Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex

Differences in alternative splicing events in the adaptive strategies of two Daphnia galeata genotypes induced by fish kairomones

BACKGROUND

Daphnia galeata is a suitable model organism for investigating predator-induced defense. Genes and pathways exhibiting differential expression between fish kairomone-treated and untreated groups in D. galeata have been identified. However, understanding of the significance of alternative splicing, a crucial process of the regulation of gene expression in eukaryotes, to this mechanism remains limited. This study measured life-history traits and conducted short-read RNA sequencing and long-read isoform sequencing of two Korean D. galeata genotypes (KB1 and KE2) to uncover the genetic mechanism underlying their phenotypic plasticity under predation stress.

RESULTS

KB1 exhibited strategies to enhance fertility and decrease body length when exposed to fish kairomones, while KE2 deployed an adaptive strategy to increase body length. Full-length transcriptomes from KB1 and KE2 yielded 65,736 and 57,437 transcripts, respectively, of which 32 differentially expressed transcripts (DETs) were shared under predation stress across both genotypes. Prominent DETs common to both genotypes were related to energy metabolism and the immune system. Additionally, differential alternative splicing (DAS) events were detected in both genotypes in response to fish kairomones. DAS genes shared between both genotypes may indicate their significant role in the post-transcriptional stress response to fish predation. Calpain-3, involved in digestion and nutrient absorption, was identified as a DAS gene in both genotypes when exposed to fish kairomones. In addition, the gene encoding thymosin beta, which is related to growth, was found to be a statistically significant DAS only in KB1, while that encoding ultraspiracle protein, also associated with growth, was only identified in KE2. Moreover, transcripts encoding proteins such as EGF-like domain-containing protein, vitellogenin fused with superoxide dismutase, and others were identified overlapping between DAS events and DETs and potentially elucidating their association with the observed phenotypic variation in each genotype.

CONCLUSIONS

Our findings highlight the crucial role of alternative splicing in modulating transcriptome landscape under predation stress in D. galeata, emphasizing the requirement for integrating gene expression and splicing analyses in evolutionary adaptation studies.

Beyond reaction norms: the temporal dynamics of phenotypic plasticity

Phenotypic plasticity can allow organisms to cope with environmental changes. Although reaction norms are commonly used to quantify plasticity along gradients of environmental conditions, they often miss the temporal dynamics of phenotypic change, especially the speed at which it occurs. Here, we argue that studying the rate of phenotypic plasticity is a crucial step to quantify and understand its adaptiveness. Iteratively measuring plastic traits allows us to describe the actual dynamics of phenotypic changes and avoid quantifying reaction norms at times that do not truly reflect the organism's capacity for plasticity. Integrating the temporal component in how we describe, quantify, and conceptualise phenotypic plasticity can change our understanding of its diversity, evolution, and consequences.

Environmental Stress and the Morphology of Daphnia pulex

AbstractMorphological variation is sometimes used as an indicator of environmental stress in animals. Here, we assessed how multiple morphological traits covaried in Daphnia pulex exposed to five common forms of environmental stress (high temperature, presence of predator cues, high salinity, low food abundance, and low Ca). We measured animal body length, body width, head width, eyespot diameter, and tail spine length along with mass in animals of five different ages (3, 6, 9, 12, and 15 d). There were strong allometric relationships among all morphological traits in reference animals and strong univariate effects of environmental stress on body mass and body length. We found that environmental stressors altered bivariate relationships between select pairwise combinations of morphological traits, with effects being dependent on animal age. Multivariate analyses further revealed high connectivity among body size-related traits but that eyespot diameter and tail spine length were less tightly associated with body size. Animals exposed to natural lake water with and without supplemental food also varied in morphology, with body size differences being suggestive of starvation and other unknown nutritional deficiencies. Yet our results demonstrate that the scaling of body morphological traits of Daphnia pulex is largely invariant with possible context-dependent plasticity in eye size and tail spine lengths. The strong coordination of traits indicates tight molecular coordination of body size during development despite strong and varied environmental stress.

Comparative transcriptome analysis of two Daphnia galeata genotypes displaying contrasting phenotypic variation induced by fish kairomones in the same environment of the Han River, Korea

BACKGROUND

Phenotypic plasticity is a crucial adaptive mechanism that enables organisms to modify their traits in response to changes in their environment. Predator-induced defenses are an example of phenotypic plasticity observed across a wide range of organisms, from single-celled organisms to vertebrates. In addition to morphology and behavior, these responses also affect life-history traits. The crustacean Daphnia galeata is a suitable model organism for studying predator-induced defenses, as it exhibits life-history traits changes under predation risk. To get a better overview of their phenotypic plasticity under predation stress, we conducted RNA sequencing on the transcriptomes of two Korean Daphnia galeata genotypes, KE1, and KB11, collected in the same environment.

RESULTS

When exposed to fish kairomones, the two genotypes exhibited phenotypic variations related to reproduction and growth, with opposite patterns in growth-related phenotypic variation. From both genotypes, a total of 135,611 unigenes were analyzed, of which 194 differentially expressed transcripts (DETs) were shared among the two genotypes under predation stress, which showed consistent, or inconsistent expression patterns in both genotypes. Prominent DETs were related to digestion and reproduction and consistently up-regulated in both genotypes, thus associated with changes in life-history traits. Among the inconsistent DETs, transcripts encode vinculin (VINC) and protein obstructor-E (OBST-E), which are associated with growth; these may explain the differences in life-history traits between the two genotypes. In addition, genotype-specific DETs could explain the variation in growth-related life-history traits between genotypes, and could be associated with the increased body length of genotype KE1.

CONCLUSIONS

The current study allows for a better understanding of the adaptation mechanisms related to reproduction and growth of two Korean D. galeata genotypes induced by predation stress. However, further research is necessary to better understand the specific mechanisms by which the uncovered DETs are related with the observed phenotypic variation in each genotype. In the future, we aim to unravel the precise adaptive mechanisms underlying predator-induced responses.

Responses to predation pressure involve similar sets of genes in two divergent species of Daphnia

Species that are not closely related can express similar inducible traits, but molecular mechanisms underlying the observed responses are often unknown, nor is it known if these mechanisms are shared between such species. Here, we compared transcriptional profiles of two Daphnia species (D. mitsukuri and D. sinensis) from different subgenera, at both juvenile and adult developmental stages. Both species were exposed to the same predation threat (fish kairomones), and both showed similar induced morphological changes (reduced body length). At the early developmental stage, response to predation risk resulted in similar changes in expression levels of 23 orthologues in both species. These orthologues, involved in 107 GO categories, changed in the same direction in both species (over- or underexpressed), in comparison to non-exposed controls. Several of these orthologues were associated with DNA replication, structural constituents of cuticle or innate immune response. In both species, the differentially expressed (DE) genes on average had higher ω (dN /dS ) values than non-DE genes, suggesting that these genes had experienced greater positive selection or lower purifying selection than non-DE genes. Overall, our results suggest that similar suites of genes, responding in similar ways to predation pressure, have been retained in Daphnia for many millions of years.

On the origin and nature of nongenetic information in eumetazoans

Nongenetic information implies all the forms of biological information not related to genes and DNA in general. Despite the deep scientific relevance of the concept, we currently lack reliable knowledge about its carriers and origins; hence, we still do not understand its true nature. Given that genes are the targets of nongenetic information, it appears that a parsimonious approach to find the ultimate source of that information is to trace back the sequential steps of the causal chain upstream of the target genes up to the ultimate link as the source of the nongenetic information. From this perspective, I examine seven nongenetically determined phenomena: placement of locus-specific epigenetic marks on DNA and histones, changes in snRNA expression patterns, neural induction of gene expression, site-specific alternative gene splicing, predator-induced morphological changes, and cultural inheritance. Based on the available evidence, I propose a general model of the common neural origin of all these forms of nongenetic information in eumetazoans.

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.

Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation

Daphnia, an ecologically important zooplankton species in lakes, shows both genetic adaptation and phenotypic plasticity in response to temperature and fish predation, but little is known about the molecular basis of these responses and their potential interactions. We performed a factorial experiment exposing laboratory-propagated Daphnia pulicaria clones from two lakes in the Sierra Nevada mountains of California to normal or high temperature (15°C or 25°C) in the presence or absence of fish kairomones, then measured changes in life history and gene expression. Exposure to kairomones increased upper thermal tolerance limits for physiological activity in both clones. Cloned individuals matured at a younger age in response to higher temperature and kairomones, while size at maturity, fecundity and population intrinsic growth were only affected by temperature. At the molecular level, both clones expressed more genes differently in response to temperature than predation, but specific genes involved in metabolic, cellular, and genetic processes responded differently between the two clones. Although gene expression differed more between clones from different lakes than experimental treatments, similar phenotypic responses to predation risk and warming arose from these clone-specific patterns. Our results suggest that phenotypic plasticity responses to temperature and kairomones interact synergistically, with exposure to fish predators increasing the tolerance of Daphnia pulicaria to stressful temperatures, and that similar phenotypic responses to temperature and predator cues can be produced by divergent patterns of gene regulation.

Evolutionary change in metabolic rate of Daphnia pulicaria following invasion by the predator Bythotrephes longimanus

Metabolic rate is a trait that may evolve in response to the direct and indirect effects of predator-induced mortality. Predators may indirectly alter selection by lowering prey densities and increasing resource availability or by intensifying resource limitation through changes in prey behavior (e.g., use of less productive areas). In the current study, we quantify the evolution of metabolic rate in the zooplankton Daphnia pulicaria following an invasive event by the predator Bythotrephes longimanus in Lake Mendota, Wisconsin, US. This invasion has been shown to dramatically impact D. pulicaria, causing a ~60% decline in their biomass. Using a resurrection ecology approach, we compared the metabolic rate of D. pulicaria clones originating prior to the Bythotrephes invasion with that of clones having evolved in the presence of Bythotrephes. We observed a 7.4% reduction in metabolic rate among post-invasive clones compared to pre-invasive clones and discuss the potential roles of direct and indirect selection in driving this change.

Genomic regions associated with adaptation to predation in Daphnia often include members of expanded gene families

Predation has been a major driver of the evolution of prey species, which consequently develop antipredator adaptations. However, little is known about the genetic basis underpinning the adaptation of prey to intensive predation. Here, we describe a high-quality chromosome-level genome assembly (approx. 145 Mb, scaffold N50 11.45 Mb) of Daphnia mitsukuri, a primary forage for many fish species. Transcriptional profiling of D. mitsukuri exposed to fish kairomone revealed that this cladoceran responds to predation risk through regulating activities of Wnt signalling, cuticle pattern formation, cell cycle regulation and anti-apoptosis pathways. Genes differentially expressed in response to predation risk are more likely to be members of expanded families. Our results suggest that expansions of multiple gene families associated with chemoreception and vision allow Daphnia to enhance detection of predation risk, and that expansions of those associated with detoxification and cuticle formation allow Daphnia to mount an efficient response to perceived predation risk. This study increases our understanding of the molecular basis of prey defences, being important evolutionary adaptations playing a stabilizing role in community dynamics.

Insights into the genetic basis of predator-induced response in Daphnia galeata

Phenotypic plastic responses allow organisms to rapidly adjust when facing environmental challenges-these responses comprise morphological, behavioral but also life-history changes. Alteration of life-history traits when exposed to predation risk have been reported often in the ecological and genomic model organism Daphnia. However, the molecular basis of this response is not well understood, especially in the context of fish predation. Here, we characterized the transcriptional profiles of two Daphnia galeata clonal lines with opposed life histories when exposed to fish kairomones. First, we conducted a differential gene expression, identifying a total of 125 candidate transcripts involved in the predator-induced response, uncovering substantial intraspecific variation. Second, we applied a gene coexpression network analysis to find clusters of tightly linked transcripts revealing the functional relations of transcripts underlying the predator-induced response. Our results showed that transcripts involved in remodeling of the cuticle, growth, and digestion correlated with the response to environmental change in D. galeata. Furthermore, we used an orthology-based approach to gain functional information for transcripts lacking gene ontology (GO) information, as well as insights into the evolutionary conservation of transcripts. We could show that our candidate transcripts have orthologs in other Daphnia species but almost none in other arthropods. The unique combination of methods allowed us to identify candidate transcripts, their putative functions, and evolutionary history associated with predator-induced responses in Daphnia. Our study opens up to the question as to whether the same molecular signature is associated with fish kairomones-mediated life-history changes in other Daphnia species.

Extra-genomic instructive influences in morphogenesis: A review of external signals that regulate growth and form

Embryonic development and regeneration accomplish a remarkable feat: individual cells work together to create or repair complex anatomical structures. What is the source of the instructive signals that specify these invariant and robust organ-level outcomes? The most frequently studied source of morphogenetic control is the host genome and its transcriptional circuits. However, it is now apparent that significant information affecting patterning also arrives from outside of the body. Both biotic and physical factors, including temperature and various molecular signals emanating from pathogens, commensals, and conspecific organisms, affect developmental outcomes. Here, we review examples in which anatomical patterning decisions are strongly impacted by lateral signals that originate from outside of the zygotic genome. The endogenous pathways targeted by these influences often show transgenerational effects, enabling them to shape the evolution of anatomies even faster than traditional Baldwin-type assimilation. We also discuss recent advances in the biophysics of morphogenetic controls and speculate on additional sources of important patterning information which could be exploited to better understand the evolution of bodies and to design novel approaches for regenerative medicine.

Ecology of predator-induced morphological defense traits in Daphnia longispina (Cladocera, Arthropoda)

Inducible defenses against predators are widespread among plants and animals. For example, some Daphnia species form neckteeth against predatory larvae of the dipteran genus Chaoborus. Though thoroughly studied in D. pulex, knowledge about neckteeth in other Daphnia species is limited. The occurrence of this trait in the D. longispina species complex is only sporadically reported and the specific shape of neckteeth or the occurrence of other morphological defense traits is scarcely known in this widespread group. Here, we explored neckteeth occurrence in a large number of D. longispina populations across Scandinavia and studied neckteeth formation and other morphological defense traits on three D. longispina clones in the laboratory. In the study region, neckteeth on juvenile D. longispina s. str. were observed frequently in permanent ponds, but only when Chaoborus spp. larvae were present. In the laboratory experiments, all three D. longispina clones developed neckteeth (very similar to D. pulex) in response to Chaoborus kairomone exposure. The D. longispina clones also developed a longer tail spine, wider body, and larger neckteeth pedestal in response to predation threat—likely as a defense against the gape-limited predator. The intensity of neckteeth expression also depended on the clone studied and the concentration of Chaoborus kairomone. Our results demonstrate that neckteeth on D. longispina can be common in nature and that D. longispina can also induce other morphological defenses against predators. The similarity of neckteeth in D. longispina and D. pulex imposes yet unresolved questions on the evolutionary origin in these distantly related Daphnia groups.

Variation in transcriptional responses to copper exposure across Daphnia pulex lineages

Copper pollution is pervasive in aquatic habitats and is particularly harmful to invertebrates sensitive to environmental changes such as Daphnia pulex. Mechanisms of toxicity and tolerance to copper are not well understood. We used RNA-sequencing to investigate these mechanisms in three genetically distinct D. pulex clonal lineages with different histories of copper exposure. Upregulated genes after copper exposure were enriched with Gene Ontology (GO) categories involved in digestion, molting and growth, whereas downregulated genes after copper exposure were enriched in the metal-regulatory system, immune response and epigenetic modifications. The three D. pulex clones in our study show largely similar transcriptional patterns in response to copper, with only a total of twenty genes differentially expressed in a single clonal lineages. We also detected lower relative expression of some genes known to be important for copper tolerance, metallothionein and glutathione-S-transferase, in a sensitive lineage sampled from an uncontaminated habitat. Daphnia-specific genes (without orthologs outside the genus) and Daphnia-specific duplications (genes duplicated in the Daphnia lineage) were overrepresented in differentially expressed genes, highlighting an important role for newly emerged genes in tolerating environmental stressors. The results indicate that the D. pulex lineages tested in this study generally respond to copper stress using the same major pathways, but that the more resistant clone with previous copper exposure might be better able to regulate key genes. This finding highlights the important nuances in gene expression among clones, shaped by historical exposure and influencing copper tolerance.

Prolonged Bat Call Exposure Induces a Broad Transcriptional Response in the Male Fall Armyworm (Spodoptera frugiperda; Lepidoptera: Noctuidae) Brain

Predation risk induces broad behavioral and physiological responses that have traditionally been considered acute and transitory. However, prolonged or frequent exposure to predators and the sensory cues of their presence they broadcast to the environment impact long-term prey physiology and demographics. Though several studies have assessed acute and chronic stress responses in varied taxa, these attempts have often involved a priori expectations of the molecular pathways involved in physiological responses, such as glucocorticoid pathways and neurohormone production in vertebrates. While relatively little is known about physiological and molecular predator-induced stress in insects, many dramatic insect defensive behaviors have evolved to combat selection by predators. For instance, several moth families, such as Noctuidae, include members equipped with tympanic organs that allow the perception of ultrasonic bat calls and facilitate predation avoidance by eliciting evasive aerial flight maneuvers. In this study, we exposed adult male fall armyworm (Spodoptera frugiperda) moths to recorded ultrasonic bat foraging and attack calls for a prolonged period and constructed a de novo transcriptome based on brain tissue from predator cue-exposed relative to control moths kept in silence. Differential expression analysis revealed that 290 transcripts were highly up- or down-regulated among treatment tissues, with many annotating to noteworthy proteins, including a heat shock protein and an antioxidant enzyme involved in cellular stress. Though nearly 50% of differentially expressed transcripts were unannotated, those that were are implied in a broad range of cellular functions within the insect brain, including neurotransmitter metabolism, ionotropic receptor expression, mitochondrial metabolism, heat shock protein activity, antioxidant enzyme activity, actin cytoskeleton dynamics, chromatin binding, methylation, axonal guidance, cilia development, and several signaling pathways. The five most significantly overrepresented Gene Ontology terms included chromatin binding, macromolecular complex binding, glutamate synthase activity, glutamate metabolic process, and glutamate biosynthetic process. As a first assessment of transcriptional responses to ecologically relevant auditory predator cues in the brain of moth prey, this study lays the foundation for examining the influence of these differentially expressed transcripts on insect behavior, physiology, and life history within the framework of predation risk, as observed in ultrasound-sensitive Lepidoptera and other 'eared' insects.

Inducible pesticide tolerance in Daphnia pulex influenced by resource availability

Pesticides are a ubiquitous contaminant in aquatic ecosystems. Despite the relative sensitivity of aquatic species to pesticides, growing evidence suggests that populations can respond to pesticides by evolving higher baseline tolerance or inducing a higher tolerance via phenotypic plasticity. While both mechanisms can allow organisms to persist when faced with pesticides, resource allocation theory suggests that tolerance may be related to resource acquisition by the organism. Using Daphnia pulex, we investigated how algal resource availability influenced the baseline and inducible tolerance of D. pulex to a carbamate insecticide, carbaryl. Individuals reared in high resource environments had a higher baseline carbaryl tolerance compared to those reared in low resource environments. However, D. pulex from low resource treatments exposed to sublethal concentrations of carbaryl early in development induced increased tolerance to a lethal concentration of carbaryl later in life. Only individuals reared in the low resource environment induced carbaryl tolerance. Collectively, this highlights the importance of considering resource availability in our understanding of pesticide tolerance.

Sensory Ecology of Predator-Induced Phenotypic Plasticity

Ecological communities are organized in trophic levels that share manifold interactions forming complex food webs. Infochemicals can further modify these interactions, e.g., by inducing defenses in prey. The micro-crustacean Daphnia is able to respond to predator-specific chemical cues indicating an increased predation risk. Daphnia shows plastic responses by adapting its morphology, behavior, and physiology, increasing organism, and population fitness. This stabilizes community structures. This review will describe the progress that has been made in understanding the high degree of plasticity observed in the model crustacean Daphnia. I summarize current knowledge on the processes of predator detection, ranging from the nature of biologically active chemical cues to the underlying neurophysiological mechanisms. With this, I aim to provide a comprehensive overview on the molecular mechanisms of ad hoc environmental phenotypic adaptation. In times of climate change and pollution understanding information transfer in aquatic systems is valuable as it will allow us to predict whether and how community structures are being affected.

Daphnia galeata responds to the exposure to an ichthyosporean gut parasite by down-regulation of immunity and lipid metabolism

BACKGROUND

Regulatory circuits of infection in the emerging experimental model system, water flea Daphnia and their microparasites, remain largely unknown. Here we provide the first molecular insights into the response of Daphnia galeata to its highly virulent and common parasite Caullerya mesnili, an ichthyosporean that infects the gut epithelium. We generated a transcriptomic dataset using RNAseq from parasite-exposed (vs. control) Daphnia, at two time points (4 and 48 h) after parasite exposure.

RESULTS

We found a down-regulation of metabolism and immunity-related genes, at 48 h (but not 4 h) after parasite exposure. These genes are involved in lipid metabolism and fatty acid biosynthesis, as well as microbe recognition (e.g. c-type lectins) and pathogen attack (e.g. gut chitin).

CONCLUSIONS

General metabolic suppression implies host energy shift from reproduction to survival, which is in agreement with the known drastic reduction in Daphnia fecundity after Caullerya infection. The down-regulation of gut chitin indicates a possible interaction between the peritrophic matrix and the evading host immune system. Our study provides the first description of host transcriptional responses in this very promising host-parasite experimental system.

Transcriptomic responses to predator kairomones in embryos of the aquatic snail Radix balthica

The ability of organisms to respond to predation threat by exhibiting induced defenses is well documented, but studies on the potential mechanistic basis for such responses are scarce. Here, we examine the transcriptomic response to predator kairomones of two functionally distinct developmental stages in embryos of the aquatic snail Radix balthica: E8-the stage at which a range-finding trial indicated that kairomone-induced accelerated growth and development first occurred; and E9-the stage at which embryos switched from ciliary- to crawling-driven locomotion. We tested whether expression profiles were influenced by kairomones and whether this influence varied between stages. We also identified potential candidate genes for investigating mechanisms underpinning induced responses. There were 6,741 differentially expressed transcripts between developmental stages, compared to just five in response to predator kairomones. However, on examination of functional enrichment in the transcripts responding to predator kairomones and adopting a less stringent significance threshold, 206 transcripts were identified relating to muscle function, growth, and development, with this response being greater at the later E9 stage. Furthermore, these transcripts included putative annotations for genes identified as responding to predator kairomones in other taxa, including C1q, lectin, and actin domains. Globally, transcript expression appeared reduced in response to predator kairomones and we hypothesize that this might be a result of metabolic suppression, as has been reported in other taxa in response to predation threat.

Toxicogenomic responses of low level anticancer drug exposures in Daphnia magna

The use of anticancer drugs in chemotherapy is increasing, leading to growing environmental concentrations of imatinib mesylate (IMA), cisplatinum (CDDP), and etoposide (ETP) in aquatic systems. Previous studies have shown that these anticancer drugs cause DNA damage in the crustacean Daphnia magna at low, environmentally relevant concentrations. To explore the mechanism of action of these compounds and the downstream effects of DNA damage on D. magna growth and development at a sensitive life stage, we exposed neonates to low level concentrations equivalent to those that elicit DNA damage (IMA: 2000 ng/L, ETP: 300 ng/L, CDDP: 10 ng/L) and performed transcriptomic analysis using an RNA-seq approach. RNA sequencing generated 14 million reads per sample, which were aligned to the D. magna genome and assembled, producing approximately 23,000 transcripts per sample. Over 90% of the transcripts showed homology to proteins in GenBank, revealing a high quality transcriptome assembly, although functional annotation was much lower. RT-qPCR was used to identify robust biomarkers and confirmed the downregulation of an angiotensin converting enzyme-like gene (ance) involved in neuropeptide regulation across all three anticancer drugs and the down-regulation of DNA topoisomerase II by ETP. RNA-seq analysis also allowed for an in depth exploration of the differential splicing of transcripts revealing that regulation of different gene isoforms predicts potential impacts on translation and protein expression, providing a more meaningful assessment of transcriptomic data. Enrichment analysis and investigation of affected biological processes suggested that the DNA damage caused by ETP and IMA influences cell cycle regulation and GPCR signaling. This dysregulation is likely responsible for effects to neurological system processes and development, and overall growth and development. Our transcriptomic approach provided insight into the mechanisms that respond to DNA damage caused by anticancer drug exposure and generated novel hypotheses on how these chemicals may impact the growth and survival of this ecologically important zooplankton species.

Comparative Transcriptome Analysis for Understanding Predator-Induced Polyphenism in the Water Flea Daphnia pulex

The crustacean Daphnia pulex is one of the best model organisms for studying inducible defense mechanisms due to their inducible morphology in response to the predator Chaoborus larvae. In this study, multiple developmental stages of D. pulex were exposed to C. flavicans larvae and transcriptome profiles of samples from late embryo to fifth instar were sequenced by the RNA-seq technique to investigate the genetic background underlying inducible defenses. In comparison, differentially expressed genes between defensive and normal morphs were identified, including 908 genes in late embryo, 1383 genes in the first-third (1–3) instar, and 1042 genes in fourth-fifth (4–5) instar. Gene ontology enrichment analysis showed that structural constituents of the cuticle and structural molecule activity genes were prominent up-regulated genes in late embryos. Down-regulated genes in late embryos and 1–3 instar comprised metabolic process, hydrolase activity, and peptidase activity gene classes. Pathway analysis indicated that small molecule neurotransmitter pathways were potentially involved in the development of inducible defenses. The characterization of genes and pathways in multiple developmental stages can improve our understanding of inducible defense responses of D. pulex to predation at the molecular level.

Contrasting gene expression programs correspond with predator-induced phenotypic plasticity within and across generations in Daphnia

Research has shown that a change in environmental conditions can alter the expression of traits during development (i.e., "within-generation phenotypic plasticity") as well as induce heritable phenotypic responses that persist for multiple generations (i.e., "transgenerational plasticity", TGP). It has long been assumed that shifts in gene expression are tightly linked to observed trait responses at the phenotypic level. Yet, the manner in which organisms couple within- and TGP at the molecular level is unclear. Here we tested the influence of fish predator chemical cues on patterns of gene expression within- and across generations using a clone of Daphnia ambigua that is known to exhibit strong TGP but weak within-generation plasticity. Daphnia were reared in the presence of predator cues in generation 1, and shifts in gene expression were tracked across two additional asexual experimental generations that lacked exposure to predator cues. Initial exposure to predator cues in generation 1 was linked to ~50 responsive genes, but such shifts were 3-4× larger in later generations. Differentially expressed genes included those involved in reproduction, exoskeleton structure and digestion; major shifts in expression of genes encoding ribosomal proteins were also identified. Furthermore, shifts within the first-generation and transgenerational shifts in gene expression were largely distinct in terms of the genes that were differentially expressed. Such results argue that the gene expression programmes involved in within- vs. transgeneration plasticity are fundamentally different. Our study provides new key insights into the plasticity of gene expression and how it relates to phenotypic plasticity in nature.

Mechanisms underlying the control of responses to predator odours in aquatic prey

In aquatic systems, chemical cues are a major source of information through which animals are able to assess the current state of their environment to gain information about local predation risk. Prey use chemicals released by predators (including cues from a predator's diet) and other prey (such as alarm cues and disturbance cues) to mediate a range of behavioural, morphological and life-history antipredator defences. Despite the wealth of knowledge on the ecology of antipredator defences, we know surprisingly little about the physiological mechanisms that control the expression of these defensive traits. Here, we summarise the current literature on the mechanisms known to specifically mediate responses to predator odours, including dietary cues. Interestingly, these studies suggest that independent pathways may control predator-specific responses, highlighting the need for greater focus on predator-derived cues when looking at the mechanistic control of responses. Thus, we urge researchers to tease apart the effects of predator-specific cues (i.e. chemicals representing a predator's identity) from those of diet-mediated cues (i.e. chemicals released from a predator's diet), which are known to mediate different ecological endpoints. Finally, we suggest some key areas of research that would greatly benefit from a more mechanistic approach.

Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia

Ecological genomics aims to understand the functional association between environmental gradients and the genes underlying adaptive traits. Many genes that are identified by genome-wide screening in ecologically relevant species lack functional annotations. Although gene functions can be inferred from sequence homology, such approaches have limited power. Here, we introduce ecological regulatory genomics by presenting an ontology-free gene prioritization method. Specifically, our method combines transcriptome profiling with high-throughput cis-regulatory sequence analysis in the water fleas Daphnia pulex and Daphnia magna. It screens coexpressed genes for overrepresented DNA motifs that serve as transcription factor binding sites, thereby providing insight into conserved transcription factors and gene regulatory networks shaping the expression profile. We first validated our method, called Daphnia-cisTarget, on a D. pulex heat shock data set, which revealed a network driven by the heat shock factor. Next, we performed RNA-Seq in D. magna exposed to the cyanobacterium Microcystis aeruginosa. Daphnia-cisTarget identified coregulated gene networks that associate with the moulting cycle and potentially regulate life history changes in growth rate and age at maturity. These networks are predicted to be regulated by evolutionary conserved transcription factors such as the homologues of Drosophila Shavenbaby and Grainyhead, nuclear receptors, and a GATA family member. In conclusion, our approach allows prioritising candidate genes in Daphnia without bias towards prior knowledge about functional gene annotation and represents an important step towards exploring the molecular mechanisms of ecological responses in organisms with poorly annotated genomes.

Reproductive switching analysis of Daphnia similoides between sexual female and parthenogenetic female by transcriptome comparison

The water flea Daphnia are planktonic crustaceans commonly found in freshwater environment that can switch their reproduction mode from parthenogenesis to sexual reproduction to adapt to the external environment. As such, Daphnia are great model organisms to study the mechanism of reproductive switching, the underlying mechanism of reproduction and development in cladocerans and other animals. However, little is known about the Daphnia's reproductive behaviour at a molecular level. We constructed a genetic database of the genes expressed in a sexual female (SF) and a parthenogenetic female (PF) of D. similoides using Illumina HiSeq 2500. A total of 1,763 differentially expressed genes (865 up- and 898 down-regulated) were detected in SF. Of the top 30 up-regulated SF unigenes, the top 4 unigenes belonged to the Chitin_bind_4 family. In contrast, of the top down-regulated SF unigenes, the top 3 unigenes belonged to the Vitellogenin_N family. This is the first study to indicate genes that may have a crucial role in reproductive switching of D. similoides, which could be used as candidate genes for further functional studies. Thus, this study provides a rich resource for investigation and elucidation of reproductive switching in D. similoides.