The marbled crayfish as a paradigm for saltational speciation by autopolyploidy and parthenogenesis in animals

Phenotypic plasticity in the monoclonal marbled crayfish is associated with very low genetic diversity but pronounced epigenetic diversity

Clonal organisms are particularly useful to investigate the contribution of epigenetics to phenotypic plasticity, because confounding effects of genetic variation are negligible. In the last decade, the apomictic parthenogenetic marbled crayfish, Procambarus virginalis, has been developed as a model to investigate the relationships between phenotypic plasticity and genetic and epigenetic diversity in detail. This crayfish originated about 30 years ago by autotriploidy from a single slough crayfish Procambarus fallax. As the result of human releases and active spreading, marbled crayfish has established numerous populations in very diverse habitats in 22 countries from the tropics to cold temperate regions. Studies in the laboratory and field revealed considerable plasticity in coloration, spination, morphometric parameters, growth, food preference, population structure, trophic position, and niche width. Illumina and PacBio whole-genome sequencing of marbled crayfish from representatives of 19 populations in Europe and Madagascar demonstrated extremely low genetic diversity within and among populations, indicating that the observed phenotypic diversity and ability to live in strikingly different environments are not due to adaptation by selection on genetic variation. In contrast, considerable differences were found between populations in the DNA methylation patterns of hundreds of genes, suggesting that the environmentally induced phenotypic plasticity is mediated by epigenetic mechanisms and corresponding changes in gene expression. Specific DNA methylation fingerprints persisted in local populations over successive years indicating the existence of epigenetic ecotypes, but there is presently no information as to whether these epigenetic signatures are transgenerationally inherited or established anew in each generation and whether the recorded phenotypic plasticity is adaptive or nonadaptive.

Combining Old and New Tricks: The Study of Genes, Neurons, and Behavior in Crayfish

For over a century the nervous system of decapod crustaceans has been a workhorse for the neurobiology community. Many fundamental discoveries including the identification of electrical and inhibitory synapses, lateral and pre-synaptic inhibition, and the Na⁺/K⁺-pump were made using lobsters, crabs, or crayfish. Key among many advantages of crustaceans for neurobiological research is the unique access to large, accessible, and identifiable neurons, and the many distinct and complex behaviors that can be observed in lab settings. Despite these advantages, recent decades have seen work on crustaceans hindered by the lack of molecular and genetic tools required for unveiling the cellular processes contributing to neurophysiology and behavior. In this perspective paper, we argue that the recently sequenced marbled crayfish, Procambarus virginalis, is suited to become a genetic model system for crustacean neuroscience. P. virginalis are parthenogenetic and produce genetically identical offspring, suggesting that germline transformation creates transgenic animal strains that are easy to maintain across generations. Like other decapod crustaceans, marbled crayfish possess large neurons in well-studied circuits such as the giant tail flip neurons and central pattern generating neurons in the stomatogastric ganglion. We provide initial data demonstrating that marbled crayfish neurons are accessible through standard physiological and molecular techniques, including single-cell electrophysiology, gene expression measurements, and RNA-interference. We discuss progress in CRISPR-mediated manipulations of the germline to knock-out target genes using the ‘Receptor-mediated ovary transduction of cargo’ (ReMOT) method. Finally, we consider the impact these approaches will have for neurophysiology research in decapod crustaceans and more broadly across invertebrates.

Physiological performance of native and invasive crayfish species in a changing environment: insights from Dynamic Energy Budget models

Crayfish are keystone species important for maintaining healthy freshwater ecosystems. Crayfish species native to Europe, such as Astacus astacus and Austropotamobius torrentium, are facing decline and are increasingly endangered by changing climate and invasions of non-native crayfish, such as Pacifastacus leniusculus and Procambarus virginalis. The success of these invasions largely depends on differences in ontogeny between the native species and the invaders and how changes in the environment will affect the ontogeny. Dynamic Energy Budget (DEB) models can be used to investigate such differences because the models capture dependence of metabolism, and therefore ontogeny, on environmental conditions. We develop DEB models for all four species and investigate key elements of ontogeny and metabolism affecting interspecific competition. We then use the DEB models to predict individual growth and reproduction in current and new conditions that are expected to arise from climate change. Although observations suggest that P. leniusculus poses the major threat to native species, our analysis identifies P. virginalis, in spite of its smaller size, as the superior competitor by a large margin-at least when considering metabolism and ontogeny. Our simulations show that climate change is set to increase the competitive edge of P. virginalis even further. Given the prospects of P. virginalis dominance, especially when considering that it is able to withstand and spread at least some crayfish plague strains that severely affect native species, additional research into P. virginalis is necessary.

Paradigm shifts in animal epigenetics: Research on non-model species leads to new insights into dependencies, functions and inheritance of DNA methylation

Recent investigations with non-model species and whole-genome approaches have challenged several paradigms in animal epigenetics. They revealed that epigenetic variation in populations is not the mere consequence of genetic variation, but is a semi-independent or independent source of phenotypic variation, depending on mode of reproduction. DNA methylation is not positively correlated with genome size and phylogenetic position as earlier believed, but has evolved differently between and within higher taxa. Epigenetic marks are usually not completely erased in the zygote and germ cells as generalized from mouse, but often persist and can be transgenerationally inherited, making them evolutionarily relevant. Gene body methylation and promoter methylation are similar in vertebrates and invertebrates with well methylated genomes but transposon silencing through methylation is variable. The new data also suggest that animals use epigenetic mechanisms to cope with rapid environmental changes and to adapt to new environments. The main benefiters are asexual populations, invaders, sessile taxa and long-lived species.

Studying phenotypic variation and DNA methylation across development, ecology and evolution in the clonal marbled crayfish: a paradigm for investigating epigenotype-phenotype relationships in macro-invertebrates

Animals can produce different phenotypes from the same genome during development, environmental adaptation and evolution, which is mediated by epigenetic mechanisms including DNA methylation. The obligatory parthenogenetic marbled crayfish, Procambarus virginalis, whose genome and methylome are fully established, proved very suitable to study this issue in detail. Comparison between developmental stages and DNA methylation revealed low expression of Dnmt methylation and Tet demethylation enzymes from the spawned oocyte to the 256 cell embryo and considerably increased expression thereafter. The global 5-methylcytosine level was 2.78% at mid-embryonic development and decreased slightly to 2.41% in 2-year-old adults. Genetically identical clutch-mates raised in the same uniform laboratory setting showed broad variation in morphological, behavioural and life history traits and differences in DNA methylation. The invasion of diverse habitats in tropical to cold-temperate biomes in the last 20 years by the marbled crayfish was associated with the expression of significantly different phenotypic traits and DNA methylation patterns, despite extremely low genetic variation on the whole genome scale, suggesting the establishment of epigenetic ecotypes. The evolution of marbled crayfish from its parent species Procambarus fallax by autotriploidy a few decades ago was accompanied by a significant increase in body size, fertility and life span, a 20% reduction of global DNA methylation and alteration of methylation in hundreds of genes, suggesting that epigenetic mechanisms were involved in speciation and fitness enhancement. The combined analysis of phenotypic traits and DNA methylation across multiple biological contexts in the laboratory and field in marbled crayfish may serve as a blueprint for uncovering the role of epigenetic mechanisms in shaping of phenotypes in macro-invertebrates.

Intergenerational Patterns of DNA Methylation in Procambarus clarkii Following Exposure to Genotoxicants: A Conjugation in Past Simple or Past Continuous?

Epigenome is susceptible to modulation by environmental pressures—namely, through alterations in global DNA methylation, impacting the organism condition and, ultimately, reverberating on the phenotype of the subsequent generations. Hence, an intergenerational study was conducted, aiming to clarify the influence of genotoxicants on global DNA methylation of the crayfish Procambarus clarkii. Two subsequent generations were exposed to the herbicide penoxsulam (Px; 23 µg·L⁻¹) and to the genotoxicant model ethyl methanesulfonate (EMS; 5 mg·L⁻¹). Px did not induce changes in DNA methylation of adult crayfish (F₀). However, the hypomethylation occurring in unexposed F₁ juveniles demonstrated that the history of exposure per se can modulate epigenome. In F₁ descendants of the Px-exposed group, methylome (hypermethylated) was more affected in males than in females. EMS-induced hypomethylation in adult females (F₀), also showed gender specificity. In addition, hypomethylation was also observed in the unexposed F₁ crayfish, indicating an intergenerational epigenetic effect. The modulatory role of past exposure to penoxsulam or to EMS also showed a dependency on the crayfish developmental stage. Overall, this research revealed that indirect experiences (events occurring in a predecessor generation) can have an impact even greater than direct experiences (present events) on the epigenetic dynamics.

Insights into the genetic regulatory network underlying neurogenesis in the parthenogenetic marbled crayfish Procambarus virginalis

Nervous system development has been intensely studied in insects (especially Drosophila melanogaster), providing detailed insights into the genetic regulatory network governing the formation and maintenance of the neural stem cells (neuroblasts) and the differentiation of their progeny. Despite notable advances over the last two decades, neurogenesis in other arthropod groups remains by comparison less well understood, hampering finer resolution of evolutionary cell type transformations and changes in the genetic regulatory network in some branches of the arthropod tree of life. Although the neurogenic cellular machinery in malacostracan crustaceans is well described morphologically, its genetic molecular characterization is pending. To address this, we established an in situ hybridization protocol for the crayfish Procambarus virginalis and studied embryonic expression patterns of a suite of key genes, encompassing three SoxB group transcription factors, two achaete-scute homologs, a Snail family member, the differentiation determinants Prospero and Brain tumor, and the neuron marker Elav. We document cell type expression patterns with notable similarities to insects and branchiopod crustaceans, lending further support to the homology of hexapod-crustacean neuroblasts and their cell lineages. Remarkably, in the crayfish head region, cell emigration from the neuroectoderm coupled with gene expression data points to a neuroblast-independent initial phase of brain neurogenesis. Further, SoxB group expression patterns suggest an involvement of Dichaete in segmentation, in concordance with insects. Our target gene set is a promising starting point for further embryonic studies, as well as for the molecular genetic characterization of subregions and cell types in the neurogenic systems in the adult crayfish brain.

Phylogeographic reconstruction of the marbled crayfish origin

The marbled crayfish (Procambarus virginalis) is a triploid and parthenogenetic freshwater crayfish species that has colonized diverse habitats around the world. Previous studies suggested that the clonal marbled crayfish population descended as recently as 25 years ago from a single specimen of P. fallax, the sexually reproducing parent species. However, the genetic, phylogeographic, and mechanistic origins of the species have remained enigmatic. We have now constructed a new genome assembly for P. virginalis to support a detailed phylogeographic analysis of the diploid parent species, Procambarus fallax. Our results strongly suggest that both parental haplotypes of P. virginalis were inherited from the Everglades subpopulation of P. fallax. Comprehensive whole-genome sequencing also detected triploid specimens in the same subpopulation, which either represent evolutionarily important intermediate genotypes or independent parthenogenetic lineages arising among the sexual parent population. Our findings thus clarify the geographic origin of the marbled crayfish and identify potential mechanisms of parthenogenetic speciation.

Ageing European lobsters (Homarus gammarus) using DNA methylation of evolutionarily conserved ribosomal DNA

Crustaceans are notoriously difficult to age because of their indeterminate growth and the moulting of their exoskeleton throughout life. The poor knowledge of population age structure in crustaceans therefore hampers accurate assessment of population dynamics and consequently sustainable fisheries management. Quantification of DNA methylation of the evolutionarily conserved ribosomal DNA (rDNA) may allow for age prediction across diverse species. However, the rDNA epigenetic clock remains to be tested in crustaceans, despite its potential to inform both ecological and evolutionary understanding, as well as conservation and management practices. Here, patterns of rDNA methylation with age were measured across 5154 bp of rDNA corresponding to 355 quality-filtered loci in the economically important European lobster (Homarus gammarus). Across 0- to 51-month-old lobsters (n = 155), there was a significant linear relationship between age and percentage rDNA methylation in claw tissue at 60% of quality-filtered loci (n = 214). An Elastic Net regression model using 46 loci allowed for the accurate and precise age estimation of individuals (R 2 = 0.98; standard deviation = 1.6 months). Applying this ageing model to antennal DNA from wild lobsters of unknown age (n = 38) resulted in predicted ages that are concordant with estimates of minimum size at age in the wild (mean estimated age = 40.1 months; range 32.8-55.7 months). Overall, the rDNA epigenetic clock shows potential as a novel, nonlethal ageing technique for European lobsters. However, further validation is required across a wider range of known-age individuals and tissue types before the model can be used in fisheries management.

Evaluating Invasive Marbled Crayfish as a Potential Livestock for Sustainable Aquaculture

The marbled crayfish (Procambarus virginalis) is a recently discovered freshwater crayfish species, which reproduces by apomictic parthenogenesis, resulting in a monoclonal, and all-female population. The animals were widely distributed through the aquarium trade and have established numerous stable wild populations through anthropogenic releases. They are highly prevalent in Madagascar, where they have become a popular source of nutritional protein. As freshwater crayfish aquaculture in open systems is a thriving, but ecologically damaging global industry, alternatives are urgently needed. Although marbled crayfish are often branded by their invasive mode of reproduction, their overall invasiveness is not higher than for other cultured crayfish species. Furthermore, their resiliency and high adaptability provide a strong rationale for evaluating them for closed, and environmentally safe aquaculture approaches. Here we describe a novel population of marbled crayfish in a former German coal mining area that is characterized by acid and polluted water. Even under these adverse conditions, animals grew to sizes, and weights that are comparable to commercially farmed freshwater crayfish. Tailored feed development and laboratory testing demonstrated highly efficient feed conversion, suggesting a considerable capacity for sustainable production in closed systems. We further show that marbled crayfish meat can be readily introduced into European meals. Finally, chemical analysis of marbled crayfish exoskeletons revealed comparably high amounts of chitin, which is a valuable source for the synthesis of chitosan and bioplastics. Our results thus suggest that production of marbled crayfish in closed systems may represent a sustainable alternative for crayfish aquaculture.

First Record of the Alien Species Procambarus virginalis Lyko, 2017 in Fresh Waters of Sardinia and Insight into Its Genetic Variability

In the fresh waters of Sardinia (Italy), the non-indigenous crayfish species Procambarus clarkii has been reported from 2005, but, starting from 2019, there have been several reports of a new non-indigenous crayfish in southern and central areas of this Mediterranean island, and its morphology suggests that this species may be the marbled crayfish Procambarus virginalis. Forty-seven individuals of this putative species were analyzed, using the mitochondrial gene Cytochrome c Oxidase subunit I as molecular marker to identify this crayfish and investigate the level of genetic variability within the recently established population. Phylogenetic and phylogeographic analyses were carried out on a dataset including sequences from the Sardinian individuals and from all congenerics available in GenBank. Results showed that the new Sardinian crayfish belong to the species P. virginalis. All the sequences belonging to P. virginalis from European countries are identical, with only few exceptions found among Sardinian individuals. In conclusion, this paper highlights the occurrence of a new further alien species in the Sardinian fresh waters, which are already characterized by the high presence of non-indigenous species.

Aversive operant conditioning alters the phototactic orientation of the marbled crayfish

Aversive learning was applied to affect the phototactic behaviour of the marbled crayfish. Animals initially showed negative phototaxis to white light and positive taxis to blue light. Using an aversive learning paradigm, we investigated the plasticity of innate behaviour following operant conditioning. The initial rate of choosing a blue-lit exit was analysed by a dual choice experiment between blue-lit and white-lit exits in pre-test conditions. During training, electrical shocks were applied to the animals when they oriented to the blue-lit exit. Memory tests were given to analyse the orientation rate to the blue-lit exit in trials 1 and 24 h after training and these rates were compared with the pre-test. In general, animals avoided the blue-lit exit in the memory tests. When training was carried out three times, the long-term memory was retained for at least 48 h, although a single bout of training was also enough to form a long-term memory. Cooling animals at 4°C or injection of cycloheximide immediately after training altered the formation of long-term memory, but had no effect on short-term memory formation. Administration of the adenylate cyclase inhibitor SQ22536, the PKA inhibitor H89 or the CREB inhibitor KG-501 immediately after training also blocked the formation of long-term memory, but had no effect on short-term memory formation. Thus, our pharmacological behavioural analyses showed that new protein synthesis was necessary to form long-term memories and that the cAMP/PKA/CREB pathway is the main signal cascade for long-term memory formation in the marbled crayfish.

Genome analysis of the monoclonal marbled crayfish reveals genetic separation over a short evolutionary timescale

The marbled crayfish (Procambarus virginalis) represents a very recently evolved parthenogenetic freshwater crayfish species that has invaded diverse habitats in Europe and in Madagascar. However, population genetic analyses have been hindered by the homogeneous genetic structure of the population and the lack of suitable tools for data analysis. We have used whole-genome sequencing to characterize reference specimens from various known wild populations. In parallel, we established a whole-genome sequencing data analysis pipeline for the population genetic analysis of nearly monoclonal genomes. Our results provide evidence for systematic genetic differences between geographically separated populations and illustrate the emerging differentiation of the marbled crayfish genome. We also used mark-recapture population size estimation in combination with genetic data to model the growth pattern of marbled crayfish populations. Our findings uncover evolutionary dynamics in the marbled crayfish genome over a very short evolutionary timescale and identify the rapid growth of marbled crayfish populations as an important factor for ecological monitoring.

Olena Maiakovska et al. provide whole-genome sequencing of the parthenogenetic and invasive marbled crayfish and develop a computational framework for data analysis of monoclonal genomes. These data and methodology allow the authors to demonstrate genetic separation between two populations and provide the first size estimate for a marbled crayfish colony, which they used to model population growth patterns.

Physiologists turned Geneticists: Identifying transcripts and genes for neuronal function in the Marbled Crayfish, Procambarus virginalis

The number of undergraduate researchers interested in pursuing neurophysiological research exceeds the research laboratory positions and hands-on course experiences available because these types of experiments often require extensive experience or expensive equipment. In contrast, genetic and molecular tools can more easily incorporate undergraduates with less time or training. With the explosion of newly sequenced genomes and transcriptomes, there is a large pool of untapped molecular and genetic information which would greatly inform neurophysiological processes. Classically trained neurophysiologists often struggle to make use of newly available genetic information for themselves and their trainees, despite the clear advantage of combining genetic and physiological techniques. This is particularly prevalent among researchers working with organisms that historically had no or only few genetic tools available. Combining these two fields will expose undergraduates to a greater variety of research approaches, concepts, and hands-on experiences. The goal of this manuscript is to provide an easily understandable and reproducible workflow that can be applied in both lab and classroom settings to identify genes involved in neuronal function. We outline clear learning objectives that can be acquired by following our workflow and assessed by peer-evaluation. Using our workflow, we identify and validate the sequence of two new Gamma Aminobutyric Acid A (GABAA) receptor subunit homologs in the recently published genome and transcriptome of the marbled crayfish, Procambarus virginalis. Altogether, this allows undergraduate students to apply their knowledge of the processes of gene expression to functional neuronal outcomes. It also provides them with opportunities to contribute significantly to physiological research, thereby exposing them to interdisciplinary approaches.

Molecular Characterization and Functional Study of Insulin-Like Androgenic Gland Hormone Gene in the Red Swamp Crayfish, Procambarus clarkii

The androgenic gland (AG) is a male-specific endocrine organ that controls the primary and secondary sexual characteristics in male crustaceans. More evidence indicates that the insulin-like androgenic gland hormone gene (IAG) is the key male sexual differentiation factor, particularly the application of RNA interference (RNAi) technology on IAG. In this study, the full-length cDNA of IAG (termed PcIAG) was isolated from the red swamp crayfish, Procambarusclarkii. Tissue distribution analysis showed that in addition to its expression in the AG of male P. clarkii, PcIAG was widely expressed in female tissues and other male tissues. The PcIAG protein was detected in the reproductive and nervous systems of adult male P. clarkii. Additionally, RNAi results showed that the PcIAG expression could be silenced efficiently, and the male sperm maturation and release possibly present a transient adverse interference at lower doses (0.1 μg/g and 1 μg/g) of PcIAG–dsRNA (PcIAG double-stranded RNA). Dramatically, the expression level of PcIAG increased sharply shortly after the injection of higher doses (5 μg/g and 10 μg/g) of PcIAG–dsRNA, which might accelerate the maturation and release of sperm. Moreover, the expression of PcSxl (P. clarkii Sex-lethal) was detected by Quantitative Real-Time PCR (qPCR) after the injection of PcIAG–dsRNA to explore whether the PcIAG gene regulates the PcSxl gene, and we found that the PcIAG did not directly regulate PcSxl in P. clarkii. The study could help accelerate the progress of PcIAG functional research and provide a useful reference for the single-sex selective breeding of P. clarkii.

How to become a successful invasive tapeworm: a case study of abandoned sexuality and exceptional chromosome diversification in the triploid carp parasite Atractolytocestus huronensis Anthony, 1958 (Caryophyllidea: Lytocestidae)

Background

A cytogenetic analysis of the new local triploid population of the caryophyllidean tapeworm Atractolytocestus huronensis, a unique parthenogenetic species with the ability to colonise new regions, was performed to understand the inner structure of its chromosome complement.

Methods

A karyotype analysis was carried out using classical Giemsa staining and C-banding combined with fluorescent DAPI staining. A hypothesis that triplets are composed from three homologue chromosomes of approximately the same length and same centromere position was tested statistically for multiple dependent variables using a non-parametric Friedman’s ANOVA. The chromosomal location of ribosomal DNA clusters within the nucleolar organization region (NORs) and telomeric (TTAGGG)_n sequences were detected by fluorescent in situ hybridization (FISH). Chromosomes were subjected to AgNO₃ staining in order to determine whether the rDNA sites represent active NORs.

Results

The cytogenetic analysis confirmed the karyotype composed from eight chromosome triplets (3n = 24) as well as the existence of a pair of NORs located on each chromosome of the second triplet. Six NORs varied their activity from cell to cell, and it was reflected in the numbers of nucleoli (from 1 to 5). A huge morphological diversification of homologue chromosomes was originally detected in six out of eight triplets; the homologue elements differed significantly either in length and/or morphology, and some of them carried discernible interstitial telomeric sequences (ITSs), while the end telomeres were minute. The heterochromatin bands with high AT content varied irregularly, and the course of aberrant spermatogenesis was evident.

Conclusions

Diversification of homologues is a unique phenomenon very likely caused by the long-term absence of a recombination and consequential accumulation of chromosome rearrangements in the genome of A. huronensis during species evolution. Unalterable asexual reproduction of the tapeworm, along with international trade in its host (carp), is facilitating its ongoing spread.

The effects of shelter quality and prior residence on marmorkrebs (marbled crayfish)

Many animals fight over a limited valuable resource. In marmorkrebs (marbled crayfish), large animals usually defeat small opponents but they are frequently beaten by small opponents that are shelter owners. A prior residence effect of marbled crayfish was analysed quantitatively in the present study. More than 2 h of residency in a shelter was sufficient for small owners to defeat large intruders. Small animals that stayed in a shelter for 24 h still tended to win following removal of the shelter 10 min before pairing with large intruders, but 2 h residents were occasionally beaten by large intruders without the support of shelters during pairings. The prior residence effect thus developed depending on the duration of residency. To clarify whether the strength of the prior residence effect was affected by the quality of a shelter, large and small owners with different combinations of high- and low-quality shelters were paired. When both large and small owners possessed a high-quality shelter, the frequency of agonistic bouts was reduced. Even if agonistic bouts occurred, the win frequency of small owners was almost equal to that of large owners. Thus, the residence effect on small owners was sufficiently strong to overcome the physical disadvantage of small animals to large opponents. By contrast, small owners of low--quality shelters were frequently beaten by large owners with the shelters of same or better quality. We conclude that the outcome of fights over the resource shelter is highly dependent on both the perception of shelter quality and body size differences.

Ecological plasticity and commercial impact of invasive marbled crayfish populations in Madagascar

Background

The marbled crayfish (Procambarus virginalis) is a monoclonal, parthenogenetically reproducing freshwater crayfish species that has formed multiple stable populations worldwide. Madagascar hosts a particularly large and rapidly expanding colony of marbled crayfish in a unique environment characterized by a very high degree of ecological diversity.

Results

Here we provide a detailed characterization of five marbled crayfish populations in Madagascar and their habitats. Our data show that the animals can tolerate a wide range of ecological parameters, consistent with their invasive potential. While we detected marbled crayfish in sympatry with endemic crayfish species, we found no evidence for the transmission of the crayfish plague pathogen, a potentially devastating oomycete. Furthermore, our results also suggest that marbled crayfish are active predators of the freshwater snails that function as intermediate hosts for human schistosomiasis. Finally, we document fishing, farming and market sales of marbled crayfish in Madagascar.

Conclusions

Our results provide a paradigm for the complex network of factors that promotes the invasive spread of marbled crayfish. The commercial value of the animals is likely to result in further anthropogenic distribution.

Electronic supplementary material

The online version of this article (10.1186/s12898-019-0224-1) contains supplementary material, which is available to authorized users.

The methylome of the marbled crayfish links gene body methylation to stable expression of poorly accessible genes

Background

The parthenogenetic marbled crayfish (Procambarus virginalis) is a novel species that has rapidly invaded and colonized various different habitats. Adaptation to different environments appears to be independent of the selection of genetic variants, but epigenetic programming of the marbled crayfish genome remains to be understood.

Results

Here, we provide a comprehensive analysis of DNA methylation in marbled crayfish. Whole-genome bisulfite sequencing of multiple replicates and different tissues revealed a methylation pattern that is characterized by gene body methylation of housekeeping genes. Interestingly, this pattern was largely tissue invariant, suggesting a function that is unrelated to cell fate specification. Indeed, integrative analysis of DNA methylation, chromatin accessibility and mRNA expression patterns revealed that gene body methylation correlated with limited chromatin accessibility and stable gene expression, while low-methylated genes often resided in chromatin with higher accessibility and showed increased expression variation. Interestingly, marbled crayfish also showed reduced gene body methylation and higher gene expression variability when compared with their noninvasive mother species, Procambarus fallax.

Conclusions

Our results provide novel insights into invertebrate gene body methylation and its potential role in adaptive gene regulation.

Electronic supplementary material

The online version of this article (10.1186/s13072-018-0229-6) contains supplementary material, which is available to authorized users.

The Influence of Heavy Metal Ions on the Viability and Metabolic Enzyme Activity of the Marbled Crayfish <i>Procambarus virginalis</i> (Lyko, 2017)

In the experiment with marbled crayfish Procambarusvirginalis (Lyko, 2017), chronic effects of various concentrations of heavy metal ions on the physiological state and enzyme activity were investigated. The obtained results showed that among the investigated heavy metals nickel ions influenced the weight indexes and mortality of crustaceans the most negatively. According to the results of the research, significant changes were noted in the individual biochemical parameters of marbled crayfish under the influence of manganese, lead and nickel ions. The most significant changes in the activity of lactate dehydrogenase were detected in muscle tissues affected by manganese and nickel ions. A significant decrease in the activity of succinate dehydrogenase in muscle of marbled crayfish was determined after the action of heavy metal ions. Investigation of changes in the activity of alkaline phosphatase under the influence of the ions of manganese, lead and nickel has its own characteristics, which indicates certain violations in the tissues of cell membranes. Changes in the activity of enzymes were also reflected in the overall protein content. Changes in these parameters may indicate a rapid biochemical response of crustaceans to the toxic effects of heavy metals.

The Influence of Heavy Metal Ions on the Viability and Metabolic Enzyme Activity of the Marbled Crayfish <i>Procambarus virginalis</i> (Lyko, 2017)

In the experiment with marbled crayfishProcambarusvirginalis(Lyko, 2017), chronic effects of various concentrations of heavy metal ions on the physiological state and enzyme activity were investigated. The obtained results showed that among the investigated heavy metals nickel ions influenced the weight indexes and mortality of crustaceans the most negatively. According to the results of the research, significant changes were noted in the individual biochemical parameters of marbled crayfish under the influence of manganese, lead and nickel ions. The most significant changes in the activity of lactate dehydrogenase were detected in muscle tissues affected by manganese and nickel ions. A significant decrease in the activity of succinate dehydrogenase in muscle of marbled crayfish was determined after the action of heavy metal ions. Investigation of changes in the activity of alkaline phosphatase under the influence of the ions of manganese, lead and nickel has its own characteristics, which indicates certain violations in the tissues of cell membranes. Changes in the activity of enzymes were also reflected in the overall protein content. Changes in these parameters may indicate a rapid biochemical response of crustaceans to the toxic effects of heavy metals.

Investigating the genetic and epigenetic basis of big biological questions with the parthenogenetic marbled crayfish: A review and perspectives

In the last 15 years, considerable attempts have been undertaken to develop the obligately parthenogenetic marbled crayfish Procambarus virginalis as a new model in biology. Its main advantage is the production of large numbers of offspring that are genetically identical to the mother, making this crustacean particularly suitable for research in epigenetics. Now, a draft genome, transcriptome and genome-wide methylome are available opening new windows for research. In this article, I summarize the biological advantages and genomic and epigenetic features of marbled crayfish and, based on first promising data, discuss what this new model could contribute to answering of ''big'' biological questions. Genome mining is expected to reveal new insights into the genetic specificities of decapod crustaceans, the genetic basis of arthropod reproduction, moulting and immunity, and more general topics such as the genetic underpinning of adaptation to fresh water, omnivory, biomineralization, sexual system change, behavioural variation, clonal genome evolution, and resistance to cancer. Epigenetic investigations with the marbled crayfish can help clarifying the role of epigenetic mechanisms in gene regulation, tissue specification, adult stem cell regulation, cell ageing, organ regeneration and disease susceptibility. Marbled crayfish is further suitable to elucidate the relationship between genetic and epigenetic variation, the transgenerational inheritance of epigenetic signatures and the contribution of epigenetic phenotype variation to the establishment of social hierarchies, environmental adaptation and speciation. These issues can be tackled by experiments with highly standardized laboratory lineages, comparison of differently adapted wild populations and the generation of genetically and epigenetically edited strains.

The gene encoding the insulin-like androgenic gland hormone in an all-female parthenogenetic crayfish

Male sexual differentiation in crustaceans is controlled by the androgenic gland (AG), a unique male endocrine organ that, in decapods, is located at the base of the 5th pereiopod. In these animals, the insulin-like androgenic gland hormone (IAG) is the major factor secreted from the AG to induce masculinization and maintain male characteristics. It has, however, recently been proposed that this hormone also plays a role in growth and ovarian development in females. In this study, we tested such a possibility by searching for the IAG gene in the marbled crayfish, a parthenogenetic animal that reproduces asexually to form an all-female genetic clone. Based on the phylogenetic relationship between the marbled crayfish and Procambarus fallax, a gonochoristic species of the same North American Cambaridae family, we searched for the IAG gene in the marbled crayfish and then fully sequenced it. The open reading frame of the gene was found to be completely identical in the two species, and their introns shared over 94% identity. It was also found that, in addition to its expression at the base of the 5th pereiopod and in the testes of male P. fallax crayfish, IAG was expressed in the muscle tissue of P. fallax males and females and even of the parthenogenetic marbled crayfish. These findings provide new insight into possible functions of IAG, in addition to its role as a masculinization-inducing factor, and also constitute the basis for a discussion of the evolutionary relationship between the above two species.

Cyclic AMP-regulated opposing and parallel effects of serotonin and dopamine on phototaxis in the Marmorkrebs (marbled crayfish)

Phototactic behaviours are observed from prokaryotes to amphibians and are a basic form of orientation. We showed that the marbled crayfish displays phototaxis in which the behavioural response reversed from negative to positive depending on external light conditions. Animals reared in a 12-L/12-D light cycle showed negative phototaxis during daytime and positive phototaxis during night-time. Animals reared under constant light conditioning showed negative phototaxis during day- and night-time, while animals reared under constant dark conditioning showed positive phototaxis during day- and night-time. Injection of serotonin leads to a reversal of negative to positive phototaxis in both light/dark-reared and light/light-reared animals while injection of dopamine induced reversed negative phototaxis in dark/dark-reared animals. Four hours of dark adaptation were enough for light/dark-reared animals to reverse phototaxis from negative to positive. Injection of a serotonin 5HT₁ receptor antagonist blocked the reverse phototaxis while serotonin 5HT₂ receptor antagonists had no effects. Similarly, dark/dark-reared animals reversed to showing negative phototaxis after 4 h of light adaptation. Injection of a dopamine DA₁ receptor antagonist blocked this reverse phototaxis, while dopamine DA₂ receptor antagonists had no effects. Injection of a cAMP analogue into light/dark-reared animals blocked reverse phototaxis after dark adaptation, while adenylate cyclase inhibitor in dark/dark-reared animals blocked reverse phototaxis after light adaptation. These results strongly suggest that serotonin mediates positive phototaxis owing to decreased cAMP levels, while dopamine-mediated negative phototaxis occurs due to increased cAMP levels. Supporting this, the ratio of serotonin to dopamine in the brain was much higher in dark/dark-reared than light/dark-reared animals.

The Behavior of Chromosomes During Parthenogenetic Oogenesis in Marmorkrebs Procambarus fallax f. virginalis

Parthenogenetic oogenesis varies among and even within species. Based on cytological mechanisms, it can largely be divided into apomixis (ameiotic parthenogenesis) producing genetically identical progeny, and automixis (meiotic parthenogenesis) producing genetically non-identical progeny. Polyploidy is common in parthenogenetic species, although the association between parthenogenesis and polyploidy throughout evolution is poorly understood. Marmorkrebs, or the marbled crayfish, was first identified as a parthenogenetic decapod and was tentatively named as Procambarus fallax f. virginalis. Previous studies revealed that Marmorkrebs is triploid and produces genetically identical offspring, suggesting that apomixis occurs during parthenogenetic oogenesis. However, the behavior of chromosomes during the process of oogenesis is still not well characterized. In this study, we observed parthenogenetic oogenesis around the time of ovulation in P. fallax f. virginalis by histology and immunohistochemistry. During oogenesis, the chromosomes were separated into two groups and behaved independently from each other, and one complete division corresponding to mitosis (the second meiosis-like division) was observed. This suggests that parthenogenetic oogenesis in Marmorkrebs exhibits gonomery, a phenomenon commonly found in apomictic parthenogenesis in polyploid animals.

Facilitation of environmental adaptation and evolution by epigenetic phenotype variation: insights from clonal, invasive, polyploid, and domesticated animals

There is increasing evidence, particularly from plants, that epigenetic mechanisms can contribute to environmental adaptation and evolution. The present article provides an overview on this topic for animals and highlights the special suitability of clonal, invasive, hybrid, polyploid, and domesticated species for environmental and evolutionary epigenetics. Laboratory and field studies with asexually reproducing animals have shown that epigenetically diverse phenotypes can be produced from the same genome either by developmental stochasticity or environmental induction. The analysis of invasions revealed that epigenetic phenotype variation may help to overcome genetic barriers typically associated with invasions such as bottlenecks and inbreeding. Research with hybrids and polyploids established that epigenetic mechanisms are involved in consolidation of speciation by contributing to reproductive isolation and restructuring of the genome in the neo-species. Epigenetic mechanisms may even have the potential to trigger speciation but evidence is still meager. The comparison of domesticated animals and their wild ancestors demonstrated heritability and selectability of phenotype modulating DNA methylation patterns. Hypotheses, model predictions, and empirical results are presented to explain how epigenetic phenotype variation could facilitate adaptation and speciation. Clonal laboratory lineages, monoclonal invaders, and adaptive radiations of different evolutionary age seem particularly suitable to empirically test the proposed ideas. A respective research agenda is presented.

Comprehensive DNA methylation analysis of the Aedes aegypti genome

Aedes aegypti mosquitoes are important vectors of viral diseases. Mosquito host factors play key roles in virus control and it has been suggested that dengue virus replication is regulated by Dnmt2-mediated DNA methylation. However, recent studies have shown that Dnmt2 is a tRNA methyltransferase and that Dnmt2-dependent methylomes lack defined DNA methylation patterns, thus necessitating a systematic re-evaluation of the mosquito genome methylation status. We have now searched the Ae. aegypti genome for candidate DNA modification enzymes. This failed to reveal any known (cytosine-5) DNA methyltransferases, but identified homologues for the Dnmt2 tRNA methyltransferase, the Mettl4 (adenine-6) DNA methyltransferase, and the Tet DNA demethylase. All genes were expressed at variable levels throughout mosquito development. Mass spectrometry demonstrated that DNA methylation levels were several orders of magnitude below the levels that are usually detected in organisms with DNA methylation-dependent epigenetic regulation. Furthermore, whole-genome bisulfite sequencing failed to reveal any evidence of defined DNA methylation patterns. These results suggest that the Ae. aegypti genome is unmethylated. Interestingly, additional RNA bisulfite sequencing provided first evidence for Dnmt2-mediated tRNA methylation in mosquitoes. These findings have important implications for understanding the mechanism of Dnmt2-dependent virus regulation.

Shelter preference in the Marmorkrebs (marbled crayfish)

For many animals, shelters are valuable source to hide from predators. To know acquisition of adequate shelter is important to understand social interactions of animals. Preferences for types of shelter used by the Marmorkrebs (marbled crayfish) were analysed behaviourally. Individual crayfish were presented with a choice between two PVC pipes with four different internal diameters (XL, L, M and S). The time spent in each shelter and the number of times crayfish entered each shelter were measured. Preference ranks of crayfish were XL = L = or > M > S. Our experiments strongly suggested that crayfish chose shelters based first on the diameter of the entrance, and then based on the length of the shelter. Crayfish recognised adequate shelters by visual cues under light conditions and utilised tactile cues from their antennae under dark conditions.