Differentially expressed genes associated with adaptation to different thermal environments in three sympatric Cuban Anolis lizards

Plasticity of Gene Expression and Thermal Tolerance: Implications for Climate Change Vulnerability in a Tropical Forest Lizard

AbstractTropical ectotherms are thought to be especially vulnerable to climate change because they have evolved in temporally stable thermal environments and therefore have decreased tolerance for thermal variability. Thus, they are expected to have narrow thermal tolerance ranges, live close to their upper thermal tolerance limits, and have decreased thermal acclimation capacity. Although models often predict that tropical forest ectotherms are especially vulnerable to rapid environmental shifts, these models rarely include the potential for plasticity of relevant traits. We measured phenotypic plasticity of thermal tolerance and thermal preference as well as multitissue transcriptome plasticity in response to warmer temperatures in a species that previous work has suggested is highly vulnerable to climate warming, the Panamanian slender anole lizard (Anolis apletophallus). We found that many genes, including heat shock proteins, were differentially expressed across tissues in response to short-term warming. Under long-term warming, the voluntary thermal maxima of lizards also increased, although thermal preference exhibited only limited plasticity. Using these data, we modeled changes in the activity time of slender anoles through the end of the century under climate change and found that plasticity should delay declines in activity time by at least two decades. Our results suggest that slender anoles, and possibly other tropical ectotherms, can alter the expression of genes and phenotypes when responding to shifting environmental temperatures and that plasticity should be considered when predicting the future of organisms under a changing climate.

Glyphosate-based herbicide (GBH) challenged thermoregulation in lizards (Eremias argus), compensatory warming could mitigate this effect

Chemical pollution and global warming are two major threats to reptiles, and these two factors can interact with each other. Glyphosate have attracted worldwide attention due to their ubiquitous occurrence, yet their impact on reptiles remains unknown. We designed a crossover experiment with different external GBH exposures (control/GBH) x different environmental temperatures (current climate treatment/warmer climate treatment) over 60 days to simulate environmental exposure in the Mongolian Racerunner lizard (Eremias argus). Preferred body temperature and active body temperature data were collected to calculate the accuracy of thermoregulation, while liver detoxification metabolic enzymes, oxidative stress system function, and the non-targeted metabolome of the brain tissue were assessed. Warmer-treated lizards adjusted their physiological levels and behavioral strategies in response to increased ambient temperatures and maintained body temperature homeostasis at moderate thermal perturbations. GBH-treated lizards suffered from oxidative damage to the brain tissue and abnormal histidine metabolism, thus their thermoregulatory accuracy reduced. Interestingly, at elevated ambient temperatures, GBH treatment did not affect on their thermoregulatory, possibly through several temperature-dependent detoxification mechanisms. Importantly, this data suggested that the subtle toxicological effects of GBH may threaten increasingly thermoregulation behavior of E. argus with species-wide repercussions, as climate change and exposure time extension.

Selection-driven adaptation to the extreme Antarctic environment in the Emperor penguin

The eco-evolutionary history of penguins is characterised by shifting from temperate to cold environments. Breeding in Antarctica, the Emperor penguin appears as an extreme outcome of this process, with unique features related to insulation, heat production and energy management. However, whether this species actually diverged from a less cold-adapted ancestor, more ecologically similar to its sister species, the King penguin, is still an open question. As the Antarctic colonisation likely resulted in vast changes in selective pressure experienced by the Emperor penguin, the relative quantification of the genomic signatures of selection, unique to each sister species, could answer this question. Applying phylogeny-based selection tests on 7651 orthologous genes, we identified a more pervasive selection shift in the Emperor penguin than in the King penguin, supporting the hypothesis that its extreme cold adaptation is a derived state. Furthermore, among candidate genes under selection, four (TRPM8, LEPR, CRB1, and SFI1) were identified before in other cold-adapted homeotherms, like the woolly Mammoth, while other 161 genes can be assigned to biological functions relevant to cold adaptation identified in previous studies. Location and structural effects of TRPM8 substitutions in Emperor and King penguin lineages support their functional role with putative divergent effects on thermal adaptation. We conclude that extreme cold adaptation in the Emperor penguin largely involved unique genetic options which, however, affect metabolic and physiological traits common to other cold-adapted homeotherms.

Draft genome of six Cuban Anolis lizards and insights into genetic changes during their diversification

Background

Detecting genomic variants and their accumulation processes during species diversification and adaptive radiation is important for understanding the molecular and genetic basis of evolution. Anolis lizards in the West Indies are good models for studying evolutionary mechanisms because of the repeated evolution of their morphology and the ecology. We performed de novo genome assembly of six Cuban Anolis lizards with different ecomorphs and thermal habitats (Anolis isolepis, Anolis allisoni, Anolis porcatus, Anolis allogus, Anolis homolechis, and Anolis sagrei). We carried out a comparative analysis of these genome assemblies to investigate the genetic changes that occurred during their diversification.

Results

We reconstructed novel draft genomes with relatively long scaffolds and high gene completeness, with the scaffold N50 ranging from 5.56 to 39.79 Mb and vertebrate Benchmarking Universal Single-Copy Orthologs completeness ranging from 77.5% to 86.9%. Comparing the repeat element compositions and landscapes revealed differences in the accumulation process between Cuban trunk-crown and trunk-ground species and separate expansions of several families of LINE in each Cuban trunk-ground species. Duplicated gene analysis suggested that the proportional differences in duplicated gene numbers among Cuban Anolis lizards may be associated with differences in their habitat ranges. Additionally, Pairwise Sequentially Markovian Coalescent analysis suggested that the effective population sizes of each species may have been affected by Cuba’s geohistory.

Conclusions

We provide draft genomes of six Cuban Anolis lizards and detected species and lineage-specific transposon accumulation and gene copy number changes that may be involved in adaptive evolution. The change processes in the past effective population size was also estimated, and the factors involved were inferred. These results provide new insights into the genetic basis of Anolis lizard diversification and are expected to serve as a stepping stone for the further elucidation of their diversification mechanisms.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02086-7.

Chromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species

Rapid technological improvements are democratizing access to high quality, chromosome-scale genome assemblies. No longer the domain of only the most highly studied model organisms, now non-traditional and emerging model species can be genome-enabled using a combination of sequencing technologies and assembly software. Consequently, old ideas built on sparse sampling across the tree of life have recently been amended in the face of genomic data drawn from a growing number of high-quality reference genomes. Arguably the most valuable are those long-studied species for which much is already known about their biology; what many term emerging model species. Here, we report a highly complete chromosome-scale genome assembly for the brown anole, Anolis sagrei – a lizard species widely studied across a variety of disciplines and for which a high-quality reference genome was long overdue. This assembly exceeds the vast majority of existing reptile and snake genomes in contiguity (N50 = 253.6 Mb) and annotation completeness. Through the analysis of this genome and population resequence data, we examine the history of repetitive element accumulation, identify the X chromosome, and propose a hypothesis for the evolutionary history of fusions between autosomes and the X that led to the sex chromosomes of A. sagrei.

A highly-complete chromosome-scale genome assembly of the brown anole, Anolis sagrei, provides insight into the evolution of sex chromosomes and is a crucial resource for this model lizard species.

Captivity induces large and population-dependent brain transcriptomic changes in wild-caught cane toads (Rhinella marina)

Gene expression levels are key molecular phenotypes at the interplay between genotype and environment. Mounting evidence suggests that short-term changes in environmental conditions, such as those encountered in captivity, can substantially affect gene expression levels. Yet, the exact magnitude of this effect, how general it is, and whether it results in parallel changes across populations are not well understood. Here, we take advantage of the well-studied cane toad, Rhinella marina, to examine the effect of short-term captivity on brain gene expression levels, and determine whether effects of captivity differ between long-colonized and vanguard populations of the cane toad's Australian invasion range. We compared the transcriptomes of wild-caught toads immediately assayed with those from toads captured from the same populations but maintained in captivity for seven months. We found large differences in gene expression levels between captive and wild-caught toads from the same population, with an over-representation of processes related to behaviour and the response to stress. Captivity had a much larger effect on both gene expression levels and gene expression variability in toads from vanguard populations compared to toads from long-colonized areas, potentially indicating an increased plasticity in toads at the leading edge of the invasion. Overall, our findings indicate that short-term captivity can induce large and population-specific transcriptomic changes, which has significant implications for studies comparing phenotypic traits of wild-caught organisms from different populations that have been held in captivity.

Differential transcriptomic responses to heat stress in surface and subterranean diving beetles

Subterranean habitats are generally very stable environments, and as such evolutionary transitions of organisms from surface to subterranean lifestyles may cause considerable shifts in physiology, particularly with respect to thermal tolerance. In this study we compared responses to heat shock at the molecular level in a geographically widespread, surface-dwelling water beetle to a congeneric subterranean species restricted to a single aquifer (Dytiscidae: Hydroporinae). The obligate subterranean beetle Paroster macrosturtensis is known to have a lower thermal tolerance compared to surface lineages (CT_max 38 °C cf. 42–46 °C), but the genetic basis of this physiological difference has not been characterized. We experimentally manipulated the thermal environment of 24 individuals to demonstrate that both species can mount a heat shock response at high temperatures (35 °C), as determined by comparative transcriptomics. However, genes involved in these responses differ between species and a far greater number were differentially expressed in the surface taxon, suggesting it can mount a more robust heat shock response; these data may underpin its higher thermal tolerance compared to subterranean relatives. In contrast, the subterranean species examined not only differentially expressed fewer genes in response to increasing temperatures, but also in the presence of the experimental setup employed here alone. Our results suggest P. macrosturtensis may be comparatively poorly equipped to respond to both thermally induced stress and environmental disturbances more broadly. The molecular findings presented here have conservation implications for P. macrosturtensis and contribute to a growing narrative concerning weakened thermal tolerances in obligate subterranean organisms at the molecular level.

Developmental dynamics of sex reprogramming by high incubation temperatures in a dragon lizard

BACKGROUND

In some vertebrate species, gene-environment interactions can determine sex, driving bipotential gonads to differentiate into either ovaries or testes. In the central bearded dragon (Pogona vitticeps), the genetic influence of sex chromosomes (ZZ/ZW) can be overridden by high incubation temperatures, causing ZZ male to female sex reversal. Previous research showed ovotestes, a rare gonadal phenotype with traits of both sexes, develop during sex reversal, leading to the hypothesis that sex reversal relies on high temperature feminisation to outcompete the male genetic cue. To test this, we conducted temperature switching experiments at key developmental stages, and analysed the effect on gonadal phenotypes using histology and transcriptomics.

RESULTS

We found sexual fate is more strongly influenced by the ZZ genotype than temperature. Any exposure to low temperatures (28 °C) caused testes differentiation, whereas sex reversal required longer exposure to high temperatures. We revealed ovotestes exist along a spectrum of femaleness to male-ness at the transcriptional level. We found inter-individual variation in gene expression changes following temperature switches, suggesting both genetic sensitivity to, and the timing and duration of the temperature cue influences sex reversal.

CONCLUSIONS

These findings bring new insights to the mechanisms underlying sex reversal, improving our understanding of thermosensitive sex systems in vertebrates.

Acute temperature adaptation mechanisms in the native reptile species Eremias argus

Reptiles are sensitive to temperature changes as ectotherm animals. The climate warming may pose more serious threat to reptiles. Although the behavior effect and reproduction biology have been well studied, little information is available about the adaptation mechanisms of reptiles to temperature stress. In this study, the native Chinese species, Eremias argus were incubated at 15 (cold stress), 25 (control group) and 35 °C (thermal stress) for 24 h. The transcriptome and metabolome technology were applied to investigate the molecular regulation mechanisms of lizards to acute temperature changes. The CIRBP and HSPA8 were hub genes in response to temperature adaptation. The increased expression of PER gene in lizard circadian rhythm is associated with tyrosine metabolism after cold or thermal stress. The poly-unsaturated fatty acids in female lizard liver were significantly increased with up-regulation of FASN and ACACA genes after thermal stress, which proved the disruption of fatty acid biosynthesis pathway in corporation with the altered body weight. The cortisol and testosterone were important steroid hormones in response to temperature changes especially in male lizard liver. The increased CIRBP gene expression in lizard gonads suppressed the KDM6B gene, which regulates the testis development and may induce sex reversal in male lizard after thermal stress. The adaptation responses of lizards to temperature stress may threaten the health status of wild population.

Thermal biology of two sympatric Lacertid lizards (Lacerta diplochondrodes and Parvilacerta parva) from Western Anatolia

Sympatric lizard species present convenient models for studying differentiation in thermal behavior and the role of morphological differences in their thermal biology. Here we studied the thermal biology of two sympatric lizard species which occur sympatrically in the Phrygian Valley of Western Anatolia. These two species differ in body size, with Lacerta diplochondrodes being larger than Parvilacerta parva. The surface body temperatures of the individuals belonging to both species were recorded when active in the field. Additionally, several environmental parameters including solar radiation, substrate temperature, air temperature and wind speed were monitored to investigate the relative effects of these abiotic parameters on the thermal biology of the two species. The surface body temperature and temperature excess (difference between body and substrate temperature) of the two species, while being relatively close to each other, showed seasonal differences. Solar radiation, substrate temperature and air temperature were the main factors influencing their thermal biology. Additionally, although body size did not have a direct effect on body temperature or temperature excess, the interaction between body size and solar radiation on temperature excess was significant. In conclusion, our study partially supports the conservation of body temperature of related lizard species.

The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos)

Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here, we explore the genetic diversity of a desert lizard that occupies a wide range of environmental conditions and that has experienced post-glacial expansion northwards along two colonization routes. Based on our analyses of a large SNP data set, we find evidence that both climate and demographic history have shaped the genetic structure of populations. Pronounced genetic differentiation was evident between populations occupying cold versus hot deserts, and we detected numerous loci with significant associations with climate. The genetic signal of founder effects, however, is still present in the genomes of the recently expanded populations, which comprise subsets of genetic variation found in the southern populations.

Detection of genes positively selected in Cuban Anolis lizards that naturally inhabit hot and open areas and currently thrive in urban areas

Species of Anolis lizards of the West Indies that naturally inhabit hot and open areas also tend to thrive in urban areas. In this study, transcriptome was sequenced for nine species of Cuban Anolis lizards that are closely related to each other, but inhabit different thermal microhabitats. Using PAML and HyPhy software, we attempted to identify genes and amino acid sites under positive selection in the common ancestral branch of A. porcatus and A. allisoni, and the branch of A. sagrei, which inhabit hot and open areas, and thrive in urban areas. Although there were no genes where positive selection was commonly detected on both of the tested branches, positive selection was detected in genes involved in the stress response (e.g., DNA damage and oxidative stress) and cardiac function, which could be related to adaptive evolution of tolerance to heat or ultraviolet radiation, on both branches. These findings suggest that adaptive evolution of the response to stress caused by heat or ultraviolet radiation might have occurred in ancestors of Anolis species inhabiting hot and open areas and might be related to the current thriving in urban areas of them.

Help, there are ‘omics’ in my comparative physiology!

‘Omics’ methods, such as transcriptomics, proteomics, lipidomics or metabolomics, yield simultaneous measurements of many related molecules in a sample. These approaches have opened new opportunities to generate and test hypotheses about the mechanisms underlying biochemical and physiological phenotypes. In this Commentary, we discuss general approaches and considerations for successfully integrating omics into comparative physiology. The choice of omics approach will be guided by the availability of existing resources and the time scale of the process being studied. We discuss the use of whole-organism extracts (common in omics experiments on small invertebrates) because such an approach may mask underlying physiological mechanisms, and we consider the advantages and disadvantages of pooling samples within biological replicates. These methods can bring analytical challenges, so we describe the most easily analyzed omics experimental designs. We address the propensity of omics studies to digress into ‘fishing expeditions’ and show how omics can be used within the hypothetico-deductive framework. With this Commentary, we hope to provide a roadmap that will help newcomers approach omics in comparative physiology while avoiding some of the potential pitfalls, which include ambiguous experiments, long lists of candidate molecules and vague conclusions.

Identification of a reptile lyssavirus in Anolis allogus provided novel insights into lyssavirus evolution

Lyssaviruses (genus Lyssavirus) are negative-strand RNA viruses belonging to the family Rhabdoviridae. Although a lyssa-like virus (frog lyssa-like virus 1 [FLLV-1]), which is distantly related to lyssaviruses, was recently identified in frogs, a large phylogenetic gap exists between those viruses, and thus the evolution of lyssaviruses is unclear. In this study, we detected a lyssa-like virus from publicly available RNA-seq data obtained using the brain and skin of Anolis allogus (Spanish flag anole), which was designated anole lyssa-like virus 1 (ALLV-1), and determined its complete coding sequence. Via mapping analysis, we demonstrated that ALLV-1 was actively replicating in the original brain and skin samples. Phylogenetic analyses revealed that ALLV-1 is more closely related to lyssaviruses than FLLV-1. Overall, the topology of the tree is compatible with that of hosts, suggesting the long-term co-divergence of lyssa-like and lyssaviruses and vertebrates. The ψ region, which is a long 3' untranslated region of unknown origin present in the G mRNA of lyssaviruses (approximately 400-700 nucleotides), is also present in the genome of ALLV-1, but it is much shorter (approximately 180 nucleotides) than those of lyssaviruses. Interestingly, FLLV-1 lacks the ψ region, suggesting that the ψ region was acquired after the divergence of the FLLV-1 and ALLV-1/lyssavirus lineages. To the best of our knowledge, this is the first report to identify a lyssa-like virus in reptiles, and thus, our findings provide novel insights into the evolution of lyssaviruses.

Genetic Constraints, Transcriptome Plasticity, and the Evolutionary Response to Climate Change

In situ adaptation to climate change will be critical for the persistence of many ectotherm species due to their relative lack of dispersal capacity. Climate change is causing increases in both the mean and the variance of environmental temperature, each of which may act as agents of selection on different traits. Importantly, these traits may not be heritable or have the capacity to evolve independently from one another. When genetic constraints prevent the "baseline" values of thermal performance traits from evolving rapidly, phenotypic plasticity driven by gene expression might become critical. We review the literature for evidence that thermal performance traits in ectotherms are heritable and have genetic architectures that permit their unconstrained evolution. Next, we examine the relationship between gene expression and both the magnitude and duration of thermal stress. Finally, we identify genes that are likely to be important for adaptation to a changing climate and determine whether they show patterns consistent with thermal adaptation. Although few studies have measured narrow-sense heritabilities of thermal performance traits, current evidence suggests that the end points of thermal reaction norms (tolerance limits) are moderately heritable and have the potential to evolve rapidly. By contrast, performance at intermediate temperatures has substantially lower evolutionary potential. Moreover, evolution in many species appears to be constrained by genetic correlations such that populations can adapt to either increases in mean temperature or temperature variability, but not both. Finally, many species have the capacity for plastic expression of the transcriptome in response to temperature shifts, with the number of differentially expressed genes increasing with the magnitude, but not the duration, of thermal stress. We use these observations to develop a conceptual model that describes the likely trajectory of genome evolution in response to changes in environmental temperature. Our results indicate that extreme weather events, rather than gradual increases in mean temperature, are more likely to drive genetic and phenotypic change in wild ectotherms.

Generation and classification of transcriptomes in two Croomia species and molecular evolution of CYC/TB1 genes in Stemonaceae

The genus Croomia (Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia (EA)-Eastern North America (ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In addition to the presence of both actinomorphic and zygomorphic flowers within the genus, species are disjunctively distributed between EA and ENA. However, due to the limited availability of genomic resources, few studies of Croomia have examined these questions. In this study, we sequenced the floral and leaf transcriptomes of the zygomorphic flowered C roomia heterosepala and the actinomorphic flowered Croomia japonica, and used comparative genomic approaches to investigate the transcriptome evolution of the two closely related species. The sequencing and de novo assembly of transcriptomes from flowers of C. heterosepala (ChFlower), flowers of C. japonica (CjFlower), and leaves of C. japonica (CjLeaf) yielded 57,193, 62,131 and 64,448 unigenes, respectively. In addition, estimation of Ka/Ks ratios for 11,566 potential orthologous groups between ChFlower and CjFlower revealed that only six pairs had Ka/Ks ratios significantly greater than 1 and are likely under positive selection. A total of 429 single copy nuclear genes (SCNGs) and 21,460 expression sequence tags-simple sequence repeats (EST-SSRs) were identified in this study. Specifically, we identified seven CYC/TB1-like genes from Stemonaceae. Phylogenetic and molecular evolution analyses indicated that these CYC/TB1-like genes formed a monophyletic clade (SteTBL1) and were subject to strong purifying selection. The shifts of floral symmetry in Stemonaceae do not appear to be correlated with TBL copy number.

Regional differences in thermal adaptation of a cold-water fish Rhynchocypris oxycephalus revealed by thermal tolerance and transcriptomic responses

Understanding how populations adapt to different thermal environments is an important issue for biodiversity conservation in the context of recent global warming. To test the hypothesis that populations from southern region are more sensitive to climate change than northern region in cold-water species, we determined the thermal tolerance of two geographical populations of a cold-water fish, Rhynchocypris oxycephalus: the Hangzhou population from southern region and the Gaizhou population from northern region, then compared their transcriptomic responses between a control and a high temperature treatment. The results showed that the thermal tolerance range and thermal tolerance polygon area of Hangzhou population were narrower than the Gaizhou population, indicating populations from southern region were possibly more vulnerable. Further transcriptomic analysis revealed that the Gaizhou population expressed more temperature responding genes than the Hangzhou population (583 VS. 484), corresponding with their higher thermal tolerance, while some of these genes (e.g. heat shock protein) showed higher expression in the Hangzhou population under control condition, suggesting individuals from southern region possibly have already responded to the present higher environmental temperature pressure. Therefore, these results confirm the prediction that populations from southern region are more sensitive to global warming, and will be important for their future conservation.

Genomic Changes Associated with Reproductive and Migratory Ecotypes in Sockeye Salmon (Oncorhynchus nerka)

Mechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here, we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associated DNA sequencing was used to genotype this sampling at 7,347 single nucleotide polymorphisms, 334 of which were identified as outlier loci and candidates for divergent selection within at least one ecotype comparison. Sixty-eight of these outliers were present in two or more comparisons, with 33 detected across multiple catchments. Of particular note, one locus was detected as the most significant outlier between shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, Fraser, and Snake). We also detected several genomic islands of divergence, some shared among comparisons, potentially showing linked signals of differential selection. The single nucleotide polymorphisms and genomic regions identified in our study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.

Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae)

Variation in gene expression can provide insights into organismal responses to environmental stress and physiological mechanisms mediating adaptation to habitats with contrasting environmental conditions. We performed an RNA-sequencing experiment to quantify gene expression patterns in fish adapted to habitats with different combinations of environmental stressors, including the presence of toxic hydrogen sulphide (H2 S) and the absence of light in caves. We specifically asked how gene expression varies among populations living in different habitats, whether population differences were consistent among organs, and whether there is evidence for shared expression responses in populations exposed to the same stressors. We analysed organ-specific transcriptome-wide data from four ecotypes of Poecilia mexicana (nonsulphidic surface, sulphidic surface, nonsulphidic cave and sulphidic cave). The majority of variation in gene expression was correlated with organ type, and the presence of specific environmental stressors elicited unique expression differences among organs. Shared patterns of gene expression between populations exposed to the same environmental stressors increased with levels of organismal organization (from transcript to gene to physiological pathway). In addition, shared patterns of gene expression were more common between populations from sulphidic than populations from cave habitats, potentially indicating that physiochemical stressors with clear biochemical consequences can constrain the diversity of adaptive solutions that mitigate their adverse effects. Overall, our analyses provided insights into transcriptional variation in a unique system, in which adaptation to H2 S and darkness coincide. Functional annotations of differentially expressed genes provide a springboard for investigating physiological mechanisms putatively underlying adaptation to extreme environments.

HSF1 and HSF3 cooperatively regulate the heat shock response in lizards

Cells cope with temperature elevations, which cause protein misfolding, by expressing heat shock proteins (HSPs). This adaptive response is called the heat shock response (HSR), and it is regulated mainly by heat shock transcription factor (HSF). Among the four HSF family members in vertebrates, HSF1 is a master regulator of HSP expression during proteotoxic stress including heat shock in mammals, whereas HSF3 is required for the HSR in birds. To examine whether only one of the HSF family members possesses the potential to induce the HSR in vertebrate animals, we isolated cDNA clones encoding lizard and frog HSF genes. The reconstructed phylogenetic tree of vertebrate HSFs demonstrated that HSF3 in one species is unrelated with that in other species. We found that the DNA-binding activity of both HSF1 and HSF3 in lizard and frog cells was induced in response to heat shock. Unexpectedly, overexpression of lizard and frog HSF3 as well as HSF1 induced HSP70 expression in mouse cells during heat shock, indicating that the two factors have the potential to induce the HSR. Furthermore, knockdown of either HSF3 or HSF1 markedly reduced HSP70 induction in lizard cells and resistance to heat shock. These results demonstrated that HSF1 and HSF3 cooperatively regulate the HSR at least in lizards, and suggest complex mechanisms of the HSR in lizards as well as frogs.

Molecular and Cellular Mechanisms of Apoptosis during Dissociated Spermatogenesis

Apoptosis is a tightly controlled process by which tissues eliminate unwanted cells. Spontaneous germ cell apoptosis in testis has been broadly investigated in mammals that have an associated spermatogenesis pattern. However, the mechanism of germ cell apoptosis in seasonally breeding reptiles following a dissociated spermatogenesis has remained enigmatic. In the present study, morphological evidence has clearly confirmed the dissociated spermatogenesis pattern in Pelodiscus sinensis. TUNEL and TEM analyses presented dynamic changes and ultrastructural characteristics of apoptotic germ cells during seasonal spermatogenesis, implying that apoptosis might be one of the key mechanisms to clear degraded germ cells. Furthermore, using RNA-Seq and digital gene expression (DGE) profiling, a large number of apoptosis-related differentially expressed genes (DEGs) at different phases of spermatogenesis were identified and characterized in the testis. DGE and RT-qPCR analysis revealed that the critical anti-apoptosis genes, such as Bcl-2, BAG1, and BAG5, showed up-regulated patterns during intermediate and late spermatogenesis. Moreover, the increases in mitochondrial transmembrane potential in July and October were detected by JC-1 staining. Notably, the low protein levels of pro-apoptotic cleaved caspase-3 and CytC in cytoplasm were detected by immunohistochemistry and western blot analyses, indicating that the CytC-Caspase model might be responsible for the effects of germ cell apoptosis on seasonal spermatogenesis. These results facilitate understanding the regulatory mechanisms of apoptosis during spermatogenesis and uncovering the biological process of the dissociated spermatogenesis system in reptiles.