Evolving gene expression: from G to E to GxE

The relative impact of parental and current environment on plant transcriptomes depends on type of stress and genotype

Through developmental plasticity, an individual organism integrates influences from its immediate environment with those due to the environment of its parents. While both effects on phenotypes are well documented, their relative impact has been little studied in natural systems, especially at the level of gene expression. We examined this issue in four genotypes of the annual plant Persicaria maculosa by varying two key resources-light and soil moisture-in both generations. Transcriptomic analyses showed that the relative effects of parent and offspring environment on gene expression (i.e. the number of differentially expressed transcripts, DETs) varied both for the two types of resource stress and among genotypes. For light, immediate environment induced more DETs than parental environment for all genotypes, although the precise proportion of parental versus immediate DETs varied among genotypes. By contrast, the relative effect of soil moisture varied dramatically among genotypes, from 8-fold more DETs due to parental than immediate conditions to 10-fold fewer. These findings provide evidence at the transcriptomic level that the relative impacts of parental and immediate environment on the developing organism may depend on the environmental factor and vary strongly among genotypes, providing potential for the interplay of these developmental influences to evolve.

Environmentally robust cis-regulatory changes underlie rapid climatic adaptation

Changes in gene expression are thought to play a major role in adaptive evolution. While it is known that gene expression is highly sensitive to the environment, very few studies have determined the influence of genetic and environmental effects on adaptive gene expression differences in natural populations. Here, we utilize allele-specific expression to characterize cis and trans gene regulatory divergence in temperate and tropical house mice in two metabolic tissues under two thermal conditions. First, we show that gene expression divergence is pervasive between populations and across thermal conditions, with roughly 5 to 10% of genes exhibiting genotype-by-environment interactions. Second, we found that most expression divergence was due to cis-regulatory changes that were stable across temperatures. In contrast, patterns of expression plasticity were largely attributable to trans-effects, which showed greater sensitivity to temperature. Nonetheless, we found a small subset of temperature-dependent cis-regulatory changes, thereby identifying loci underlying expression plasticity. Finally, we performed scans for selection in wild house mice to identify genomic signatures of rapid adaptation. Genomic outliers were enriched in genes with evidence for cis-regulatory divergence. Notably, these genes were associated with phenotypes that affected body weight and metabolism, suggesting that cis-regulatory changes are a possible mechanism for adaptive body size evolution between populations. Our results show that gene expression plasticity, largely controlled in trans, may facilitate the colonization of new environments, but that evolved changes in gene expression are largely controlled in cis, illustrating the genetic and nongenetic mechanisms underlying the establishment of populations in new environments.

Transition from Transient DNA Rereplication to Inherited Gene Amplification Following Prolonged Environmental Stress

Cells require the ability to adapt to changing environmental conditions, however, it is unclear how these changes elicit stable permanent changes in genomes. We demonstrate that, in response to environmental metal exposure, the metallothionein (MT) locus undergoes DNA rereplication generating transient site-specific gene amplifications (TSSGs). Chronic metal exposure allows transition from MT TSSG to inherited MT gene amplification through homologous recombination within and outside of the MT locus. DNA rereplication of the MT locus is suppressed by H3K27me3 and EZH2. Long-term ablation of EZH2 activity eventually leads to integration and inheritance of MT gene amplifications without the selective pressure of metal exposure. The rereplication and inheritance of MT gene amplification is an evolutionarily conserved response to environmental metal from yeast to human. Our results describe a new paradigm for adaptation to environmental stress where targeted, transient DNA rereplication precedes stable inherited gene amplification.

Daphnia as a model organism to probe biological responses to nanomaterials-from individual to population effects via adverse outcome pathways

The importance of the cladoceran Daphnia as a model organism for ecotoxicity testing has been well-established since the 1980s. Daphnia have been increasingly used in standardised testing of chemicals as they are well characterised and show sensitivity to pollutants, making them an essential indicator species for environmental stress. The mapping of the genomes of D. pulex in 2012 and D. magna in 2017 further consolidated their utility for ecotoxicity testing, including demonstrating the responsiveness of the Daphnia genome to environmental stressors. The short lifecycle and parthenogenetic reproduction make Daphnia useful for assessment of developmental toxicity and adaption to stress. The emergence of nanomaterials (NMs) and their safety assessment has introduced some challenges to the use of standard toxicity tests which were developed for soluble chemicals. NMs have enormous reactive surface areas resulting in dynamic interactions with dissolved organic carbon, proteins and other biomolecules in their surroundings leading to a myriad of physical, chemical, biological, and macromolecular transformations of the NMs and thus changes in their bioavailability to, and impacts on, daphnids. However, NM safety assessments are also driving innovations in our approaches to toxicity testing, for both chemicals and other emerging contaminants such as microplastics (MPs). These advances include establishing more realistic environmental exposures via medium composition tuning including pre-conditioning by the organisms to provide relevant biomolecules as background, development of microfluidics approaches to mimic environmental flow conditions typical in streams, utilisation of field daphnids cultured in the lab to assess adaption and impacts of pre-exposure to pollution gradients, and of course development of mechanistic insights to connect the first encounter with NMs or MPs to an adverse outcome, via the key events in an adverse outcome pathway. Insights into these developments are presented below to inspire further advances and utilisation of these important organisms as part of an overall environmental risk assessment of NMs and MPs impacts, including in mixture exposure scenarios.

Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata

Understanding what factors influence plastic and genetic variation is valuable for predicting how organisms respond to changes in the selective environment. Here, using gene expression and DNA methylation as molecular phenotypes, we study environmentally induced variation among Arabidopsis lyrata plants grown at lowland and alpine field sites. Our results show that gene expression is highly plastic, as many more genes are differentially expressed between the field sites than between populations. These environmentally responsive genes evolve under strong selective constraint – the strength of purifying selection on the coding sequence is high, while the rate of adaptive evolution is low. We find, however, that positive selection on cis-regulatory variants has likely contributed to the maintenance of genetically variable environmental responses, but such variants segregate only between distantly related populations. In contrast to gene expression, DNA methylation at genic regions is largely insensitive to the environment, and plastic methylation changes are not associated with differential gene expression. Besides genes, we detect environmental effects at transposable elements (TEs): TEs at the high-altitude field site have higher expression and methylation levels, suggestive of a broad-scale TE activation. Compared to the lowland population, plants native to the alpine environment harbor an excess of recent TE insertions, and we observe that specific TE families are enriched within environmentally responsive genes. Our findings provide insight into selective forces shaping plastic and genetic variation. We also highlight how plastic responses at TEs can rapidly create novel heritable variation in stressful conditions.

Disentangling the developmental origins of a novel phenotype: enhancement versus reversal of environmentally induced gene expression

Increasing evidence suggests that many novel traits might have originated via plasticity-led evolution (PLE). Yet, little is known of the developmental processes that underpin PLE, especially in its early stages. One such process is 'phenotypic accommodation', which occurs when, in response to a change in the environment, an organism experiences adjustments across variable parts of its phenotype that improve its fitness. Here, we asked if environmentally induced changes in gene expression are enhanced or reversed during phenotypic accommodation of a novel, complex phenotype in spadefoot toad tadpoles (Spea multiplicata). More genes than expected were affected by both the environment and phenotypic accommodation in the liver and brain. However, although phenotypic accommodation primarily reversed environmentally induced changes in gene expression in liver tissue, it enhanced these changes in brain tissue. Thus, depending on the tissue, phenotypic accommodation may either minimize functional disruption via reversal of gene expression patterns or promote novelty via enhancement of existing expression patterns. Our study thereby provides insights into the developmental origins of a novel phenotype and the incipient stages of PLE.

Gene expression studies of plastic and evolutionary responses to global warming

Phenotypic plasticity can be a rapid response for coping with global warming, yet may be insufficient to protect species from extinction. Evolutionary adaptation may reinforce adaptive or oppose maladaptive plastic responses. With advances in technology whole transcriptomes can provide us with an unprecedented overview of genes and functional processes underlying the interplay between plasticity and evolution. We advocate that insects provide ideal opportunities to study plasticity in non-adapted and thermally adapted populations to infer reaction norms across the whole transcriptome ('reactionomes'). This can advance our understanding of how the interplay between plasticity and evolution shapes responses to warming. So far, a limited number of studies suggest predominantly maladaptive plastic responses to novel environments that are reduced with time, but much more research is needed to infer general patterns.

The dynamic effect of genetic variation on the in vivo ER stress transcriptional response in different tissues

The genetic regulation of gene expression varies greatly across tissue-type and individuals and can be strongly influenced by the environment. Many variants, under healthy control conditions, may be silent or even have the opposite effect under diseased stress conditions. This study uses an in vivo mouse model to investigate how the effect of genetic variation changes with cellular stress across different tissues. Endoplasmic reticulum stress occurs when misfolded proteins accumulate in the endoplasmic reticulum. This triggers the unfolded protein response, a large transcriptional response which attempts to restore homeostasis. This transcriptional response, despite being a conserved, basic cellular process, is highly variable across different genetic backgrounds, making it an ideal system to study the dynamic effects of genetic variation. In this study, we sought to better understand how genetic variation alters expression across tissues, in the presence and absence of endoplasmic reticulum stress. The use of different mouse strains and their F1s allow us to also identify context-specific cis- and trans- regulatory variation underlying variable transcriptional responses. We found hundreds of genes that respond to endoplasmic reticulum stress in a tissue- and/or genotype-dependent manner. The majority of the regulatory effects we identified were acting in cis-, which in turn, contribute to the variable endoplasmic reticulum stress- and tissue-specific transcriptional response. This study demonstrates the need for incorporating environmental stressors across multiple different tissues in future studies to better elucidate the effect of any particular genetic factor in basic biological pathways, like the endoplasmic reticulum stress response.

Relationship between gene expression networks and muscle contractile physiology differences in Anolis lizards

Muscles facilitate most animal behavior, from eating to fleeing. However, to generate the variation in behavior necessary for survival, different muscles must perform differently; for instance, sprinting requires multiple rapid muscle contractions, whereas biting may require fewer contractions but greater force. Here, we use a transcriptomic approach to identify genes associated with variation in muscle contractile physiology among different muscles from the same individual. We measured differential gene expression between a leg and jaw muscle of Anolis lizards known to differ in muscle contractile physiology and performance. For each individual, one muscle was used to measure muscle contractile physiology, including contractile velocity (V_max and V₄₀), specific tension, power ratio, and twitch time, whereas the contralateral muscle was used to extract RNA for transcriptomic sequencing. Using the transcriptomic data, we found clear clustering of muscle type. Expression of genes clustered in gene ontology (GO) terms related to muscle contraction and extracellular matrix was, on average, negatively correlated with V_max and slower twitch times but positively correlated to power ratio and V₄₀. Conversely, genes related to the GO terms related to aerobic respiration were downregulated in muscles with higher power ratio and V₄₀, and over-expressed as twitch time decreased. Determining the molecular mechanisms that underlie variation in muscle contractile physiology can begin to explain how organisms are able to optimize behavior under variable conditions. Future studies pursuing the effects of differential gene expression across muscle types in different environments might inform researchers about how differences develop across species, populations, and individuals varying in ecological history.

Differential expression analyses reveal extensive transcriptional plasticity induced by temperature in New Zealand silver trevally (Pseudocaranx georgianus)

Ectotherm species, such as marine fishes, depend on environmental temperature to regulate their vital functions. In finfish aquaculture production, being able to predict physiological responses in growth and other economic traits to temperature is crucial to address challenges inherent in the selection of grow-out locations. This will become an even more significant issue under the various predicted future climate change scenarios. In this study, we used the marine teleost silver trevally (Pseudocaranx georgianus), a species currently being explored as a candidate for aquaculture in New Zealand, as a model to study plasticity in gene expression patterns and growth in response to different temperatures. Using a captive study population, temperature conditions were experimentally manipulated for 1 month to mimic seasonal extremes. Phenotypic differences in growth were measured in 400 individuals, and gene expression patterns of pituitary gland and liver were determined in a subset of 100 individuals. Results showed that growth increased 50% in the warmer compared with the colder condition, suggesting that temperature has a large impact on metabolic activities associated with growth. A total of 265,116,678 single-end RNA sequence reads were aligned to the trevally genome, and 28,416 transcript models were developed (27,887 of these had GenBank accessions, and 17,980 unique gene symbols). Further filtering reduced this set to 8597 gene models. 39 and 238 differentially expressed genes (DEGs) were found in the pituitary gland and the liver, respectively (|log2FC| > 0.26, p-value < 0.05). Of these, 6 DEGs showed a common expression pattern between both tissues, all involved in housekeeping functions. Temperature-modulated growth responses were linked to major pathways affecting metabolism, cell regulation and signalling, previously shown to be important for temperature tolerance in other fish species. An interesting finding of this study was that genes linked to the reproductive system were up-regulated in both tissues in the high treatment, indicating the onset of sexual maturation. Few studies have investigated the thermal plasticity of the gene expression in the main organs of the somatotropic axis simultaneously. Our findings indicate that trevally exhibit substantial growth differences and predictable plastic regulatory responses to different temperature conditions. We identified a set of genes that provide a list of candidates for further investigations for selective breeding objectives and how populations may adapt to increasing temperatures.

Differential effects of steroid hormones on levels of broad-sense heritability in a wild bird: possible mechanism of environment × genetic variance interaction?

Genetic variation is one of the key concepts in evolutionary biology and an important prerequisite of evolutionary change. However, we know very little about processes that modulate its levels in wild populations. In particular, we still are to understand why genetic variances often depend on environmental conditions. One of possible environment-sensitive modulators of observed levels of genetic variance are maternal effects. In this study we attempt to experimentally test the hypothesis that maternally transmitted agents (e.g. hormones) may influence the expression of genetic variance in quantitative traits in the offspring. We manipulated the levels of steroid hormones (testosterone and corticosterone) in eggs laid by blue tits in a wild population. Our experimental setup allowed for full crossing of genetic and rearing effects with the experimental manipulation. We observed that birds treated with corticosterone exhibited a significant decrease in broad-sense genetic variance of tarsus length, and an increase in this component in body mass on the 2nd day post-hatching. Our study indicates, that maternally transmitted substances such as hormones may have measurable impact on the levels of genetic variance and hence, on the evolutionary potential of quantitative traits.

Long-lasting effects of chronic exposure to chemical pollution on the hologenome of the Manila clam

Chronic exposure to pollutants affects natural populations, creating specific molecular and biochemical signatures. In the present study, we tested the hypothesis that chronic exposure to pollutants might have substantial effects on the Manila clam hologenome long after removal from contaminated sites. To reach this goal, a highly integrative approach was implemented, combining transcriptome, genetic and microbiota analyses with the evaluation of biochemical and histological profiles of the edible Manila clam Ruditapes philippinarum, as it was transplanted for 6 months from the polluted area of Porto Marghera (PM) to the clean area of Chioggia (Venice lagoon, Italy). One month post-transplantation, PM clams showed several modifications to its resident microbiota, including an overrepresentation of the opportunistic pathogen Arcobacter spp. This may be related to the upregulation of several immune genes in the PM clams, potentially representing a host response to the increased abundance of deleterious bacteria. Six months after transplantation, PM clams demonstrated a lower ability to respond to environmental/physiological stressors related to the summer season, and the hepatopancreas-associated microbiota still showed different compositions among PM and CH clams. This study confirms that different stressors have predictable effects in clams at different biological levels and demonstrates that chronic exposure to pollutants leads to long-lasting effects on the animal hologenome. In addition, no genetic differentiation between samples from the two areas was detected, confirming that PM and CH clams belong to a single population. Overall, the obtained responses were largely reversible and potentially related to phenotypic plasticity rather than genetic adaptation. The results here presented will be functional for the assessment of the environmental risk imposed by chemicals on an economically important bivalve species.

Transcriptome-Wide Gene Expression Plasticity in Stipa grandis in Response to Grazing Intensity Differences

Organisms have evolved effective and distinct adaptive strategies to survive. Stipa grandis is a representative species for studying the grazing effect on typical steppe plants in the Inner Mongolia Plateau. Although phenotypic (morphological and physiological) variations in S. grandis in response to long-term grazing have been identified, the molecular mechanisms underlying adaptations and plastic responses remain largely unknown. Here, we performed a transcriptomic analysis to investigate changes in gene expression of S. grandis under four different grazing intensities. As a result, a total of 2357 differentially expressed genes (DEGs) were identified among the tested grazing intensities, suggesting long-term grazing resulted in gene expression plasticity that affected diverse biological processes and metabolic pathways in S. grandis. DEGs were identified in RNA-Seq and qRT-PCR analyses that indicated the modulation of the Calvin–Benson cycle and photorespiration metabolic pathways. The key gene expression profiles encoding various proteins (e.g., ribulose-1,5-bisphosphate carboxylase/oxygenase, fructose-1,6-bisphosphate aldolase, glycolate oxidase, etc.) involved in these pathways suggest that they may synergistically respond to grazing to increase the resilience and stress tolerance of S. grandis. Our findings provide scientific clues for improving grassland use and protection and identifying important questions to address in future transcriptome studies.

Extensive alternative splicing triggered by mitonuclear mismatch in naturally introgressed Rhinolophus bats

Mitochondrial function needs strong interactions of mitochondrial and nuclear (mitonuclear) genomes, which can be disrupted by mitonuclear mismatch due to mitochondrial DNA (mtDNA) introgression between two formerly isolated populations or taxa. This mitonuclear disruption may cause severe cellular stress in mismatched individuals. Gene expression changes and alternative splicing (AS) are two important transcriptional regulations to respond to environmental or cellular stresses. We previously identified a naturally introgressed population in the intermediate horseshoe bat (Rhinolophus affinis). Individuals from this population belong to R. a. himalayanus and share almost identical nuclear genetic background; however, some of them had mtDNA from another subspecies (R. a. macrurus). With this unique natural system, we examined gene expression changes in six tissues between five mitonuclear mismatched and five matched individuals. A small number of differentially expressed genes (DEGs) were identified, and functional enrichment analysis revealed that most DEGs were related to immune response although some may be involved in response to oxidative stress. In contrast, we identified extensive AS events and alternatively spliced genes (ASGs) between mismatched and matched individuals. Functional enrichment analysis revealed that multiple ASGs were directly or indirectly associated with energy production in mitochondria which is vital for survival of organism. To our knowledge, this is the first study to examine the role of AS in responding to cellular stress caused by mitonuclear mismatch in natural populations. Our results suggest that AS may play a more important role than gene expression regulation in responding to severe environmental or cellular stresses.

The somatic molecular evolution of cancer: Mutation, selection, and epistasis

Cancer progression has been attributed to somatic changes in single-nucleotide variants, copy-number aberrations, loss of heterozygosity, chromosomal instability, epistatic interactions, and the tumor microenvironment. It is not entirely clear which of these changes are essential and which are ancillary to cancer. The dynamic nature of cancer evolution in a patient can be illuminated using several concepts and tools from classical evolutionary biology. Neutral mutation rates in cancer cells are calculable from genomic data such as synonymous mutations, and selective pressures are calculable from rates of fixation occurring beyond the expectation by neutral mutation and drift. However, these cancer effect sizes of mutations are complicated by epistatic interactions that can determine the likely sequence of gene mutations. In turn, longitudinal phylogenetic analyses of somatic cancer progression offer an opportunity to identify key moments in cancer evolution, relating the timing of driver mutations to corresponding landmarks in the clinical timeline. These analyses reveal temporal aspects of genetic and phenotypic change during tumorigenesis and across clinical timescales. Using a related framework, clonal deconvolution, physical locations of clones, and their phylogenetic relations can be used to infer tumor migration histories. Additionally, genetic interactions with the tumor microenvironment can be analyzed with longstanding approaches applied to organismal genotype-by-environment interactions. Fitness landscapes for cancer evolution relating to genotype, phenotype, and environment could enable more accurate, personalized therapeutic strategies. An understanding of the trajectories underlying the evolution of neoplasms, primary, and metastatic tumors promises fundamental advances toward accurate and personalized predictions of therapeutic response.

A quantitative genetics approach to validate lab- versus field-based behavior in novel environments

Conclusions about the adaptive nature of repeatable variation in behavior (i.e., “personality”) are often derived from laboratory-based assays. However, the expression of genetic variation differs between laboratory and field. Laboratory-based behavior might not predict field-based behavior thus, cross-context validation is required. We estimated the cross-context correlation between behavior expressed by wild great tits (Parus major) in established laboratory versus field novel environment assays. Both assays have been used as proxies for “exploration tendency.” Behavior in both contexts had similar repeatability (R = 0.35 vs. 0.37) but differed in heritability (h2 = 0.06 vs. 0.23), implying differences in selection pressures. Unexpectedly, there was no cross-context correlation. Laboratory- and field-based behavior thus reflected expressions of two distinct underlying characters. Post hoc simulations revealed that sampling bias did not explain the lack of correlation. Laboratory-based behavior may reflect fear and exploration, but field-based behavior may reflect escape behavior instead, though other functional interpretations cannot be excluded. Thus, in great tits, activity expressed in laboratory versus field novel environment assays is modulated by multiple quasi-independent characters. The lack of cross-context correlation shown here may also apply to other setups, other repeatable behaviors, and other taxa. Our study thus implies care should be taken in labeling behaviors prior to firm validation studies.

Adaptive and maladaptive expression plasticity underlying herbicide resistance in an agricultural weed

Plastic phenotypic responses to environmental change are common, yet we lack a clear understanding of the fitness consequences of these plastic responses. Here, we use the evolution of herbicide resistance in the common morning glory (Ipomoea purpurea) as a model for understanding the relative importance of adaptive and maladaptive gene expression responses to herbicide. Specifically, we compare leaf gene expression changes caused by herbicide to the expression changes that evolve in response to artificial selection for herbicide resistance. We identify a number of genes that show plastic and evolved responses to herbicide and find that for the majority of genes with both plastic and evolved responses, plastic responses appear to be adaptive. We also find that selection for herbicide response increases gene expression plasticity. Overall, these results show the importance of adaptive plasticity for herbicide resistance in a common weed and that expression changes in response to strong environmental change can be adaptive.

Predicting whether and how organisms will adapt to environmental change is a crucial goal. However, this goal can be complicated because environmental change can alter traits, in a process called plasticity. The extent and fitness consequences of plasticity will have important effects on the adaptive process. In this study, we use adaptation to herbicide in the agricultural weed, the common morning glory, as a model for understanding the extent and fitness consequences of plasticity in gene expression. We find evidence that gene expression plasticity is adaptive in the presence of herbicide, suggesting that understanding plasticity is crucial for understanding how organisms adapt to new environments.

Species diversity and spatial distribution of CL/VL vectors: assessing bioclimatic effect on expression plasticity of genes possessing vaccine properties isolated from wild-collected sand flies in endemic areas of Iran

Background

Leishmaniasis is one of the ten most important neglected tropical diseases worldwide. Understanding the distribution of vectors of visceral and cutaneous leishmaniasis (VL/CL) is one of the significant strategic frameworks to control leishmaniasis. In this study, the extent of the bioclimatic variability was investigated to recognize a rigorous cartographic of the spatial distribution of VL/CL vectors as risk-maps using ArcGIS modeling system. Moreover, the effect of bioclimatic diversity on the fold change expression of genes possessing vaccine traits (SP15 and LeIF) was evaluated in each bioclimatic region using real-time PCR analysis.

Methods

The Inverse Distance Weighting interpolation method was used to obtain accurate geography map in closely-related distances. Bioclimatic indices were computed and vectors spatial distribution was analyzed in ArcGIS10.3.1 system. Species biodiversity was calculated based on Shannon diversity index using Rv.3.5.3. Expression fold change of SP15 and LeIF genes was evaluated using cDNA synthesis and RT-qPCR analysis.

Results

Frequency of Phlebotomus papatasi was predominant in plains areas of Mountainous bioclimate covering the CL hot spots. Mediterranean region was recognized as an important bioclimate harboring prevalent patterns of VL vectors. Semi-arid bioclimate was identified as a major contributing factor to up-regulate salivary-SP15 gene expression (P = 0.0050, P < 0.05). Also, Mediterranean bioclimate had considerable effect on up-regulation of Leishmania-LeIF gene in gravid and semi-gravid P. papatasi population (P = 0.0109, P < 0.05).

Conclusions

The diversity and spatial distribution of CL/VL vectors associated with bioclimatic regionalization obtained in our research provide epidemiological risk maps and establish more effectively control measures against leishmaniasis. Oscillations in gene expression indicate that each gene has its own features, which are profoundly affected by bioclimatic characteristics and physiological status of sand flies. Given the efficacy of species-specific antigens for vaccine production, it is essential to consider bioclimatic factors that have a fundamental role in affecting the regulatory regions of environmentally responsive loci for genes used in vaccine design.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06129-0.

A framework for understanding gene expression plasticity and its influence on stress tolerance

Phenotypic plasticity can serve as a stepping stone towards adaptation. Recently, studies have shown that gene expression contributes to emergent stress responses such as thermal tolerance, with tolerant and susceptible populations showing distinct transcriptional profiles. However, given the dynamic nature of gene expression, interpreting transcriptomic results in a way that elucidates the functional connection between gene expression and the observed stress response is challenging. Here, we present a conceptual framework to guide interpretation of gene expression reaction norms in the context of stress tolerance. We consider the evolutionary and adaptive potential of gene expression reaction norms and discuss the influence of sampling timing, transcriptomic resilience, as well as complexities related to life history when interpreting gene expression dynamics and how these patterns relate to host tolerance. We highlight corals as a case study to demonstrate the value of this framework for non-model systems. As species face rapidly changing environmental conditions, modulating gene expression can serve as a mechanistic link from genetic and cellular processes to the physiological responses that allow organisms to thrive under novel conditions. Interpreting how or whether a species can employ gene expression plasticity to ensure short-term survival will be critical for understanding the global impacts of climate change across diverse taxa.

Rapid evolutionary changes in gene expression in response to climate fluctuations

There is now abundant evidence of rapid evolution in natural populations, but the genetic mechanisms of these changes remain unclear. One possible route to rapid evolution is through changes in the expression of genes that influence traits under selection. We examined contemporary evolutionary gene expression changes in plant populations responding to environmental fluctuations. We compared genome‐wide gene expression, using RNA‐seq, in two populations of Brassica rapa collected over four time points between 1997 and 2014, during which precipitation in southern California fluctuated dramatically and phenotypic and genotypic changes occurred. By combining transcriptome profiling with the resurrection approach, we directly examined evolutionary changes in gene expression over time. For both populations, we found a substantial number of differentially expressed genes between generations, indicating rapid evolution in the expression of many genes. Using existing gene annotations, we found that many changes occurred in genes involved in regulating stress responses and flowering time. These appeared related to the fluctuations in precipitation and were potentially adaptive. However, the evolutionary changes in gene expression differed across generations within and between populations, indicating largely independent evolutionary trajectories across populations and over time. Our study provides strong evidence for rapid evolution in gene expression, and indicates that changes in gene expression can be one mechanism of rapid evolutionary responses to selection episodes. This study also illustrates that combining resurrection studies with transcriptomics is a powerful approach for investigating evolutionary changes at the gene regulatory level, and will provide new insights into the genetic basis of contemporary evolution.

see also the Perspective by Emily B. Josephs.

Restoring ancestral phenotypes is a general pattern in gene expression evolution during adaptation to new environments in Tribolium castaneum

Plasticity and evolution are two processes allowing populations to respond to environmental changes, but how both are related and impact each other remains controversial. We studied plastic and evolutionary responses in gene expression of Tribolium castaneum after exposure of the beetles to new environments that differed from ancestral conditions in temperature, humidity or both. Using experimental evolution with 10 replicated lines per condition, we were able to demonstrate adaptation after 20 generations. We measured whole-transcriptome gene expression with RNA-sequencing to infer evolutionary and plastic changes. We found more evidence for changes in mean expression (shift in the intercept of reaction norms) in adapted lines than for changes in plasticity (shifts in slopes). Plasticity was mainly preserved in selected lines and was responsible for a large part of the phenotypic divergence in expression between ancestral and new conditions. However, we found that genes with the largest evolutionary changes in expression also evolved reduced plasticity and often showed expression levels closer to the ancestral stage. Results obtained in the three different conditions were similar, suggesting that restoration of ancestral expression levels during adaptation is a general evolutionary pattern. With a larger sample in the most stressful condition, we were able to detect a positive correlation between the proportion of genes with reversion of the ancestral plastic response and mean fitness per selection line.

Transcriptional Control of Quality Differences in the Lipid-Based Cuticle Barrier in Drosophila suzukii and Drosophila melanogaster

Cuticle barrier efficiency in insects depends largely on cuticular lipids. To learn about the evolution of cuticle barrier function, we compared the basic properties of the cuticle inward and outward barrier function in adults of the fruit flies Drosophila suzukii and Drosophila melanogaster that live on fruits sharing a similar habitat. At low air humidity, D. suzukii flies desiccate faster than D. melanogaster flies. We observed a general trend indicating that in this respect males are less robust than females in both species. Xenobiotics penetration occurs at lower temperatures in D. suzukii than in D. melanogaster. Likewise, D. suzukii flies are more susceptible to contact insecticides than D. melanogaster flies. Thus, both the inward and outward barriers of D. suzukii are less efficient. Consistently, D. suzukii flies have less cuticular hydrocarbons (CHC) that participate as key components of the cuticle barrier. Especially, the relative amounts of branched and desaturated CHCs, known to enhance desiccation resistance, show reduced levels in D. suzukii. Moreover, the expression of snustorr (snu) that encodes an ABC transporter involved in barrier construction and CHC externalization, is strongly suppressed in D. suzukii. Hence, species-specific genetic programs regulate the quality of the lipid-based cuticle barrier in these two Drosophilae. Together, we conclude that the weaker inward and outward barriers of D. suzukii may be partly explained by differences in CHC composition and by a reduced Snu-dependent transport rate of CHCs to the surface. In turn, this suggests that snu is an ecologically adjustable and therefore relevant gene in cuticle barrier efficiency.

Adaptation of plasticity to projected maximum temperatures and across climatically defined bioregions

Resilience to environmental stressors due to climate warming is influenced by local adaptations, including plastic responses. The recent literature has focused on genomic signatures of climatic adaptation, but little is known about how plastic capacity may be influenced by biogeographic and evolutionary processes. We investigate phenotypic plasticity as a target of climatic selection, hypothesizing that lineages that evolved in warmer climates will exhibit greater plastic adaptive resilience to upper thermal stress. This was experimentally tested by comparing transcriptomic responses within and among temperate, subtropical, and desert ecotypes of Australian rainbowfish subjected to contemporary and projected summer temperatures. Critical thermal maxima were estimated, and ecological niches delineated using bioclimatic modeling. A comparative phylogenetic expression variance and evolution model was used to assess plastic and evolved changes in gene expression. Although 82% of all expressed genes were found in the three ecotypes, they shared expression patterns in only 5 out of 236 genes that responded to the climate change experiment. A total of 532 genes showed signals of adaptive (i.e., genetic-based) plasticity due to ecotype-specific directional selection, and 23 of those responded to projected summer temperatures. Network analyses demonstrated centrality of these genes in thermal response pathways. The greatest adaptive resilience to upper thermal stress was shown by the subtropical ecotype, followed by the desert and temperate ecotypes. Our findings indicate that vulnerability to climate change will be highly influenced by biogeographic factors, emphasizing the value of integrative assessments of climatic adaptive traits for accurate estimation of population and ecosystem responses.

Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species

The wild currant tomato Solanum pimpinellifolium inhabits a wide range of abiotic habitats across its native range of Ecuador and Peru. Although it has served as a key genetic resource for the improvement of domestic cultivars, little is known about the genetic basis of traits underlying local adaptation in this species, nor what abiotic variables are most important for driving differentiation. Here we use redundancy analysis (RDA) and other multivariate statistical methods (structural equation modelling [SEM] and generalized dissimilarity modelling [GDM]) to quantify the relationship of genomic variation (6,830 single nucleotide polymorphisms [SNPs]) with climate and geography, among 140 wild accessions. RDA, SEM and GDM each identified environment as explaining more genomic variation than geography, suggesting that local adaptation to heterogeneous abiotic habitats may be an important source of genetic diversity in this species. Environmental factors describing temporal variation in precipitation and evaporative demand explained the most SNP variation among accessions, indicating that these forces may represent key selective agents. Lastly, by studying how SNP-environment associations vary throughout the genome (44,064 SNPs), we mapped the location and investigated the functions of loci putatively contributing to climatic adaptations. Together, our findings indicate an important role for selection imposed by the abiotic environment in driving genomic differentiation between populations.

Rapid evolution in plant-microbe interactions - a molecular genomics perspective

Rapid (co-)evolution at multiple timescales is a hallmark of plant-microbe interactions. The mechanistic basis for the rapid evolution largely rests on the features of the genomes of the interacting partners involved. Here, we review recent insights into genomic characteristics and mechanisms that enable rapid evolution of both plants and phytopathogens. These comprise fresh insights in allelic series of matching pairs of resistance and avirulence genes, the generation of novel pathogen effectors, the recently recognised small RNA warfare, and genomic aspects of secondary metabolite biosynthesis. In addition, we discuss the putative contributions of permissive host environments, transcriptional plasticity and the role of ploidy on the interactions. We conclude that the means underlying the rapid evolution of plant-microbe interactions are multifaceted and depend on the particular nature of each interaction.

Transcriptome analysis reveals plasticity in gene regulation due to environmental cues in Primula sikkimensis, a high altitude plant species

BACKGROUND

Studying plasticity in gene expression in natural systems is crucial, for predicting and managing the effects of climate change on plant species. To understand the contribution of gene expression level variations to abiotic stress compensation in a Himalaya plant (Primula sikkimensis), we carried out a transplant experiment within (Ambient), and beyond (Below Ambient and Above Ambient) the altitudinal range limit of species. We sequenced nine transcriptomes (three each from each altitudinal range condition) using Illumina sequencing technology. We compared the fitness variation of transplants among three transplant conditions.

RESULTS

A large number of significantly differentially expressed genes (DEGs) between below ambient versus ambient (109) and above ambient versus ambient (85) were identified. Transcripts involved in plant growth and development were mostly up-regulated in below ambient conditions. Transcripts involved in signalling, defence, and membrane transport were mostly up-regulated in above ambient condition. Pathway analysis revealed that most of the genes involved in metabolic processes, secondary metabolism, and flavonoid biosynthesis were differentially expressed in below ambient conditions, whereas most of the genes involved in photosynthesis and plant hormone signalling were differentially expressed in above ambient conditions. In addition, we observed higher reproductive fitness in transplant individuals at below ambient condition compared to above ambient conditions; contrary to what we expect from the cold adaptive P. sikkimensis plants.

CONCLUSIONS

We reveal P. sikkimensis's capacity for rapid adaptation to climate change through transcriptome variation, which may facilitate the phenotypic plasticity observed in morphological and life history traits. The genes and pathways identified provide a genetic resource for understanding the temperature stress (both the hot and cold stress) tolerance mechanism of P. sikkimensis in their natural environment.

Empirical measures of mutational effects define neutral models of regulatory evolution in Saccharomyces cerevisiae

Understanding how phenotypes evolve requires disentangling the effects of mutation generating new variation from the effects of selection filtering it. Tests for selection frequently assume that mutation introduces phenotypic variation symmetrically around the population mean, yet few studies have tested this assumption by deeply sampling the distributions of mutational effects for particular traits. Here, we examine distributions of mutational effects for gene expression in the budding yeast Saccharomyces cerevisiae by measuring the effects of thousands of point mutations introduced randomly throughout the genome. We find that the distributions of mutational effects differ for the 10 genes surveyed and are inconsistent with normality. For example, all 10 distributions of mutational effects included more mutations with large effects than expected for normally distributed phenotypes. In addition, some genes also showed asymmetries in their distribution of mutational effects, with new mutations more likely to increase than decrease the gene's expression or vice versa. Neutral models of regulatory evolution that take these empirically determined distributions into account suggest that neutral processes may explain more expression variation within natural populations than currently appreciated.

Environmental and Evolutionary Drivers of the Modular Gene Regulatory Network Underlying Phenotypic Plasticity for Stress Resistance in the Nematode Caenorhabditis remanei

Organisms can cope with stressful environments via a combination of phenotypic plasticity at the individual level and adaptation at the population level. Changes in gene expression can play an important role in both. Significant advances in our understanding of gene regulatory plasticity and evolution have come from comparative studies in the field and laboratory. Experimental evolution provides another powerful path by which to learn about how differential regulation of genes and pathways contributes to both acclimation and adaptation. Here we present results from one such study using the nematode Caenorhabditis remanei We selected one set of lines to withstand heat stress and another oxidative stress. We then compared transcriptional responses to acute heat stress of both and an unselected control to the ancestral population using a weighted gene coexpression network analysis, finding that the transcriptional response is primarily dominated by a plastic response that is shared in the ancestor and all evolved populations. In addition, we identified several modules that respond to artificial selection by (1) changing the baseline level of expression, (2) altering the magnitude of the plastic response, or (3) a combination of the two. Our findings therefore reveal that while patterns of transcriptional response can be perturbed with short bouts of intense selection, the overall ancestral structure of transcriptional plasticity is largely maintained over time.

Modeling Gene-Environment Interaction for the Risk of Non-hodgkin Lymphoma

Background: Non-hodgkin lymphoma (NHL) is one of the most common and deadly cancers. There is limited analysis of gene-environment interactions for the risk of NHL. This study intends to explore the interactions between genetic variants and environmental factors, and how they contribute to NHL risk.

Methods: A case-control study was performed in Shanghai, China. The cases were diagnosed between 2003 and 2008 with patients aged 18 years or older. Samples and SNPs which did not satisfy quality control were excluded from the analysis. Weighted and unweighted genetic risk scores (GRS) and environmental risk scores were generated using clustering analysis algorithm. Univariate and multivariable logistic regression analyses were conducted. Moreover, genetics and environment interactions (G × E) were tested on the NHL cases and controls.

Results: After quality control, there are 22 SNPs, 11 environmental variables and 5 demographical variables to be explored. For logistic regression analyses, 5 SNPs (rs1800893, rs4251961, rs1800630, rs13306698, rs1799931) and environmental tobacco smoking showed statistically significant associations with the risk of NHL. Odds ratio (OR) and 95% confidence interval (CI) was 10.82 (4.34–28.88) for rs13306698, 2.84 (1.66–4.95) for rs1800893, and 2.54 (1.43–4.58) for rs4251961. For G × E analysis, the interaction between smoking and dichotomized weighted GRS showed statistically significant association with NHL (OR = 0.23, 95% CI = [0.09, 0.61]).

Conclusions: Several genetic and environmental risk factors and their interactions associated with the risk of NHL have been identified. Replication in other cohorts is needed to validate the results.

Transcriptome response of Atlantic salmon (Salmo salar) to competition with ecologically similar non-native species

Non-native species may be introduced either intentionally or unintentionally, and their impact can range from benign to highly disruptive. Non-native salmonids were introduced into Lake Ontario, Canada, to provide recreational fishing opportunities; however, the establishment of those species has been proposed as a significant barrier to the reintroduction of native Atlantic salmon (Salmo salar) due to intense interspecific competition. In this study, we compared population differences of Atlantic salmon in transcriptome response to interspecific competition. We reared Atlantic salmon from two populations (LaHave River and Sebago Lake) with fish of each of three non-native salmonids (Chinook salmon Oncorhynchus tshawytscha, rainbow trout O. mykiss, and brown trout S. trutta) in artificial streams. We used RNA-seq to assess transcriptome differences between the Atlantic salmon populations and the responses of these populations to the interspecific competition treatments after 10 months of competition in the stream tanks. We found that population differences in gene expression were generally greater than the effects of interspecific competition. Interestingly, we found that the two Atlantic salmon populations exhibited similar responses to interspecific competition based on functional gene ontologies, but the specific genes within those ontologies were different. Our transcriptome analyses suggest that the most stressful competitor (as measured by the highest number of differentially expressed genes) differs between the two study populations. Our transcriptome characterization highlights the importance of source population selection for conservation applications, as organisms with different evolutionary histories can possess different transcriptional responses to the same biotic stressors. The results also indicate that generalized predictions of the response of native species to interactions with introduced species may not be appropriate without incorporating potential population-specific response to introduced species.

Cis-Regulatory Divergence in Gene Expression between Two Thermally Divergent Yeast Species

Gene regulation is a ubiquitous mechanism by which organisms respond to their environment. While organisms are often found to be adapted to the environments they experience, the role of gene regulation in environmental adaptation is not often known. In this study, we examine divergence in cis-regulatory effects between two Saccharomycesspecies, S. cerevisiaeand S. uvarum, that have substantially diverged in their thermal growth profile. We measured allele specific expression (ASE) in the species’ hybrid at three temperatures, the highest of which is lethal to S. uvarumbut not the hybrid or S. cerevisiae. We find that S. uvarumalleles can be expressed at the same level as S. cerevisiaealleles at high temperature and most cis-acting differences in gene expression are not dependent on temperature. While a small set of 136 genes show temperature-dependent ASE, we find no indication that signatures of directional cis-regulatory evolution are associated with temperature. Within promoter regions we find binding sites enriched upstream of temperature responsive genes, but only weak correlations between binding site and expression divergence. Our results indicate that temperature divergence between S. cerevisiaeand S. uvarumhas not caused widespread divergence in cis-regulatory activity, but point to a small subset of genes where the species’ alleles show differences in magnitude or opposite responses to temperature. The difficulty of explaining divergence in cis-regulatory sequences with models of transcription factor binding sites and nucleosome positioning highlights the importance of identifying mutations that underlie cis-regulatory divergence between species.

Effects of mutation and selection on plasticity of a promoter activity in Saccharomyces cerevisiae

Phenotypic plasticity is an evolvable property of biological systems that can arise from environment-specific regulation of gene expression. To better understand the evolutionary and molecular mechanisms that give rise to plasticity in gene expression, we quantified the effects of 235 single-nucleotide mutations in the Saccharomyces cerevisiae TDH3 promoter (P_TDH3 ) on the activity of this promoter in media containing glucose, galactose, or glycerol as a carbon source. We found that the distributions of mutational effects differed among environments because many mutations altered the plastic response exhibited by the wild-type allele. Comparing the effects of these mutations with the effects of 30 P_TDH3 polymorphisms on expression plasticity in the same environments provided evidence of natural selection acting to prevent the plastic response in P_TDH3 activity between glucose and galactose from becoming larger. The largest changes in expression plasticity were observed between fermentable (glucose or galactose) and nonfermentable (glycerol) carbon sources and were caused by mutations located in the RAP1 and GCR1 transcription factor binding sites. Mutations altered expression plasticity most frequently between the two fermentable environments, with mutations causing significant changes in plasticity between glucose and galactose distributed throughout the promoter, suggesting they might affect chromatin structure. Taken together, these results provide insight into the molecular mechanisms underlying gene-by-environment interactions affecting gene expression as well as the evolutionary dynamics affecting natural variation in plasticity of gene expression.

Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut

Recent studies of interactions between hosts and their resident microbes have revealed important ecological and evolutionary consequences that emerge from these complex interspecies relationships, including diseases that occur when the interactions go awry. Given the preponderance of these interactions, we hypothesized that effects of the microbiota on gene expression in the developing gut—an important aspect of host biology—would be pervasive, and that these effects would be both comparable in magnitude to and contingent on effects of the host genetic background. To evaluate the effects of the microbiota, host genotype, and their interaction on gene expression in the gut of a genetically diverse, gnotobiotic host model, the threespine stickleback (Gasterosteus aculeatus), we compared RNA-seq data among 84 larval fish. Surprisingly, we found that stickleback population and family differences explained substantially more gene expression variation than the presence of microbes. Expression levels of 72 genes, however, were affected by our microbiota treatment. These genes, including many associated with innate immunity, comprise a tractable subset of host genetic factors for precise, systems-level study of host–microbe interactions in the future. Importantly, our data also suggest subtle signatures of a statistical interaction between host genotype and the microbiota on expression patterns of genetic pathways associated with innate immunity, coagulation and complement cascades, focal adhesion, cancer, and peroxisomes. These genotype-by-environment interactions may prove to be important leads to the understanding of host genetic mechanisms commonly at the root of sometimes complex molecular relationships between hosts and their resident microbes.

The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi

Changes in gene expression have been hypothesized to play an important role in the evolution of divergent morphologies. To test this hypothesis in a model system, we examined differences in fruiting body morphology of five filamentous fungi in the Sordariomycetes, culturing them in a common garden environment and profiling genome-wide gene expression at five developmental stages. We reconstructed ancestral gene expression phenotypes, identifying genes with the largest evolved increases in gene expression across development. Conducting knockouts and performing phenotypic analysis in two divergent species typically demonstrated altered fruiting body development in the species that had evolved increased expression. Our evolutionary approach to finding relevant genes proved far more efficient than other gene deletion studies targeting whole genomes or gene families. Combining gene expression measurements with knockout phenotypes facilitated the refinement of Bayesian networks of the genes underlying fruiting body development, regulation of which is one of the least understood processes of multicellular development.

Genetic architecture of gene transcription in two Atlantic salmon (Salmo salar) populations

Gene expression regulation has an important role in short-term acclimation and long-term adaptation to changing environments. However, the genetic architecture of gene expression has received much less attention than that of traditional phenotypic traits. In this study, we used a 5 × 5 full-factorial breeding design within each of two Atlantic salmon (Salmo salar) populations to characterize the genetic architecture of gene transcription. The two populations (LaHave and Sebago) are being used for reintroduction efforts into Lake Ontario, Canada. We used high-throughput quantitative real-time PCR to measure gene transcription levels for 22 genes in muscle tissue of Atlantic salmon fry. We tested for population differences in gene transcription and partitioned the transcription variance into additive genetic, non-additive genetic and maternal effects within each population. Interestingly, average additive genetic effects for gene transcription were smaller than those reported for traditional phenotypic traits in salmonids, suggesting that the evolutionary potential of gene transcription is lower than that of traditional traits. Contrary to expectations for early life stage traits, maternal effects were small. In general, the LaHave population had higher additive genetic effects for gene transcription than the Sebago population had, indicating that the LaHave fish have a higher adaptive potential to respond to the novel selection pressures associated with reintroduction into a novel environment. This study highlights not only the profound variation in gene transcription possible among salmonid populations but also the among-population variation in the underlying genetic architecture of such traits.

Animal tracking meets migration genomics: transcriptomic analysis of a partially migratory bird species

Seasonal migration is a widespread phenomenon, which is found in many different lineages of animals. This spectacular behaviour allows animals to avoid seasonally adverse environmental conditions to exploit more favourable habitats. Migration has been intensively studied in birds, which display astonishing variation in migration strategies, thus providing a powerful system for studying the ecological and evolutionary processes that shape migratory behaviour. Despite intensive research, the genetic basis of migration remains largely unknown. Here, we used state-of-the-art radio-tracking technology to characterize the migratory behaviour of a partially migratory population of European blackbirds (Turdus merula) in southern Germany. We compared gene expression of resident and migrant individuals using high-throughput transcriptomics in blood samples. Analyses of sequence variation revealed a nonsignificant genetic structure between blackbirds differing by their migratory phenotype. We detected only four differentially expressed genes between migrants and residents, which might be associated with hyperphagia, moulting and enhanced DNA replication and transcription. The most pronounced changes in gene expression occurred between migratory birds depending on when, in relation to their date of departure, blood was collected. Overall, the differentially expressed genes detected in this analysis may play crucial roles in determining the decision to migrate, or in controlling the physiological processes required for the onset of migration. These results provide new insights into, and testable hypotheses for, the molecular mechanisms controlling the migratory phenotype and its underlying physiological mechanisms in blackbirds and other migratory bird species.

Gene expression plasticity as a mechanism of coral adaptation to a variable environment

Local adaptation is ubiquitous, but the molecular mechanisms that give rise to this ecological phenomenon remain largely unknown. A year-long reciprocal transplant of mustard hill coral (Porites astreoides) between a highly environmentally variable inshore habitat and a more stable offshore habitat demonstrated that populations exhibit phenotypic signatures that are consistent with local adaptation. We characterized the genomic basis of this adaptation in both coral hosts and their intracellular symbionts (Symbiodinium sp.) using genome-wide gene expression profiling. Populations differed primarily in their capacity for plasticity: following transplantation to a novel environment, inshore-origin coral expression profiles became significantly more similar to the local population's profiles than those in offshore-origin corals. Furthermore, elevated plasticity of the environmental stress response expression was correlated with lower susceptibility to a natural summer bleaching event, suggesting that plasticity is adaptive in the inshore environment. Our results reveal a novel genomic mechanism of resilience to a variable environment, demonstrating that corals are capable of a more diverse molecular response to stress than previously thought.

Immune genes and divergent antimicrobial peptides in flies of the subgenus Drosophila

Background

Drosophila is an important model for studying the evolution of animal immunity, due to the powerful genetic tools developed for D. melanogaster. However, Drosophila is an incredibly speciose lineage with a wide range of ecologies, natural histories, and diverse natural enemies. Surprisingly little functional work has been done on immune systems of species other than D. melanogaster. In this study, we examine the evolution of immune genes in the speciose subgenus Drosophila, which diverged from the subgenus Sophophora (that includes D. melanogaster) approximately 25–40 Mya. We focus on D. neotestacea, a woodland species used to study interactions between insects and parasitic nematodes, and combine recent transcriptomic data with infection experiments to elucidate aspects of host immunity.

Results

We found that the vast majority of genes involved in the D. melanogaster immune response are conserved in D. neotestacea, with a few interesting exceptions, particularly in antimicrobial peptides (AMPs); until recently, AMPs were not thought to evolve rapidly in Drosophila. Unexpectedly, we found a distinct diptericin in subgenus Drosophila flies that appears to have evolved under diversifying (positive) selection. We also describe the presence of the AMP drosocin, which was previously thought to be restricted to the subgenus Sophophora, in the subgenus Drosophila. We challenged two subgenus Drosophila species, D. neotestacea and D. virilis with bacterial and fungal pathogens and quantified AMP expression.

Conclusions

While diptericin in D. virilis was induced by exposure to gram-negative bacteria, it was not induced in D. neotestacea, showing that conservation of immune genes does not necessarily imply conservation of the realized immune response. Our study lends support to the idea that invertebrate AMPs evolve rapidly, and that Drosophila harbor a diverse repertoire of AMPs with potentially important functional consequences.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0805-y) contains supplementary material, which is available to authorized users.

Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes

Little is known of how gene expression and its plasticity evolves as populations adapt to different environmental regimes. Expression is expected to evolve adaptively in all populations but only those populations experiencing environmental heterogeneity are expected to show adaptive evolution of plasticity. We measured the transcriptome in a cadmium-enriched diet and a salt-enriched diet for experimental populations of Drosophila melanogaster that evolved for ~130 generations in one of four selective regimes: two constant regimes maintained in either cadmium or salt diets and two heterogeneous regimes that varied either temporally or spatially between the two diets. For populations evolving in constant regimes, we find a strong signature of counter-gradient evolution; the evolved expression differences between populations adapted to alternative diets is opposite to the plastic response of the ancestral population that is naïve to both diets. Based on expression patterns in the ancestral populations, we identify a set of genes for which we predict selection in heterogeneous regimes to result in increases in plasticity and we find the expected pattern. In contrast, a set of genes where we predicted reduced plasticity did not follow expectation. Nonetheless, both gene sets showed a pattern consistent with adaptive expression evolution in heterogeneous regimes, highlighting the difference between observing “optimal” plasticity and improvements in environment-specific expression. Looking across all genes, there is evidence in all regimes of differences in biased allele expression across environments (“allelic plasticity”) and this is more common among genes with plasticity in total expression.

Different developmental environments change how genes are expressed and what phenotypes are produced. Here we examine how the responsiveness of gene expression to different environments (“expression plasticity”) evolves in populations adapted to constant environments or heterogeneous ones (temporal or spatial heterogeneity) using experimental populations of D. melanogaster. We find the plastic response of the ancestral population that is naïve to both environments is generally opposed by the evolved differences between populations adapted to alternative environments. Populations that live in heterogeneous environments show evidence of adaptive expression evolution in genes predicted to evolve changes in plasticity.

Thermal plasticity in Drosophila melanogaster populations from eastern Australia: quantitative traits to transcripts

The flexibility afforded to genotypes in different environments by phenotypic plasticity is of interest to biologists studying thermal adaptation because of the thermal lability of many traits. Differences in thermal performance and reaction norms can provide insight into the evolution of thermal adaptation to explore broader questions such as species distributions and persistence under climate change. One approach is to study the effects of temperature on fitness, morphological and more recently gene expression traits in populations from different climatic origins. The diverse climatic conditions experienced by Drosophila melanogaster along the eastern Australian temperate-tropical gradient are ideal given the high degree of continuous trait differentiation, but reaction norm variation has not been well studied in this system. Here, we reared a tropical and temperate population from the ends of the gradient over six developmental temperatures and examined reaction norm variation for five quantitative traits including thermal performance for fecundity, and reaction norms for thermotolerance, body size, viability and 23 transcript-level traits. Despite genetic variation for some quantitative traits, we found no differentiation between the populations for fecundity thermal optima and breadth, and the reaction norms for the other traits were largely parallel, supporting previous work suggesting that thermal evolution occurs by changes in trait means rather than by reaction norm shifts. We examined reaction norm variation in our expanded thermal regime for a gene set shown to previously exhibit GxE for expression plasticity in east Australian flies, as well as key heat-shock genes. Although there were differences in curvature between the populations suggesting a higher degree of thermal plasticity in expression patterns than for the quantitative traits, we found little evidence to support a role for genetic variation in maintaining expression plasticity.

Differential expression profiles of the salivary proteins SP15 and SP44 from Phlebotomus papatasi

Background

Sand fly saliva has been shown to help parasite establishment and to induce immune responses in vertebrate hosts. In the current study, we investigated the pattern of expression of two Phlebotomus papatasi salivary transcripts in specific physiological and seasonal conditions at a hyperendemic area of zoonotic cutaneous leishmaniasis (ZCL) in Iran.

Methods

Sand flies were collected during 2012–2013, and grouped according to physiological stages such as unfed, fed, semi-gravid, gravid, parous, nulliparous, infected or non-infected with Leishmania major and also based on the season in which they were collected. Quantitative Real-Time PCR was applied for assessment of the expression of two relevant salivary transcripts, PpSP15 and PpSP44, associated to protection from and exacerbation of ZCL, respectively.

Results

The expression of PpSP15 and PpSP44 transcripts was significantly up-regulated (1.74 and 1.4 folds, respectively) in blood fed compared to unfed flies. Among four groups of fed, unfed, semi-gravid and gravid flies, the lowest levels of PpSP15 and PpSP44 expression were observed in gravid flies. Additionally, the expression levels of both PpSP15 and PpSP44 transcripts in P. papatasi collected during summer were significantly up-regulated (3.7 and 4.4 folds, respectively) compared to spring collections. In addition, the PpSP15 transcript exhibited a significant up-regulation (P < 0.05) in non-infected flies compared to those infected with L. major.

Conclusions

This study contributes to our knowledge of the differential expression of salivary genes among different groups within a P. papatasi population under natural field conditions. Cutaneous and visceral leishmaniasis are of public health importance in many parts of Iran and neighbouring countries where P. papatasi is the proven and dominant sand fly vector for ZCL, the most prevalent and endemic form of the disease in Iran. Therefore, the current study could be helpful in understanding the influence of salivary genes on Leishmania transmission by phlebotomine sand flies. Our findings demonstrate the differential expression of salivary transcripts under various physiological conditions potentially influencing the sand fly capacity for parasite transmission as well as the outcome of disease.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1633-z) contains supplementary material, which is available to authorized users.

Age-related association of venom gene expression and diet of predatory gastropods

Background

Venomous organisms serve as wonderful systems to study the evolution and expression of genes that are directly associated with prey capture. To evaluate the relationship between venom gene expression and prey utilization, we examined these features among individuals of different ages of the venomous, worm-eating marine snail Conus ebraeus. We determined expression levels of six genes that encode venom components, used a DNA-based approach to evaluate the identity of prey items, and compared patterns of venom gene expression and dietary specialization.

Results

C. ebraeus exhibits two major shifts in diet with age—an initial transition from a relatively broad dietary breadth to a narrower one and then a return to a broader diet. Venom gene expression patterns also change with growth. All six venom genes are up-regulated in small individuals, down-regulated in medium-sized individuals, and then either up-regulated or continued to be down-regulated in members of the largest size class. Venom gene expression is not significantly different among individuals consuming different types of prey, but instead is coupled and slightly delayed with shifts in prey diversity.

Conclusion

These results imply that changes in gene expression contribute to intraspecific variation of venom composition and that gene expression patterns respond to changes in the diversity of food resources during different growth stages.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0592-5) contains supplementary material, which is available to authorized users.

Effects of Gene Duplication, Positive Selection, and Shifts in Gene Expression on the Evolution of the Venom Gland Transcriptome in Widow Spiders

Gene duplication and positive selection can be important determinants of the evolution of venom, a protein-rich secretion used in prey capture and defense. In a typical model of venom evolution, gene duplicates switch to venom gland expression and change function under the action of positive selection, which together with further duplication produces large gene families encoding diverse toxins. Although these processes have been demonstrated for individual toxin families, high-throughput multitissue sequencing of closely related venomous species can provide insights into evolutionary dynamics at the scale of the entire venom gland transcriptome. By assembling and analyzing multitissue transcriptomes from the Western black widow spider and two closely related species with distinct venom toxicity phenotypes, we do not find that gene duplication and duplicate retention is greater in gene families with venom gland biased expression in comparison with broadly expressed families. Positive selection has acted on some venom toxin families, but does not appear to be in excess for families with venom gland biased expression. Moreover, we find 309 distinct gene families that have single transcripts with venom gland biased expression, suggesting that the switching of genes to venom gland expression in numerous unrelated gene families has been a dominant mode of evolution. We also find ample variation in protein sequences of venom gland–specific transcripts, lineage-specific family sizes, and ortholog expression among species. This variation might contribute to the variable venom toxicity of these species.

Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses

Differentially evolved responses to various stress conditions in plants are controlled by complex regulatory circuits of transcriptional activators, and repressors, such as transcription factors (TFs). To understand the general and condition-specific activities of the TFs and their regulatory relationships with the target genes (TGs), we have used a homogeneous stress gene expression dataset generated on ten natural ecotypes of the model plant Arabidopsis thaliana, during five single and six combined stress conditions. Knowledge-based profiles of binding sites for 25 stress-responsive TF families (187 TFs) were generated and tested for their enrichment in the regulatory regions of the associated TGs. Condition-dependent regulatory sub-networks have shed light on the differential utilization of the underlying network topology, by stress-specific regulators and multifunctional regulators. The multifunctional regulators maintain the core stress response processes while the transient regulators confer the specificity to certain conditions. Clustering patterns of transcription factor binding sites (TFBS) have reflected the combinatorial nature of transcriptional regulation, and suggested the putative role of the homotypic clusters of TFBS towards maintaining transcriptional robustness against cis-regulatory mutations to facilitate the preservation of stress response processes. The Gene Ontology enrichment analysis of the TGs reflected sequential regulation of stress response mechanisms in plants.