that introgression has introduced substantial sequence and structural variation into the cultivated sunflower gene pool, including >3,000 new genes. While introgressions reduced genetic load at protein-coding sequences, they mostly had negative impacts on yield and quality traits. Introgressions found at high frequency in the cultivated gene pool had larger effects than low-frequency introgressions, suggesting that the former likely were targeted by artificial selection. Also, introgressions from more distantly related species were more likely to be maladaptive than those from the wild progenitor of cultivated sunflower. Thus, breeding efforts should focus, as far as possible, on closely related and fully compatible wild relatives.

Genetic architecture of rust resistance in a wheat (Triticum turgidum) diversity panel

INTRODUCTION

Wheat rust diseases are widespread and affect all wheat growing areas around the globe. Breeding strategies focus on incorporating genetic disease resistance. However, pathogens can quickly evolve and overcome the resistance genes deployed in commercial cultivars, creating a constant need for identifying new sources of resistance.

METHODS

We have assembled a diverse tetraploid wheat panel comprised of 447 accessions of three Triticum turgidum subspecies and performed a genome-wide association study (GWAS) for resistance to wheat stem, stripe, and leaf rusts. The panel was genotyped with the 90K Wheat iSelect single nucleotide polymorphism (SNP) array and subsequent filtering resulted in a set of 6,410 non-redundant SNP markers with known physical positions.

RESULTS

Population structure and phylogenetic analyses revealed that the diversity panel could be divided into three subpopulations based on phylogenetic/geographic relatedness. Marker-trait associations (MTAs) were detected for two stem rust, two stripe rust and one leaf rust resistance loci. Of them, three MTAs coincide with the known rust resistance genes Sr13, Yr15 and Yr67, while the other two may harbor undescribed resistance genes.

DISCUSSION

The tetraploid wheat diversity panel, developed and characterized herein, captures wide geographic origins, genetic diversity, and evolutionary history since domestication making it a useful community resource for mapping of other agronomically important traits and for conducting evolutionary studies.

Dual domestications and origin of traits in grapevine evolution

We elucidate grapevine evolution and domestication histories with 3525 cultivated and wild accessions worldwide. In the Pleistocene, harsh climate drove the separation of wild grape ecotypes caused by continuous habitat fragmentation. Then, domestication occurred concurrently about 11,000 years ago in Western Asia and the Caucasus to yield table and wine grapevines. The Western Asia domesticates dispersed into Europe with early farmers, introgressed with ancient wild western ecotypes, and subsequently diversified along human migration trails into muscat and unique western wine grape ancestries by the late Neolithic. Analyses of domestication traits also reveal new insights into selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These data demonstrate the role of the grapevines in the early inception of agriculture across Eurasia.

Evolutionary Conservation and Transcriptome Analyses Attribute Perenniality and Flowering to Day-Length Responsive Genes in Bulbous Barley (Hordeum bulbosum)

Rapid population growth and dramatic climatic turnovers are challenging global crop production. These challenges are spurring plant breeders to enhance adaptation and sustainability of major crops. One intriguing approach is to turn annual systems into perennial ones, yet long-term classical breeding efforts to induce perenniality have achieved limited success. Here, we report the results of our investigation of the genetic basis of bulb formation in the nonmodel organism Hordeum bulbosum, a perennial species closely related to barley. To identify candidate genes that regulate bulb formation in H. bulbosum, we applied two complementary approaches. First, we explored the evolutionary conservation of expressed genes among annual Poaceae species. Next, we assembled a reference transcriptome for H. bulbosum and conducted a differential expression (DE) analysis before and after stimulating bulb initiation. Low conservation was identified in genes related to perenniality in H. bulbosum compared with other species, including bulb development and sugar accumulation genes. We also inspected these genes using a DE analysis, which enabled identification of additional genes responsible for bulb initiation and flowering regulation. We propose a molecular model for the regulation of bulb formation involving storage organ development and starch biosynthesis genes. The high conservation observed along a major part of the pathway between H. bulbosum and barley suggests a potential for the application of biotechnological techniques to accelerate breeding toward perenniality in barley.

Emmer Wheat Eco-Geographic and Genomic Congruence Shapes Phenotypic Performance under Mediterranean Climate

Emmer wheat (Triticum turgidum ssp. dicoccum) is one of the world’s oldest domesticated crops, and it harbors a potentially rich reservoir of agronomic and nutritional quality trait variations. The growing global demand for plant-based health-food niche markets has promoted new commercial interest in ancient grains, including Emmer wheat. Although T. dicoccum can also perform well under harsh environments, its cultivation along the Mediterranean agro-ecosystems is sparse. Here, we analyze a unique tetraploid wheat collection (n = 121) representing a wide geographic range of Emmer accessions, using 9897 DArTseq markers and on-field phenotypic characterization to quantify the extent of diversity among populations and the interactions between eco-geographic, genetic, and phenotypic attributes. Population genomic inferences based on the DArTseq data indicated that the collection could be split into four distinguished clusters in accordance with their eco-geographic origin although significant phenotypic variation was observed within clusters. Superior early vegetative vigor, shorter plant height, and early phenology were observed among emmer wheat accessions from Ethiopia compared to accessions from northern regions. This adaptive advantage highlights the potential of emmer wheat as an exotic germplasm for wheat improvement through breeding. The direct integration of such germplasm into conventional or organic farming agro-systems under the Mediterranean basin climate is also discussed.

Are we there yet? Driving the road to evolutionary graph-pangenomics

With increase in the number of sequenced genomes, it is now recognized that graph-based pangenomes can provide a comprehensive platform to study diversity in a population or species, from point mutations to large chromosomal rearrangements. By incorporating concepts from graph theory, a graph-pangenome can be studied directly to identify genomic regions and genes that underlie important evolutionary processes and traits. Here, I discuss how basic concepts in graph theory can be implemented to address questions in evolutionary genomics and guide future breeding efforts. Despite its compelling versatility, a graph-pangenome assembly is still challenging especially in species with large complex genomes. As technology is rapidly improving, the graph-pangenome is expected to become a central platform in genomics studies and applications. Thus, development of tools and methods that exploit the graph structure are urged to pave the route to evolutionary graph-pangenomics.

Wild sunflower goes viral: citizen science and comparative genomics allow tracking the origin and establishment of invasive sunflower in the Levant

Globalization and intensified volume of trade and transport around the world are accelerating the rate of biological invasions. It is therefore increasingly important to understand the processes through which invasive species colonize new habitats, often to the detriment of native flora. The initial steps of an invasion are particularly critical, as the introduced species relies on limited genetic diversity to adapt to a new environment. However, our understanding of this critical stage of the invasion is currently limited. We used a citizen science approach and social media to survey the distribution of invasive sunflower in Israel. We then sampled and sequenced a representative collection and compared it with available genomic data sets of North American wild sunflower, landraces and cultivars. We show that invasive wild sunflower is rapidly establishing throughout Israel, probably from a single, recent introduction from Texas, while maintaining high genetic diversity through ongoing gene flow. Since its introduction, invasive sunflower has spread quickly to most regions, and differentiation was detected despite extensive gene flow between clusters. Our findings suggest that rapid spread followed by continuous gene flow between diverging populations can serve as an efficient mechanism for maintaining sufficient genetic diversity at the early stages of invasion, promoting rapid adaptation and establishment in the new territory.

Fitness dependence preserves selection for recombination across diverse mixed mating strategies

Meiotic recombination and the factors affecting its rate and fate in nature have inspired many studies in theoretical evolutionary biology. Classical theoretical models have inferred that recombination can be favored under a rather restricted parameter range. Thus, the ubiquity of recombination in nature remains an open question. However, these models assumed constant recombination with an equal rate across all individuals within the population, whereas empirical evidence suggests that recombination may display certain sensitivity to ecological stressors and/or genotype fitness. Models assuming condition-dependent recombination show that such a strategy can often be favored over constant recombination. Moreover, in our recent model with panmictic populations subjected to purifying selection, fitness-dependent recombination was quite often favored even when any constant recombination was rejected. By using numerical modeling, we test whether such a 'recombination-rescuing potential' of fitness dependence holds also beyond panmixia, given the recognized effect of mating strategy on the evolution of recombination. We show that deviations from panmixia generally increase the recombination-rescuing potential of fitness dependence, with the strongest effect under intermediate selfing or high clonality. We find that under partial clonality, the evolutionary advantage of fitness-dependent recombination is determined mostly by selection against heterozygotes and additive-by-additive epistasis, while under partial selfing, additive-by-dominance epistasis is also a driver.

High rate of self-improving phenotypes in children with non-syndromic congenital ichthyosis: case series from south-western Germany

BACKGROUND

Non-syndromic congenital ichthyosis describes a heterogeneous group of hereditary skin disorders associated with erythroderma and scaling at birth. Although both severe and mild courses are known, the prediction of the natural history in clinical practice may be challenging.

OBJECTIVES

To determine clinical course and genotype-phenotype correlations in children affected by non-syndromic congenital ichthyosis in a case series from south-western Germany.

METHODS

We performed a retrospective observational study of 32 children affected by non-syndromic congenital ichthyoses seen in our genodermatosis clinic between 2011 and 2020. Follow-ups included assessment of weight and severity of skin involvement utilizing a modified Ichthyosis Area Severity Index (mIASI). mIASI was calculated as a sum comprising the previously published IASI score and an additional novel score to evaluate palmoplantar involvement. Linear regression was assessed using Pearson correlation, and statistical analysis was performed using the Wilcoxon-Mann-Whitney test.

RESULTS

This study included 23 patients with autosomal recessive congenital ichthyosis, seven with keratinopathic ichthyosis and two with harlequin ichthyosis. Cutaneous manifestations improved in more than 70% of the children during the follow-up. Especially in patients with mutations in ALOXE3 and ALOX12B, mIASI scores dropped significantly. The most common phenotype observed in this study was designated 'mild fine scaling ichthyosis'. Severe palmoplantar involvement occurred in patients with KRT1 and ABCA12 mutations; most patients demonstrated hyperlinearity as a sign of dryness and scaling. Weight was mainly in the normal range and negatively correlated with the severity of skin involvement.

CONCLUSIONS

Congenital ichthyosis that self-improves and evolves with mild fine scaling ichthyosis was the most common phenotype observed in our patients. This type might be underdiagnosed if the genetic diagnosis is not performed in the first year of life. mIASI is an easy and fast instrument for scoring disease severity and adding additional points for palmoplantar involvement might be valuable.

Demographic and ecogeographic factors limit wild grapevine spread at the southern edge of its distribution range

The spatial distribution of plants is constrained by demographic and ecogeographic factors that determine the range and abundance of the species. Wild grapevine (Vitis vinifera ssp. sylvestris) is distributed from Switzerland in the north to Israel in the south. However, little is known about the ecogeographic constraints of this species and its genetic and phenotypic characteristics, especially at the southern edge of its distribution range in the Levant region. In this study, we explore the population structure of southern Levantine wild grapevines and the correlation between demographic and ecogeographic characteristics. Based on our genetic analysis, the wild grapevine populations in this region can be divided into two major subgroups in accordance with a multivariate spatial and ecogeographical clustering model. The identified subpopulations also differ in morphological traits, mainly leaf hairiness which may imply adaptation to environmental stress. The findings suggest that the Upper Jordan River population was spread to the Sea of Galilee area and that a third smaller subpopulation at the south of the Golan Heights may represent a distinguished gene pool or a recent establishment of a new population. A spatial distribution model indicated that distance to water sources, Normalized difference vegetation index, and precipitation are the main environmental factors constraining V. v. sylvestris distribution at its southern distribution range. These factors in addition to limited gene flow between populations prevent further spread of wild grapevines southwards to semi-arid regions.

Tapping Diversity From the Wild: From Sampling to Implementation

The diversity observed among crop wild relatives (CWRs) and their ability to flourish in unfavorable and harsh environments have drawn the attention of plant scientists and breeders for many decades. However, it is also recognized that the benefit gained from using CWRs in breeding is a potential rose between thorns of detrimental genetic variation that is linked to the trait of interest. Despite the increased interest in CWRs, little attention was given so far to the statistical, analytical, and technical considerations that should guide the sampling design, the germplasm characterization, and later its implementation in breeding. Here, we review the entire process of sampling and identifying beneficial genetic variation in CWRs and the challenge of using it in breeding. The ability to detect beneficial genetic variation in CWRs is strongly affected by the sampling design which should be adjusted to the spatial and temporal variation of the target species, the trait of interest, and the analytical approach used. Moreover, linkage disequilibrium is a key factor that constrains the resolution of searching for beneficial alleles along the genome, and later, the ability to deplete linked deleterious genetic variation as a consequence of genetic drag. We also discuss how technological advances in genomics, phenomics, biotechnology, and data science can improve the ability to identify beneficial genetic variation in CWRs and to exploit it in strive for higher-yielding and sustainable crops.

ANALYSIS OF THE FIRST COLIBRI FUEL RODS OSCILLATION CAMPAIGN IN THE CROCUS REACTOR FOR THE EUROPEAN PROJECT CORTEX

The Horizon2020 European project CORTEX aims at developing an innovative core monitoring technique that allows detecting anomalies in nuclear reactors, such as excessive vibrations of core internals, flow blockage, or coolant inlet perturbations. The technique will be mainly based on using the fluctuations in neutron flux recorded by in-core and ex-core instrumentation, from which the anomalies will be differentiated depending on their type, location and characteristics. The project will result in a deepened understanding of the physical processes involved, allowing utilities to detect operational problems at a very early stage. In this framework, neutron noise computational methods and models are developed. In parallel, mechanical noise experimental campaigns are carried out in two zero-power reactors: AKR-2 and CROCUS. The aim is to produce high quality neutron noise-specific experimental data for the validation of the models. In CROCUS, the COLIBRI experimental program was developed to investigate experimentally the radiation noise induced by fuel rods vibrations. In this way, the 2018 first CORTEX campaign in CROCUS consisted in experiments with a perturbation induced by a fuel rods oscillator. Eighteen fuel rods located at the periphery of the core fuel lattice were oscillated between ±0.5 mm and ±2.0 mm around their central position at a frequency ranging from 0.1 Hz to 2 Hz. Signals from 11 neutron detectors which were set at positions in-core and ex-core in the water reflector, were recorded. The present article documents the results in noise level of the experimental campaign. Neutron noise levels are compared for several oscillation frequencies and amplitudes, and at the various detector locations concluding to the observation of a spatial dependency of the noise in amplitude.

Genetic and phenotypic analyses indicate that resistance to flooding stress is uncoupled from performance in cultivated sunflower

Given the rising risk of extreme weather caused by climate change, enhancement of abiotic stress resistance in crops is increasingly urgent. But will the development of stress-resistant cultivars come at the cost of yield under ideal conditions? We hypothesize that this need not be inevitable, because resistance alleles with minimal pleiotropic costs may evade artificial selection and be retained in crop germplasm. Genome-wide association (GWA) analyses for variation in plant performance and flooding response were conducted in cultivated sunflower, a globally important oilseed. We observed broad variation in flooding responses among genotypes. Flooding resistance was not strongly correlated with performance in control conditions, suggesting no inherent trade-offs. Consistent with this finding, we identified a subset of loci conferring flooding resistance, but lacking antagonistic effects on growth. Genetic diversity loss at candidate genes underlying these loci was significantly less than for other resistance genes during cultivated sunflower evolution. Despite bottlenecks associated with domestication and improvement, low-cost resistance alleles remain within the cultivated sunflower gene pool. Thus, development of cultivars that are both flooding-tolerant and highly productive should be straightforward. Results further indicate that estimates of pleiotropic costs from GWA analyses explain, in part, patterns of diversity loss in crop genomes.

Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance

Domesticated plants and animals often display dramatic responses to selection, but the origins of the genetic diversity underlying these responses remain poorly understood. Despite domestication and improvement bottlenecks, the cultivated sunflower remains highly variable genetically, possibly due to hybridization with wild relatives. To characterize genetic diversity in the sunflower and to quantify contributions from wild relatives, we sequenced 287 cultivated lines, 17 Native American landraces and 189 wild accessions representing 11 compatible wild species. Cultivar sequences failing to map to the sunflower reference were assembled de novo for each genotype to determine the gene repertoire, or 'pan-genome', of the cultivated sunflower. Assembled genes were then compared to the wild species to estimate origins. Results indicate that the cultivated sunflower pan-genome comprises 61,205 genes, of which 27% vary across genotypes. Approximately 10% of the cultivated sunflower pan-genome is derived through introgression from wild sunflower species, and 1.5% of genes originated solely through introgression. Gene ontology functional analyses further indicate that genes associated with biotic resistance are over-represented among introgressed regions, an observation consistent with breeding records. Analyses of allelic variation associated with downy mildew resistance provide an example in which such introgressions have contributed to resistance to a globally challenging disease.

Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley

The cereal grass barley was domesticated about 10,000 years before the present in the Fertile Crescent and became a founder crop of Neolithic agriculture. Here we report the genome sequences of five 6,000-year-old barley grains excavated at a cave in the Judean Desert close to the Dead Sea. Comparison to whole-exome sequence data from a diversity panel of present-day barley accessions showed the close affinity of ancient samples to extant landraces from the Southern Levant and Egypt, consistent with a proposed origin of domesticated barley in the Upper Jordan Valley. Our findings suggest that barley landraces grown in present-day Israel have not experienced major lineage turnover over the past six millennia, although there is evidence for gene flow between cultivated and sympatric wild populations. We demonstrate the usefulness of ancient genomes from desiccated archaeobotanical remains in informing research into the origin, early domestication and subsequent migration of crop species.

Why Close a Bacterial Genome? The Plasmid of Alteromonas Macleodii HOT1A3 is a Vector for Inter-Specific Transfer of a Flexible Genomic Island

Genome sequencing is rapidly becoming a staple technique in environmental and clinical microbiology, yet computational challenges still remain, leading to many draft genomes which are typically fragmented into many contigs. We sequenced and completely assembled the genome of a marine heterotrophic bacterium, Alteromonas macleodii HOT1A3, and compared its full genome to several draft genomes obtained using different reference-based and de novo methods. In general, the de novo assemblies clearly outperformed the reference-based or hybrid ones, covering >99% of the genes and representing essentially all of the gene functions. However, only the fully closed genome (∼4.5 Mbp) allowed us to identify the presence of a large, 148 kbp plasmid, pAM1A3. While HOT1A3 belongs to A. macleodii, typically found in surface waters (“surface ecotype”), this plasmid consists of an almost complete flexible genomic island (fGI), containing many genes involved in metal resistance previously identified in the genomes of Alteromonas mediterranea (“deep ecotype”). Indeed, similar to A. mediterranea, A. macleodii HOT1A3 grows at concentrations of zinc, mercury, and copper that are inhibitory for other A. macleodii strains. The presence of a plasmid encoding almost an entire fGI suggests that wholesale genomic exchange between heterotrophic marine bacteria belonging to related but ecologically different populations is not uncommon.

Hybridization and extinction

Hybridization may drive rare taxa to extinction through genetic swamping, where the rare form is replaced by hybrids, or by demographic swamping, where population growth rates are reduced due to the wasteful production of maladaptive hybrids. Conversely, hybridization may rescue the viability of small, inbred populations. Understanding the factors that contribute to destructive versus constructive outcomes of hybridization is key to managing conservation concerns. Here, we survey the literature for studies of hybridization and extinction to identify the ecological, evolutionary, and genetic factors that critically affect extinction risk through hybridization. We find that while extinction risk is highly situation dependent, genetic swamping is much more frequent than demographic swamping. In addition, human involvement is associated with increased risk and high reproductive isolation with reduced risk. Although climate change is predicted to increase the risk of hybridization‐induced extinction, we find little empirical support for this prediction. Similarly, theoretical and experimental studies imply that genetic rescue through hybridization may be equally or more probable than demographic swamping, but our literature survey failed to support this claim. We conclude that halting the introduction of hybridization‐prone exotics and restoring mature and diverse habitats that are resistant to hybrid establishment should be management priorities.

Transcriptome profiling of wheat glumes in wild emmer, hulled landraces and modern cultivars

Background

Wheat domestication is considered as one of the most important events in the development of human civilization. Wheat spikelets have undergone significant changes during evolution under domestication, resulting in soft glumes and larger kernels that are released easily upon threshing. Our main goal was to explore changes in transcriptome expression in glumes that accompanied wheat evolution under domestication.

Methods

A total of six tetraploid wheat accessions were selected for transcriptome profiling based on their rachis brittleness and glumes toughness. RNA pools from glumes of the central spikelet at heading time were used to construct cDNA libraries for sequencing. The trimmed reads from each library were separately aligned to the reference sub-genomes A and B, which were extracted from wheat survey sequence. Differentially expression analysis and functional annotation were performed between wild and domesticated wheat, to identity candidate genes associated with evolution under domestication. Selected candidate genes were validated using real time PCR.

Results

Transcriptome profiles of wild emmer wheat, wheat landraces, and wheat cultivars were compared using next generation sequencing (RNA-seq). We have found a total of 194,893 transcripts, of which 73,150 were shared between wild, landraces, and cultivars. From 781 differentially expressed genes (DEGs), 336 were down-regulated and 445 were up-regulated in the domesticated compared to wild wheat genotypes. Gene Ontology (GO) annotation assigned 293 DEGs (37.5 %) to GO term groups, of which 134 (17.1 %) were down-regulated and 159 (20.4 %) up-regulated in the domesticated wheat. Some of the down-regulated DEGs in domesticated wheat are related to the biosynthetic pathways that eventually define the mechanical strength of the glumes, such as cell wall, lignin, pectin and wax biosynthesis. The reduction in gene expression of such genes, may explain the softness of the glumes in the domesticated forms. In addition, we have identified genes involved in nutrient remobilization that may affect grain size and other agronomic traits evolved under domestication.

Conclusions

The comparison of RNA-seq profiles between glumes of wheat groups differing in glumes toughness and rachis brittleness revealed a few DEGs that may be involved in glumes toughness and nutrient remobilization. These genes may be involved in processes of wheat improvement under domestication.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1996-0) contains supplementary material, which is available to authorized users.

RNA-Seq analysis identifies genes associated with differential reproductive success under drought-stress in accessions of wild barley Hordeum spontaneum

BACKGROUND

The evolutionary basis of reproductive success in different environments is of major interest in the study of plant adaptation. Since the reproductive stage is particularly sensitive to drought, genes affecting reproductive success during this stage are key players in the evolution of adaptive mechanisms. We used an ecological genomics approach to investigate the reproductive response of drought-tolerant and sensitive wild barley accessions originating from different habitats in the Levant.

RESULTS

We sequenced mRNA extracted from spikelets at the flowering stage in drought-treated and control plants. The barley genome was used for a reference-guided assembly and differential expression analysis. Our approach enabled to detect biological processes affecting grain production under drought stress. We detected novel candidate genes and differentially expressed alleles associated with drought tolerance. Drought associated genes were shown to be more conserved than non-associated genes, and drought-tolerance genes were found to evolve more rapidly than other drought associated genes.

CONCLUSIONS

We show that reproductive success under drought stress is not a habitat-specific trait but a shared physiological adaptation that appeared to evolve recently in the evolutionary history of wild barley. Exploring the genomic basis of reproductive success under stress in crop wild progenitors is expected to have considerable ecological and economical applications.

Identification of conserved drought-adaptive genes using a cross-species meta-analysis approach

BACKGROUND

Drought is the major environmental stress threatening crop-plant productivity worldwide. Identification of new genes and metabolic pathways involved in plant adaptation to progressive drought stress at the reproductive stage is of great interest for agricultural research.

RESULTS

We developed a novel Cross-Species meta-Analysis of progressive Drought stress at the reproductive stage (CSA:Drought) to identify key drought adaptive genes and mechanisms and to test their evolutionary conservation. Empirically defined filtering criteria were used to facilitate a robust integration of 17 deposited microarray experiments (148 arrays) of Arabidopsis, rice, wheat and barley. By prioritizing consistency over intensity, our approach was able to identify 225 differentially expressed genes shared across studies and taxa. Gene ontology enrichment and pathway analyses classified the shared genes into functional categories involved predominantly in metabolic processes (e.g. amino acid and carbohydrate metabolism), regulatory function (e.g. protein degradation and transcription) and response to stimulus. We further investigated drought related cis-acting elements in the shared gene promoters, and the evolutionary conservation of shared genes. The universal nature of the identified drought-adaptive genes was further validated in a fifth species, Brachypodium distachyon that was not included in the meta-analysis. qPCR analysis of 27, randomly selected, shared orthologs showed similar expression pattern as was found by the CSA:Drought.In accordance, morpho-physiological characterization of progressive drought stress, in B. distachyon, highlighted the key role of osmotic adjustment as evolutionary conserved drought-adaptive mechanism.

CONCLUSIONS

Our CSA:Drought strategy highlights major drought-adaptive genes and metabolic pathways that were only partially, if at all, reported in the original studies included in the meta-analysis. These genes include a group of unclassified genes that could be involved in novel drought adaptation mechanisms. The identified shared genes can provide a useful resource for subsequent research to better understand the mechanisms involved in drought adaptation across-species and can serve as a potential set of molecular biomarkers for progressive drought experiments.

What we still don't know about invasion genetics

Publication of The Genetics of Colonizing Species in 1965 launched the field of invasion genetics and highlighted the value of biological invasions as natural ecological and evolutionary experiments. Here, we review the past 50 years of invasion genetics to assess what we have learned and what we still don't know, focusing on the genetic changes associated with invasive lineages and the evolutionary processes driving these changes. We also suggest potential studies to address still-unanswered questions. We now know, for example, that rapid adaptation of invaders is common and generally not limited by genetic variation. On the other hand, and contrary to prevailing opinion 50 years ago, the balance of evidence indicates that population bottlenecks and genetic drift typically have negative effects on invasion success, despite their potential to increase additive genetic variation and the frequency of peak shifts. Numerous unknowns remain, such as the sources of genetic variation, the role of so-called expansion load and the relative importance of propagule pressure vs. genetic diversity for successful establishment. While many such unknowns can be resolved by genomic studies, other questions may require manipulative experiments in model organisms. Such studies complement classical reciprocal transplant and field-based selection experiments, which are needed to link trait variation with components of fitness and population growth rates. We conclude by discussing the potential for studies of invasion genetics to reveal the limits to evolution and to stimulate the development of practical strategies to either minimize or maximize evolutionary responses to environmental change.

Laminopathy-inducing mutations reduce nuclear import of expressed prelamin A

Lamins are structural components of the nuclear lamina and integral parts of the nucleoplasm. The tripartite domain structure partitions the molecule into an amino-terminal head, central rod and a carboxy-terminal tail domain. The tail domain contains a nuclear localization sequence and in most lamins an additional CaaX motif, which is necessary to post-translationally process prelamin to mature lamin. As players of nuclear and cellular integrity, lamins must possess unrestrained access to the nucleus. To study whether nuclear trafficking of lamins is compromised in laminopathies, we determined relative nuclear import activities between expressed prelamin A and selected laminopathy-inducing mutants thereof. Furthermore, the impact of inhibition of maturation on nuclear import of expressed prelamin A was examined. To perform quantitative transport measurements, import competent but lamina incorporation-deficient GFP- or DsRed-tagged prelamin A deletion mutants were used, which lacked the head and rod domain (ΔHR-prelamin A). Nuclear accumulation of ΔHR-prelamin A carrying the lipodystrophy and metabolic syndrome-inducing mutations R419C and L421P or progeria-causing deletions was significantly reduced, but that of the maturation-deficient mutant ΔHR-prelamin A SSIM was significantly increased. In the case of the full length prelamin A mutants R419C and L421P altered subcellular localization and reduced lamina incorporation were detected, with the prelamin A-binding protein Narf being redistributed into R419-containing aggregates. The results suggest that impaired nuclear transport of certain prelamin A mutants may represent a contributing factor in the pathogenesis of certain laminopathies.

Phenotypic landscapes: phenological patterns in wild and cultivated barley

Phenotypic variation in natural populations is the outcome of the joint effects of environmentally induced adaptations and neutral processes on the genetic architecture of quantitative traits. In this study, we examined the role of adaptation in shaping wild barley phenotypic variation along different environmental gradients. Detailed phenotyping of 164 wild barley (Hordeum spontaneum) accessions from Israel (of the Barley1K collection) and 18 cultivated barley (H. vulgare) varieties was conducted in common garden field trials. Cluster analysis based on phenotypic data indicated that wild barley in this region can be differentiated into three ecotypes in accordance with their ecogeographical distribution: north, coast and desert. Population differentiation (Q(ST) ) for each trait was estimated using a hierarchical Bayesian model and compared to neutral differentiation (F(ST) ) based on 42 microsatellite markers. This analysis indicated that the three clusters diverged in morphological but not in reproductive characteristics. To address the issue of phenotypic variation along environmental gradients, climatic and soil gradients were compared with each of the measured traits given the geographical distance between sampling sites using a partial Mantel test. Flowering time and plant growth were found to be differentially correlated with climatic and soil characteristic gradients, respectively. The H. vulgare varieties were superior to the H. spontaneum accessions in yield components, yet resembled the Mediterranean types in vegetative characteristics and flowering time, which may indicate the geographical origin of domesticated barley.

Ultrasound and microstructures--a promising combination?

Short diffusion paths and high specific interfacial areas in microstructured devices can increase mass transfer rates and thus accelerate multiphase reactions. This effect can be intensified by the application of ultrasound. Herein, we report on the design and testing of a novel versatile setup for a continuous ultrasound-supported multiphase process in microstructured devices on a preparative scale. The ultrasonic energy is introduced indirectly into the microstructured device through pressurized water as transfer medium. First, we monitored the influence of ultrasound on the slug flow of a liquid/liquid two-phase system in a channel with a high-speed camera. To quantify the influence of ultrasound, the hydrolysis of p-nitrophenyl acetate was utilized as a model reaction. Microstructured devices with varying channel diameter, shape, and material were applied with and without ultrasonication at flow rates in the mL min(-1) range. The continuous procedures were then compared and evaluated by performing a simplified life cycle assessment.

Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns

The blind subterranean mole rat (Spalax ehrenbergi superspecies) is a model animal for survival under extreme environments due to its ability to live in underground habitats under severe hypoxic stress and darkness. Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of S. ehrenbergi. cDNA pools from muscle and brain tissues isolated from animals exposed to hypoxic and normoxic conditions were sequenced using Sanger, GS FLX, and GS FLX Titanium technologies. Assembly of the sequences yielded over 51,000 isotigs with homology to ∼12,000 mouse, rat or human genes. Based on these results, it was possible to detect large numbers of splice variants, SNPs, and novel transcribed regions. In addition, multiple differential expression patterns were detected between tissues and treatments. The results presented here will serve as a valuable resource for future studies aimed at identifying genes and gene regions evolved during the adaptive radiation associated with underground life of the blind mole rat.

Dust-induced modulation of the atomic emission in a dusty argon discharge

The spectral emission of argon atoms in a dusty rf discharge plasma has been determined. For that purpose, the spatially and temporally resolved emission of the argon atoms during the rf cycle was measured using a gated intensified charge-coupled device camera. While dust particles of 2-3 microm diameter trapped in the sheath lead to an increased plasma emission during the sheath expansion phase, larger particles of 10-12 microm diameter result in a decreased emission. This behavior is explained by the combined action of electron density reduction due to the charging dynamics in the sheath and the increase of electron temperature to compensate plasma losses at the dust.

Strong correlation of wild barley (Hordeum spontaneum) population structure with temperature and precipitation variation

In this study, we present the genetic analysis of a new collection of wild barley (Hordeum spontaneum) using 42 simple sequence repeat (SSR) markers that represent the seven chromosomes. The Barley1K (B1K) infrastructure consists of 1020 accessions collected in a hierarchical sampling mode (HSM) from 51 sites across Israel and represents the wide adaptive niche of the modern barley's ancestor. According to the genetic structure analysis, the sampled sites can be divided into seven groups, and sampled microsites located on opposing slopes or in different soil types did not show significant genetic differentiation. Although the genetic analysis indicates a simple isolation-by-distance model among the populations, examination of the genetic populations' structure with abiotic parameters in an ordination analysis revealed that the combination of elevation, mid-day temperature and rainfall explains a high proportion of the variance in the principal components analysis. Our findings demonstrate that the current populations have therefore been shaped and distinguished by non-selective forces such as migration; however, we suggest that aridity and temperature gradients played major roles as selective forces in the adaptation of wild barley in this part of the Fertile Crescent. This unique collection is a prelude for the investigation of the molecular basis underlying plant adaptation and responsiveness to harsh environments.

Quantitative analysis of localization and nuclear aggregate formation induced by GFP-lamin A mutant proteins in living HeLa cells

Although A-type lamins are ubiquitously expressed, their role in the tissue-specificity of human laminopathies remains enigmatic. In this study, we generate a series of transfection constructs encoding missense lamin A mutant proteins fused to green fluorescent protein and investigate their subnuclear localization using quantitative live cell imaging. The mutant constructs used included the laminopathy-inducing lamin A rod domain mutants N195K, E358K, M371K, R386K, the tail domain mutants G465D, R482L, and R527P, and the Hutchinson-Gilford progeria syndrome-causing deletion mutant, progerin (LaA delta50). All mutant derivatives induced nuclear aggregates, except for progerin, which caused a more lobulated phenotype of the nucleus. Quantitative analysis revealed that the frequency of nuclear aggregate formation was significantly higher (two to four times) for the mutants compared to the wild type, although the level of lamin fusion proteins within nuclear aggregates was not. The distribution of endogenous A-type lamins was altered by overexpression of the lamin A mutants, coexpression experiments revealing that aberrant localization of the N195K and R386K mutants had no effect on the subnuclear distribution of histones H2A or H2B, or on nuclear accumulation of H2A overexpressed as a DsRed2 fusion protein. The GFP-lamin fusion protein-expressing constructs will have important applications in the future, enabling live cell imaging of nuclear processes involving lamins and how this may relate to the pathogenesis of laminopathies.

Laminopathy-inducing lamin A mutants can induce redistribution of lamin binding proteins into nuclear aggregates

Lamins, members of the family of intermediate filaments, form a supportive nucleoskeletal structure underlying the nuclear envelope and can also form intranuclear structures. Mutations within the A-type lamin gene cause a variety of degenerative diseases which are collectively referred to as laminopathies. At the molecular level, laminopathies have been shown to be linked to a discontinuous localization pattern of A-type lamins, with some laminopathies containing nuclear lamin A aggregates. Since nuclear aggregate formation could lead to the mislocalization of proteins interacting with A-type lamins, we set out to examine the effects of FLAG-lamin A N195K and R386K protein aggregate formation on the subnuclear distribution of the retinoblastoma protein (pRb) and the sterol responsive element binding protein 1a (SREBP1a) after coexpression as GFP-fusion proteins in HeLa cells. We observed strong recruitment of both proteins into nuclear aggregates. Nuclear aggregate recruitment of the NPC component nucleoporin NUP153 was also observed and found to be dependent on the N-terminus. That these effects were specific was implied by the fact that a number of other coexpressed karyophilic GFP-fusion proteins, such as the nucleoporin NUP98 and kanadaptin, did not coaggregate with FLAG-lamin A N195K or R386K. Immunofluorescence analysis further indicated that the precursor form of lamin A, pre-lamin A, could be found in intranuclear aggregates. Our results imply that redistribution into lamin A-/pre-lamin A-containing aggregates of proteins such as pRb and SREBP1a could represent a key aspect underlying the molecular pathogenesis of certain laminopathies.

High incidence and unique features of antigen receptor gene rearrangements in TEL-AML1-positive leukemias

The t(12;21) translocation resulting in the TEL-AML1 gene fusion is found in 25% of childhood B-cell precursor (BCP) acute lymphoblastic leukemias (ALL). Since TEL-AML1 has been reported to induce cell cycle retardation and thus may influence somatic recombination, we analyzed 214 TEL-AML1-positive ALL by PCR for rearrangements of the immunoglobulin (Ig) and T-cell receptor (TCR) genes. As a control group, 174 childhood BCP ALL without a TEL-AML1 were used. The majority of TEL-AML1-positive leukemias had a higher number of Ig/TCR rearrangements than control ALL. They also had a more mature immunogenotype characterized by their high frequency of complete IGH, IGK-Kde, and TCRG rearrangements. While IGK-Kde and TCRG were more frequently rearranged on both alleles at higher age, IGH and TCRD rearrangements decreased in their incidence along with a decrease in biallelic IGH rearrangements. This suggests that the recombination process continues in these leukemias leading to ongoing rearrangements and possibly also deletions of antigen receptor genes. We here provide first evidence that somatic recombination of antigen receptor genes is affected by the TEL-AML1 fusion, and that further age-related differences are probably caused by the longer latency period of the prenatally initiated TEL-AML1-positive leukemias in older children.

Roles of cytoskeletal and junctional plaque proteins in nuclear signaling

Cytoplasmic junctional plaque proteins play an important role at intercellular junctions. They link transmembrane cell adhesion molecules to components of the cytoskeleton, thereby playing an important role in the control of many cellular processes. Recent studies on the subcellular distribution of some plaque proteins have revealed that a number of these proteins are able to localize in the nucleus. This dual location indicates that in addition to promoting adhesive interactions, plaque proteins may also play a direct role in nuclear processes, and in particular in the transfer of signals from the membrane to the nucleus. Therefore, translocation of plaque proteins into the nucleus in response to extracellular signals could represent a novel and direct mechanism by which signals can be transmitted from the plasma membrane to the nucleus. This could allow cells to respond to changing environmental conditions in a rapid and efficient way. In addition, conditional sequestration of karyophilic proteins at the sites of cell-cell and cell-substratum adhesion may represent a general mechanism for the regulation of nucleocytoplasmic transport.

Luminescence characteristics of dental ceramics for retrospective dosimetry: a preliminary study

Ceramic materials that are widely employed in dental prosthetics and repairs exhibit luminescent properties. Because of their use in the body, these materials are potentially of interest in situations where retrospective dosimetry for individuals is required but where monitoring was not planned. The luminescent properties of dental ceramics obtained from Germany, Spain and the UK were examined. Linear dose-response characteristics were obtained in the range < 100 mGy to 10 Gy using thermoluminescence (TL), optically stimulated luminescence (OSL) and infrared-stimulated luminescence (IRSL) measurement techniques. Measurements of time-resolved luminescence were also performed to examine the nature of the luminescence recombination under visible (470 nm) and IR (855 nm) stimulation. The results obtained by TL and optically stimulated techniques suggest that there may be deeper traps than previously observed in certain types of dental ceramic. Such traps may be less susceptible to optical and athermal fading than was reported in earlier studies.

Protein kinase C mu selectively activates the mitogen-activated protein kinase (MAPK) p42 pathway

Here we show that human protein kinase C mu (PKC mu) activates the mitogen-activated protein kinase (MAPK). Transient expression of constitutive active PKC mu leads to an activation of Raf-1 kinase as demonstrated by in vitro phosphorylation of MAPK. PKC mu enhances transcriptional activity of a basal thymidine kinase promotor containing serum response elements (SREs) as shown by luciferase reporter gene assays. SRE driven gene activation by PKC mu is triggered by the Elk-1 ternary complex factor. PKC mu-mediated activation of SRE driven transcription can be inhibited by the MEK1 inhibitor PD98059. In contrast to the activation of the p42/ERK1 MAPK cascade, transient expression of constitutive active PKC mu does neither affect c-jun N-terminal kinase nor p38 MAPK.

Hsp70-RAP46 interaction in downregulation of DNA binding by glucocorticoid receptor

Receptor-associating protein 46 (RAP46) is a cochaperone that regulates the transactivation function of several steroid receptors. It is transported into the nucleus by a liganded glucocorticoid receptor where it downregulates DNA binding and transactivation by this receptor. The N- and C-termini of RAP46 are both implicated in its negative regulatory function. In metabolic labelling experiments, we have shown that the N-terminus of RAP46 is modified by phosphorylation, but this does not contribute to the downregulation of glucocorticoid receptor activity. However, deletion of a sequence that binds 70 kDa heat shock protein (Hsp70) and the constitutive isoform of Hsp70 (Hsc70) at the C-terminus of RAP46 abrogated its negative regulatory action. Surface plasmon resonance studies showed that RAP46 binds the glucocorticoid receptor only when it has interacted with Hsp70/Hsc70, and confocal immunofluorescence analyses revealed a nuclear transport of Hsp70/Hsc70 by the liganded receptor. Together these findings demonstrate an important contribution of Hsp70/Hsc70 in the binding of RAP46 to the glucocorticoid receptor and suggest a role for this molecular chaperone in the RAP46-mediated downregulation of glucocorticoid receptor activity.

BAG-1M: a potential specificity determinant of corticosteroid receptor action

BAG-1M is a eukaryotic cochaperone that associates with several proteins, including the glucocorticoid receptor (GR). It down-regulates GR-mediated transactivation by a mechanism that requires its prior recruitment by the liganded receptor from cytoplasm into the nucleus. In the nucleus, it uses a repeated sequence motif ([EEX4]8) at its NH2 terminus to inhibit DNA binding, as well as transactivation functions of the receptor. The mineralocorticoid receptor (MR), a structural and functional homologue of the GR, is unable to translocate BAG-1M into the nucleus, and its transactivation function is also not affected by this protein. This differential regulation of GR and MR activity could be relevant in classic mineralocorticoid tissues such as the kidney in which GR activity needs to be repressed to allow the MR to exert its action. In in situ hybridization studies, we show that BAG-1M is expressed in the kidney. Its expression pattern, especially in the developing kidney, correlated well with that of the GR. We therefore postulate that BAG-1M may be a specificity determinant in GR and MR action, and may feature prominently in the control of GR activity in kidney development.