The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development

Evolution of diapause in the African turquoise killifish by remodeling the ancient gene regulatory landscape

Suspended animation states allow organisms to survive extreme environments. The African turquoise killifish has evolved diapause as a form of suspended development to survive a complete drought. However, the mechanisms underlying the evolution of extreme survival states are unknown. To understand diapause evolution, we performed integrative multi-omics (gene expression, chromatin accessibility, and lipidomics) in the embryos of multiple killifish species. We find that diapause evolved by a recent remodeling of regulatory elements at very ancient gene duplicates (paralogs) present in all vertebrates. CRISPR-Cas9-based perturbations identify the transcription factors REST/NRSF and FOXOs as critical for the diapause gene expression program, including genes involved in lipid metabolism. Indeed, diapause shows a distinct lipid profile, with an increase in triglycerides with very-long-chain fatty acids. Our work suggests a mechanism for the evolution of complex adaptations and offers strategies to promote long-term survival by activating suspended animation programs in other species.

The African Turquoise Killifish: A Scalable Vertebrate Model for Aging and Other Complex Phenotypes

The African turquoise killifish Nothobranchius furzeri is currently the shortest-lived vertebrate that can be bred in captivity. Because of its short life span of only 4-6 months, rapid generation time, high fecundity, and low cost of maintenance, the African turquoise killifish has emerged as an attractive model organism that combines the scalability of invertebrate models with the unique features of vertebrate organisms. A growing community of researchers is using the African turquoise killifish for studies in diverse fields, including aging, organ regeneration, development, "suspended animation," evolution, neuroscience, and disease. A wide range of techniques is now available for killifish research, from genetic manipulations and genomic tools to specialized assays for studying life span, organ biology, response to injury, etc. This protocol collection provides detailed descriptions of the methods that are generally applicable to all killifish laboratories and those that are limited to specific disciplines. Here, we give an overview of the features that render the African turquoise killifish a unique fast-track vertebrate model organism.

Living in Temporary Ponds Loading Giant Genomes: The Neotropical Annual Killifish Genus Austrolebias as New Outstanding Evolutionary Model

The term Annual killifish describes a short-lived and amazing group of vertebrates inhabiting temporary ponds exposed to an extremely variable environment during its short lifespan in South America and Africa, leading to the death of the entire adult population during the dry season. Austrolebias is a specious genus of the family Rivulidae, with ∼58 currently recognized species, extensively distributed in the temperate Neotropical region. Herein, we reviewed different aspects of the evolutionary biology with emphasis on the genome dynamic linked to the burst speciation process in this genus. Austrolebias constitutes an excellent model to study the genomic evolutionary processes underlying speciation events, since all the species of this genus analyzed so far share an unusually large genome size, with an average DNA content of 5.95 ± 0.45 picograms per diploid cell (mean C-value of about 2.98 pg). The drastic nuclear DNA–increasing would be associated with a considerable proportion of transposable elements (TEs) found in the Austrolebias genomes. The genomic proportion of the moderately repetitive DNA in the A. charrua genome represents approximately twice (45%) the amount of the repetitive components of the highly related sympatric and syntopic rivulinae taxon Cynopoecilus melanotaenia (25%), as well as from other rivulids and actinopterygian fish. These events could explain the great genome instability, the high genetic diversity, chromosome variability, as well as the morphological diversity in species of Austrolebias. Thus, species of this genus represent new model systems linking different evolutionary processes: drastic genome increase, massive TEs genomic representation, high chromosome instability, occurrence of natural hybridization between sister species, and burst speciation events.

Genome of the Rio Pearlfish (Nematolebias whitei), a bi-annual killifish model for Eco-Evo-Devo in extreme environments

The Rio Pearlfish, Nematolebias whitei, is a bi-annual killifish species inhabiting seasonal pools in the Rio de Janeiro region of Brazil that dry twice per year. Embryos enter dormant diapause stages in the soil, waiting for the inundation of the habitat which triggers hatching and commencement of a new life cycle. Rio Pearlfish represents a convergent, independent origin of annualism from other emerging killifish model species. While some transcriptomic datasets are available for Rio Pearlfish, thus far, a sequenced genome has been unavailable. Here, we present a high quality, 1.2 Gb chromosome-level genome assembly, genome annotations, and a comparative genomic investigation of the Rio Pearlfish as representative of a vertebrate clade that evolved environmentally cued hatching. We show conservation of 3D genome structure across teleost fish evolution, developmental stages, tissues, and cell types. Our analysis of mobile DNA shows that Rio Pearlfish, like other annual killifishes, possesses an expanded transposable element profile with implications for rapid aging and adaptation to harsh conditions. We use the Rio Pearlfish genome to identify its hatching enzyme gene repertoire and the location of the hatching gland, a key first step in understanding the developmental genetic control of hatching. The Rio Pearlfish genome expands the comparative genomic toolkit available to study convergent origins of seasonal life histories, diapause, and rapid aging phenotypes. We present the first set of genomic resources for this emerging model organism, critical for future functional genetic, and multiomic explorations of “Eco-Evo-Devo” phenotypes of resilience and adaptation to extreme environments.

Functional genomics of abiotic environmental adaptation in lacertid lizards and other vertebrates

Understanding the genomic basis of adaptation to different abiotic environments is important in the context of climate change and resulting short-term environmental fluctuations. Using functional and comparative genomics approaches, we here investigated whether signatures of genomic adaptation to a set of environmental parameters are concentrated in specific subsets of genes and functions in lacertid lizards and other vertebrates. We first identify 200 genes with signatures of positive diversifying selection from transcriptomes of 24 species of lacertid lizards and demonstrate their involvement in physiological and morphological adaptations to climate. To understand how functionally similar these genes are to previously predicted candidate functions for climate adaptation and to compare them with other vertebrate species, we then performed a meta-analysis of 1,100 genes under selection obtained from -omics studies in vertebrate species adapted to different abiotic factors. We found that the vertebrate gene set formed a tightly connected interactome, which was to 23% enriched in previously predicted functions of adaptation to climate, and to a large part (18%) involved in organismal stress response. We found a much higher degree of identical genes being repeatedly selected among different animal groups (43.6%), and of functional similarity and post-translational modifications than expected by chance, and no clear functional division between genes used for ectotherm and endotherm physiological strategies. In total, 171 out of 200 genes of Lacertidae were part of this network. These results highlight an important role of a comparatively small set of genes and their functions in environmental adaptation and narrow the set of candidate pathways and markers to be used in future research on adaptation and stress response related to climate change.

Distinct Gene Expression Patterns of Two Heat Shock Protein 70 Members During Development, Diapause, and Temperature Stress in the Freshwater Crustacean Daphnia magna

Dormancy is a lifecycle delay that allows organisms to escape suboptimal environmental conditions. As a genetically programmed type of dormancy, diapause is usually accompanied by metabolic depression and enhanced tolerance toward adverse environmental factors. However, the drivers and regulators that steer an organism’s development into a state of suspended animation to survive environmental stress have not been fully uncovered. Heat shock proteins 70 (HSP70s), which are often produced in response to various types of stress, have been suggested to play a role in diapause. Considering the diversity of the Hsp70 family, different family members may have different functions during diapause. In the present study, we demonstrate the expression of two hsp70 genes (A and B together with protein localization of B) throughout continuous and diapause interrupted development of Daphnia magna. Before and after diapause, the expression of Dmhsp70-A is low. Only shortly before diapause and during diapause, Dmhsp70-A is significantly upregulated and may therefore be involved in diapause preparation and maintenance. In contrast, Dmhsp70-B is expressed only in developing embryos but not in diapausing embryos. During continuous development, the protein of this Hsp70 family member is localized in the cytosol. When we expose both embryo types to heat stress, expression of both hsp70 genes increases only in developing embryos, and the protein of family member B is translocated to the nucleus. In this stress formation, this protein provides effective protection of nucleoplasmic DNA. As we also see this localization in diapausing embryos, it seems that Daphnia embryo types share a common subcellular strategy when facing dormancy or heat shock, i.e., they protect their DNA by HSP70B nuclear translocation. Our study underlines the distinctive roles that different Hsp70 family members play throughout continuous and diapause interrupted development.

Pinniped Ontogeny as a Window into the Comparative Physiology and Genomics of Hypoxia Tolerance

Diving physiology has received considerable scientific attention as it is a central element of the extreme phenotype of marine mammals. Many scientific discoveries have illuminated physiological mechanisms supporting diving, such as massive, internally bound oxygen stores and dramatic cardiovascular regulation. However, the cellular and molecular mechanisms that support the diving phenotype remain mostly unexplored as logistic and legal restrictions limit the extent of scientific manipulation possible. With next-generation sequencing (NGS) tools becoming more widespread and cost-effective, there are new opportunities to explore the diving phenotype. Genomic investigations come with their own challenges, particularly those including cross-species comparisons. Studying the regulatory pathways that underlie diving mammal ontogeny could provide a window into the comparative physiology of hypoxia tolerance. Specifically, in pinnipeds, which shift from terrestrial pups to elite diving adults, there is potential to characterize the transcriptional, epigenetic, and posttranslational differences between contrasting phenotypes while leveraging a common genome. Here we review the current literature detailing the maturation of the diving phenotype in pinnipeds, which has primarily been explored via biomarkers of metabolic capability including antioxidants, muscle fiber typing, and key aerobic and anaerobic metabolic enzymes. We also discuss how NGS tools have been leveraged to study phenotypic shifts within species through ontogeny, and how this approach may be applied to investigate the biochemical and physiological mechanisms that develop as pups become elite diving adults. We conclude with a specific example of the Antarctic Weddell seal by overlapping protein biomarkers with gene regulatory microRNA datasets.

GABA metabolism is crucial for long-term survival of anoxia in annual killifish embryos

In most vertebrates, a lack of oxygen quickly leads to irreparable damages to vital organs, such as the brain and heart. However, there are some vertebrates that have evolved mechanisms to survive periods of no oxygen (anoxia). The annual killifish (Austrofundulus limnaeus) survives in ephemeral ponds in the coastal deserts of Venezuela and their embryos have the remarkable ability to tolerate anoxia for months. When exposed to anoxia, embryos of A. limnaeus respond by producing significant amounts of γ-aminobutyric acid (GABA). This study aims to understand the role of GABA in supporting the metabolic response to anoxia. To explore this, we investigated four developmentally distinct stages of A. limnaeus embryos that vary in their anoxia tolerance. We measured GABA and lactate concentrations across development in response to anoxia and aerobic recovery. We then inhibited enzymes responsible for the production and degradation of GABA and observed GABA and lactate concentrations, as well as embryo mortality. Here, we show for the first time that GABA metabolism affects anoxia tolerance in A. limnaeus embryos. Inhibition of enzymes responsible for GABA production (glutamate decarboxylase) and degradation (GABA-transaminase and succinic acid semialdehyde dehydrogenase) led to increased mortality, supporting a role for GABA as an intermediate product and not a metabolic end-product. We propose multiple roles for GABA during anoxia and aerobic recovery in A. limnaeus embryos, serving as a neurotransmitter, an energy source, and an anti-oxidant.

No water, no problem: stage-specific metabolic responses to dehydration stress in annual killifish embryos

Annual killifish survive in temporary ponds by producing drought-tolerant embryos that can enter metabolic dormancy (diapause). Survival of dehydration stress is achieved through severe reduction of evaporative water loss. We assessed dehydration stress tolerance in diapausing and developing Austrofundulus limnaeus embryos. We measured oxygen consumption rates under aquatic and aerial conditions to test the hypothesis that there is a trade-off between water retention and oxygen permeability. Diapausing embryos survive dehydrating conditions for over 1.5 years, and post-diapause stages can survive for over 100 days. Diapausing embryos respond to dehydration stress by increasing oxygen consumption rates while post-diapause embryos exhibit the same or reduced rates compared with aquatic embryos. Thus, water retention does not always limit oxygen diffusion. Aerial incubation coupled with hypoxia causes some embryos to arrest development. The observed stage-specific responses are consistent with an intrinsic bet-hedging strategy in embryos that would increase developmental variation in a potentially adaptive manner.

Metabolomics analysis of annual killifish (Austrofundulus limnaeus) embryos during aerial dehydration stress

The annual killifish, Austrofundulus limnaeus, survives in ephemeral ponds in the coastal deserts of Venezuela. Persistence through the dry season is dependent on drought-resistant eggs embedded in the pond sediments during the rainy season. The ability of these embryos to enter drastic metabolic dormancy (diapause) during normal development enables A. limnaeus to survive conditions lethal to most other aquatic vertebrates; critical to the survival of the species is the ability of embryos to survive months and perhaps years without access to liquid water. Little is known about the molecular mechanisms that aid in survival of the dry season. This study aims to gain insight into the mechanisms facilitating survival of dehydration stress due to aerial exposure by examining metabolite profiles of dormant and developing embryos. There is strong evidence for unique metabolic profiles based on developmental stage and length of aerial exposure. Actively developing embryos exhibit more robust changes; however, dormant embryos respond in an active manner and significantly alter their metabolic profile. A number of metabolites accumulate in aerial-exposed embryos that may play an important role in survival, including the identification of known antioxidants and neuroprotectants. In addition, a number of unique metabolites not yet discussed in the dehydration literature are identified, such as lanthionine and 2-hydroxyglutarate. Despite high oxygen availability, embryos accumulate the anaerobic end product lactate. This paper offers an overview of the metabolic changes occurring that may support embryonic survival during dehydration stress due to aerial incubation, which can be functionally tested using genetic and pharmacological approaches.

MitosRNAs and extreme anoxia tolerance in embryos of the annual killifish Austrofundulus limnaeus

Embryos of the annual killifish Austrofundulus limnaeus are the most anoxia-tolerant vertebrate. Annual killifish inhabit ephemeral ponds, producing drought and anoxia-tolerant embryos, which allows the species to persist generation after generation. Anoxia tolerance and physiology vary by developmental stage, creating a unique opportunity for comparative study within the species. A recent study of small ncRNA expression in A. limnaeus embryos in response to anoxia and aerobic recovery revealed small ncRNAs with expression patterns that suggest a role in supporting anoxia tolerance. MitosRNAs, small ncRNAs derived from the mitochondrial genome, emerged as an interesting group of these sequences. MitosRNAs derived from mitochondrial tRNAs were differentially expressed in developing embryos and isolated cells exhibiting extreme anoxia tolerance. In this study we focus on expression of mitosRNAs derived from tRNA-cysteine, and their subcellular and organismal localization in order to consider possible function. These tRNA-cys mitosRNAs appear enriched in the mitochondria, particularly near the nucleus, and also appear to be present in the cytoplasm. We provide evidence that mitosRNAs are generated in the mitochondria in response to anoxia, though the precise mechanism of biosynthesis remains unclear. MitosRNAs derived from tRNA-cys localize to numerous tissues, and increase in the anterior brain during anoxia. We hypothesize that these RNAs may play a role in regulating gene expression that supports extreme anoxia tolerance.

Establishment and characterization of an anoxia-tolerant cell line, PSU-AL-WS40NE, derived from an embryo of the annual killifish Austrofundulus limnaeus

Most animal cells rely on aerobic metabolism for survival and are damaged or die within minutes without oxygen. Embryos of the annual killifish Austrofundulus limnaeus, however, survive months without oxygen. Determining how their cells survive without oxygen has the potential to revolutionize our understanding of the cellular mechanisms supporting vertebrate anoxia tolerance and the evolution of such tolerance. Therefore, we aimed to establish and characterize an anoxia-tolerant cell line from A. limnaeus for investigating mechanisms of vertebrate anoxia tolerance. The PSU-AL-WS40NE cell line of neuroepithelial identity was established from embryonic tissue of A. limnaeus using a tissue explant. The cells can survive for at least 49 d without oxygen or replenishment of growth medium, compared to only 3 d of anoxic survival for two mammalian cell lines. PSU-AL-WS40NE cells accumulate lactate during anoxia, indicating use of common metabolic pathways for anaerobic metabolism. Additionally, they express many of the same small noncoding RNAs that are stress-responsive in whole embryos of A. limnaeus and mammalian cells, as well as anoxia-responsive small noncoding RNAs derived from the mitochondrial genome (mitosRNAs). The establishment of the cell line provides a unique tool for investigating cellular mechanisms of vertebrate anoxia tolerance, and has the potential to transform our understanding of the role of oxidative metabolism in cell biology.

Netting the Stress Responses in Fish

In the last decade, the concept of animal stress has been stressed thin to accommodate the effects of short-term changes in cell and tissue physiology, major behavioral syndromes in individuals and ecological disturbances in populations. Seyle's definition of stress as "the nonspecific (common) result of any demand upon the body" now encompasses homeostasis in a broader sense, including all the hierarchical levels in a networked biological system. The heterogeneity of stress responses thus varies within individuals, and stressors become multimodal in terms of typology, source and effects, as well as the responses that each individual elicits to cope with the disturbance. In fish, the time course of changes after stress strongly depends on several factors, including the stressful experiences in early life, the vertical transmission of stressful-prone phenotypes, the degree of individual phenotypic plasticity, the robustness and variety of the epigenetic network related to environmentally induced changes, and the intrinsic behavioral responses (individuality/personality) of each individual. The hierarchical heterogeneity of stress responses demands a code that may decrypt and simplify the analysis of both proximate and evolutionary causes of a particular stress phenotype. We propose an analytical framework, the stressotope, defined as an adaptive scenario dominated by common environmental selective pressures that elicit common multilevel acute stress-induced responses and produce a measurable allostatic load in the organism. The stressotope may constitute a blueprint of embedded interactions between stress-related variations in cell states, molecular mediators and systemic networks, a map of circuits that reflect the inherited and acquired stress responses in an ever-changing, microorganismal-loaded medium. Several features of the proposed model are discussed as a starting point to pin down the maximum common stress responses across immune-neuroendocrine relevant physiological levels and scenarios, including the characterization of behavioral responses, in fish.

Antioxidant capacity and anoxia-tolerance in Austrofundulus limnaeus embryos

Embryos of Austrofundulus limnaeus can tolerate extreme environmental stresses by entering into a state of metabolic and developmental arrest known as diapause. Oxidative stress is ubiquitous in aerobic organisms and the unique biology and ecology of A. limnaeus likely results in frequent and repeated exposures to oxidative stress during development. Antioxidant capacity of A. limnaeus was explored during development by measuring antioxidant capacity due to small molecules and several enzymatic antioxidant systems. Diapause II embryos can survive for several days in 1% hydrogen peroxide without indications of negative effects. Surprisingly, both small and large molecule antioxidant systems are highest during early development and may be due to maternal provisioning. Antioxidant capacity is largely invested in small molecules during early development and in enzymatic systems during late development. The switch in antioxidant mechanisms and decline in small molecule antioxidants during development correlates with the loss of extreme anoxia tolerance.

Temperature-dependent vitamin D signaling regulates developmental trajectory associated with diapause in an annual killifish

The mechanisms that integrate environmental signals into developmental programs remain largely uncharacterized. Nuclear receptors (NRs) are ligand-regulated transcription factors that orchestrate the expression of complex phenotypes. The vitamin D receptor (VDR) is an NR activated by 1α,25-dihydroxyvitamin D₃ [1,25(OH)₂D₃], a hormone derived from 7-dehydrocholesterol (7-DHC). VDR signaling is best known for regulating calcium homeostasis in mammals, but recent evidence suggests a diversity of uncharacterized roles. In response to incubation temperature, embryos of the annual killifish Austrofundulus limnaeus can develop along two alternative trajectories: active development and diapause. These trajectories diverge early in development, from a biochemical, morphological, and physiological perspective. We manipulated incubation temperature to induce the two trajectories and profiled changes in gene expression using RNA sequencing and weighted gene coexpression network analysis. We report that transcripts involved in 1,25(OH)₂D₃ synthesis and signaling are expressed in a trajectory-specific manner. Furthermore, exposure of embryos to vitamin D₃ analogs and Δ4-dafachronic acid directs continuous development under diapause-inducing conditions. Conversely, blocking synthesis of 1,25(OH)₂D₃ induces diapause in A. limnaeus and a diapause-like state in zebrafish, suggesting vitamin D signaling is critical for normal vertebrate development. These data support vitamin D signaling as a molecular pathway that can regulate developmental trajectory and metabolic dormancy in a vertebrate. Interestingly, the VDR is homologous to the daf-12 and ecdysone NRs that regulate dormancy in Caenorhabditis elegans and Drosophila We suggest that 7-DHC-derived hormones and their associated NRs represent a conserved pathway for the integration of environmental information into developmental programs associated with life history transitions in animals.

Dispersion/reaggregation in early development of annual killifishes: Phylogenetic distribution and evolutionary significance of a unique feature

Annual killifishes are members of the Aplocheiloidea and live in ephemeral habitats that desiccate regularly during the dry season and refill during the rainy season. Populations of these fishes survive the dry season by producing drought-resistant diapausing eggs that are buried in the substrate. When the pool refills during the rainy season the juveniles hatch, grow rapidly and reproduce until the pool desiccates again during the next dry season. The association with such unpredictable habitats has led to the evolution to a variety of developmental adaptations such as a dispersed/reaggregation phase of the deep blastomeres, three possible diapause stages, extreme tolerance to high salinity and anoxia, an efficient DNA repair system and an extremely short life span. Here, we review the course of the dispersed/reaggregation phase, its evolution and phylogenetic distribution and diversity within the Aplocheiloidea. The phenomenon of blastomere dispersion/reaggregation in these fishes was first described in the 1960s and 70s. Blastomeres of most teleost fishes segregate into three groups that give rise to the enveloping cell layer, the yolk syncytial layer and the deep blastomeres that will form the embryo itself. When epiboly commences, the deep blastomeres form a more or less coherent cell sheet with a so called embryonic shield at it marginal zone marking the area where gastrulation takes place. In annual killifishes, the deep blastomeres segregate when epiboly starts and disperse when epiboly commences. After epiboly has been completed, the deep blastomeres are randomly distributed and migrate all over the enveloping cell layer. After several days they start to reaggregate and form the actual embryo that starts gastrulation. The evolutionary origin and mechanism behind this peculiar developmental pathway have puzzled developmental biologists for almost 50 years. However, several of these annual killifishes (Nothobranchius furzeri, Austrofundulus limnaeus, Austrolebias charrua and Austrolebias bellottii) have become model organisms in studies on developmental physiology, aging and stress tolerance. This has led to the establishment of modern genetic techniques such as transgenesis and cell fate mapping that are now used to tackle questions about the origin and mechanisms behind the dispersal/reaggregation phase.