RELIC THERMOSENSITIVE GENE EXPRESSION IN A TURTLE WITH GENOTYPIC SEX DETERMINATION

How do maternal androgens and estrogens affect sex determination in reptiles with temperature-dependent sex?

Temperature sex determination (TSD) in reptiles has been studied to elucidate the mechanisms by which temperature is transformed into a biological signal that determines the sex of the embryo. Temperature is thought to trigger signals that alter gene expression and hormone metabolism, which will determine the development of female or male gonads. In this review, we focus on collecting and discussing important and recent information on the role of maternal steroid hormones in sex determination in oviparous reptiles such as crocodiles, turtles, and lizards that possess TSD. In particular, we focus on maternal androgens and estrogens deposited in the egg yolk and their metabolites that could also influence the sex of offspring. Finally, we suggest guidelines for future research to help clarify the link between maternal steroid hormones and offspring sex.

Context-dependent thermolability of sex determination in a lacertid lizard with heteromorphic sex chromosomes

Developmental conditions can profoundly impact key life history traits of the individual. In cases where offspring sex is driven by developmental reaction norms, permanent changes to the phenotype can fundamentally alter life history trajectories. Sex determination mechanisms in reptiles are remarkably diverse, including well-characterised genetic and temperature-dependent sex determination. In rarer, but increasingly more commonly documented cases, sex can also be determined by a combination of the two, with temperature overriding the genetically determined sex. Thus, sex-by-temperature interactions is a mechanism that can be contextually labile, where reaction norms of sex against developmental environment might only be observable under certain conditions. We examine the effects of incubation temperature on hatchling sex in an oviparous lizard with clearly defined heteromorphic sex chromosomes presumed to determine sex solely on a genetic basis. We also test the repeatability of our results by replicating incubation experiments across 3 years. We show that warmer temperatures may override chromosomal sex and cause an overproduction of daughters. However, this effect was inconsistent among years, with high temperature only resulting in a daughter-significant bias in one year. Warm-incubated daughters were more efficient at converting yolk into tissue, which would allow for greater resource allocation to other fitness-related processes, such as growth. This suggests that thermolabile sex determination could be a trait under selection. More energy-efficient embryos also produced faster-growing offspring, suggesting that energy utilization patterns of the embryo were maintained into the juvenile stage, which could have important implications for the ontogenetic development and evolution of life histories.

A Cautionary Tale of Sexing by Methylation: Hybrid Bisulfite-Conversion Sequencing of Immunoprecipitated Methylated DNA in Chrysemys picta Turtles with Temperature-Dependent Sex Determination Reveals Contrasting Patterns of Somatic and Gonadal Methylation, but No Unobtrusive Sex Diagnostic

Background: The gonads of Chrysemys picta, a turtle with temperature-dependent sex determination (TSD), exhibit differential DNA methylation between males and females, but whether the same is true in somatic tissues remains unknown. Such differential DNA methylation in the soma would provide a non-lethal sex diagnostic for TSD turtle hatchings who lack visually detectable sexual dimorphism when young. Methods: Here, we tested multiple approaches to study DNA methylation in tail clips of Chrysemys picta hatchlings, to identify differentially methylated candidate regions/sites that could serve as molecular sex markers To detect global differential methylation in the tails we used methylation-sensitive ELISA, and to test for differential local methylation we developed a novel hybrid method by sequencing immunoprecipitated and bisulfite converted DNA (MeDIP-BS-seq) followed by PCR validation of candidate regions/sites after digestion with a methylation-sensitive restriction enzyme. Results: We detected no global differences in methylation between males and females via ELISA. While we detected inter-individual variation in DNA methylation in the tails, this variation was not sexually dimorphic, in contrast with hatchling gonads. Conclusions: Results highlight that differential DNA methylation is tissue-specific and plays a key role in gonadal formation (primary sexual development) and maintenance post-hatching, but not in the somatic tail tissue.

Tenuous transcriptional threshold of human sex determination. II. SRY exploits water-mediated clamp at the edge of ambiguity

Y-encoded transcription factor SRY initiates male differentiation in therian mammals. This factor contains a high-mobility-group (HMG) box, which mediates sequence-specific DNA binding with sharp DNA bending. A companion article in this issue described sex-reversal mutations at box position 72 (residue 127 in human SRY), invariant as Tyr among mammalian orthologs. Although not contacting DNA, the aromatic ring seals the domain's minor wing at a solvent-exposed junction with a basic tail. A seeming paradox was posed by the native-like biochemical properties of inherited Swyer variant Y72F: its near-native gene-regulatory activity is consistent with the father's male development, but at odds with the daughter's XY female somatic phenotype. Surprisingly, aromatic rings (Y72, F72 or W72) confer higher transcriptional activity than do basic or polar side chains generally observed at solvated DNA interfaces (Arg, Lys, His or Gln). Whereas biophysical studies (time-resolved fluorescence resonance energy transfer and heteronuclear NMR spectroscopy) uncovered only subtle perturbations, dissociation of the Y72F complex was markedly accelerated relative to wild-type. Studies of protein-DNA solvation by molecular-dynamics (MD) simulations of an homologous high-resolution crystal structure (SOX18) suggest that Y72 para-OH anchors a network of water molecules at the tail-DNA interface, perturbed in the variant in association with nonlocal conformational fluctuations. Loss of the Y72 anchor among SRY variants presumably "unclamps" its basic tail, leading to (a) rapid DNA dissociation despite native affinity and (b) attenuated transcriptional activity at the edge of sexual ambiguity. Conservation of Y72 suggests that this water-mediated clamp operates generally among SRY and metazoan SOX domains.

Thermosensitive sex chromosome dosage compensation in ZZ/ZW softshell turtles, Apalone spinifera

Sex chromosome dosage compensation (SCDC) overcomes gene-dose imbalances that disturb transcriptional networks, as when ZW females or XY males are hemizygous for Z/X genes. Mounting data from non-model organisms reveal diverse SCDC mechanisms, yet their evolution remains obscure, because most informative lineages with variable sex chromosomes are unstudied. Here, we discovered SCDC in turtles and an unprecedented thermosensitive SCDC in eukaryotes. We contrasted RNA-seq expression of Z-genes, their autosomal orthologues, and control autosomal genes in Apalone spinifera (ZZ/ZW) and Chrysemys picta turtles with temperature-dependent sex determination (TSD) (proxy for ancestral expression). This approach disentangled chromosomal context effects on Z-linked and autosomal expression, from lineage effects owing to selection or drift. Embryonic Apalone SCDC is tissue- and age-dependent, regulated gene-by-gene, complete in females via Z-upregulation in both sexes (Type IV) but partial and environmentally plastic via Z-downregulation in males (accentuated at colder temperature), present in female hatchlings and a weakly suggestive in adult liver (Type I). Results indicate that embryonic SCDC evolved with/after sex chromosomes in Apalone's family Tryonichidae, while co-opting Z-gene upregulation present in the TSD ancestor. Notably, Apalone's SCDC resembles pygmy snake's, and differs from the full-SCDC of Anolis lizards who share homologous sex chromosomes (XY), advancing our understanding of how XX/XY and ZZ/ZW systems compensate gene-dose imbalance. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.

Podocnemis expansa Turtles Hint to a Unifying Explanation for the Evolution of Temperature-Dependent Sex Determination in Long-Lived and Short-Lived Vertebrates

The adaptive significance of temperature-dependent sex determination (TSD) remains elusive for many long-lived reptiles. Various hypotheses proposed potential ecological drivers of TSD. The Charnov-Bull'77 model remains the most robust and explains the maintenance of TSD in short-lived vertebrates, where sex ratios correlate with seasonal temperatures within years that confer sex-specific fitness (colder springs produce females who grow larger and gain in fecundity, whereas warmer summers produce males who mature at smaller size). Yet, evidence of fitness differentials correlated with incubation temperature is scarce for long-lived taxa. Here, it is proposed that the Charnov-Bull'77 model applies similarly to long-lived taxa, but at a longer temporal scale, by revisiting ecological and genetic data from the long-lived turtle Podocnemis expansa. After ruling out multiple alternatives, it is hypothesized that warmer-drier years overproduce females and correlate with optimal resource availability in the flood plains, benefitting daughters more than sons, whereas resources are scarcer (due to reduced flowering/fruiting) during colder-rainier years that overproduce males, whose fitness is less impacted by slower growth rates. New technical advances and collaborative interdisciplinary efforts are delineated that should facilitate testing this hypothesis directly, illuminating the understanding of TSD evolution in P. expansa and other long-lived TSD reptiles.

Turtle Insights into the Evolution of the Reptilian Karyotype and the Genomic Architecture of Sex Determination

Sex chromosome evolution remains an evolutionary puzzle despite its importance in understanding sexual development and genome evolution. The seemingly random distribution of sex-determining systems in reptiles offers a unique opportunity to study sex chromosome evolution not afforded by mammals or birds. These reptilian systems derive from multiple transitions in sex determination, some independent, some convergent, that lead to the birth and death of sex chromosomes in various lineages. Here we focus on turtles, an emerging model group with growing genomic resources. We review karyotypic changes that accompanied the evolution of chromosomal systems of genotypic sex determination (GSD) in chelonians from systems under the control of environmental temperature (TSD). These transitions gave rise to 31 GSD species identified thus far (out of 101 turtles with known sex determination), 27 with a characterized sex chromosome system (13 of those karyotypically). These sex chromosomes are varied in terms of the ancestral autosome they co-opted and thus in their homology, as well as in their size (some are macro-, some are micro-chromosomes), heterogamety (some are XX/XY, some ZZ/ZW), dimorphism (some are virtually homomorphic, some heteromorphic with larger-X, larger W, or smaller-Y), age (the oldest system could be ~195 My old and the youngest < 25 My old). Combined, all data indicate that turtles follow some tenets of classic theoretical models of sex chromosome evolution while countering others. Finally, although the study of dosage compensation and molecular divergence of turtle sex chromosomes has lagged behind research on other aspects of their evolution, this gap is rapidly decreasing with the acceleration of ongoing research and growing genomic resources in this group.

Alternative splicing and thermosensitive expression of Dmrt1 during urogenital development in the painted turtle, Chrysemys picta

BACKGROUND

The doublesex and mab-3 related transcription factor 1 (Dmrt1) is a highly conserved gene across numerous vertebrates and invertebrates in sequence and function. Small aminoacid changes in Dmrt1 are associated with turnovers in sex determination in reptiles. Dmrt1 is upregulated in males during gonadal development in many species, including the painted turtle, Chrysemys picta, a reptile with temperature-dependent sex determination (TSD). Dmrt1 is reported to play different roles during sex determination and differentiation, yet whether these functions are controlled by distinct Dmrt1 spliceoforms remains unclear. While Dmrt1 isoforms have been characterized in various vertebrates, no study has investigated their existence in any turtle.

METHODS

We examine the painted turtle to identify novel Dmrt1 isoforms that may be present during urogenital development using PCR, profile their expression by RNA-seq across five embryonic stages at male- and female-producing temperatures, and validate their expression pattern via qPCR with transcript-specific fluorescent probes.

RESULTS

A novel Dmrt1 spliceoform was discovered for the first time in chelonians, lacking exons 2 and 3 (Dmrt1 ΔEx2Ex3). Dmrt1 canonical and ΔEx2Ex3 transcripts were differentialy expressed by temperature at stages 19 and 22 in developing gonads of painted turtles, after the onset of sex determination, and displayed a significant male-biased expression pattern. This transcriptional pattern differs from studies in other turtles and vertebrates that reported Dmrt1 differential expression before or at the onset of sex determination. This study provides the first insight into Dmrt1 transcriptional diversity in turtles and opens the door for future functional studies of the alternative Dmrt1 transcript uncovered here.

CONCLUSIONS

The discovery of an isoform in turtles indicate that alternative splicing may be a common feature of Dmrt1 across vertebrates, as isoforms are also found in crocodilians, birds, mammals and fish, and this variation remains unexplained. The relatively late-onset of Dmrt1 expression observed here contrasts with other turtles, indicating that Dmrt1 is not the topmost male sex -determining factor in C. picta. When placed in a phylogenetic context, this discrepancy underscores the divergent regulation of Dmrt1, and of sexual development more generally, across vertebrates.

Mechanisms related to sexual determination by temperature in reptiles

A number of strategies have emerged that appear to relate to the evolution of mechanisms for sexual determination in vertebrates, among which are genetic sex determination caused by sex chromosomes and environmental sex determination, where environmental factors influence the phenotype of the sex of an individual. Within the reptile group, some orders such as: Chelonia, Crocodylia, Squamata and Rhynchocephalia, manifest one of the most intriguing and exciting environmental sexual determination mechanisms that exists, comprising temperature-dependent sex determination (TSD), where the temperature of incubation that the embryo experiences during its development is fundamental to establishing the sex of the individual. This makes them an excellent model for the study of sexual determination at the molecular, cellular and physiological level, as well as in terms of their implications at an evolutionary and ecological level. There are different hypotheses concerning how this process is triggered and this review aims to describe any new contributions to particular TSD hypotheses, analyzing them from the "eco-evo-devo" perspective.

Thermal Response of Epigenetic Genes Informs Turtle Sex Determination with and without Sex Chromosomes

Vertebrate sexual fate can be established by environmental cues (e.g., temperature-dependent sex determination, TSD) or by genetic content (genotypic sex determination, GSD). While methylation is implicated in TSD, the influence of broader epigenetic processes in sexual development remains obscure. Here, we investigated for the first time the embryonic gonadal expression of the genome-wide epigenetic machinery in turtles, including genes and noncoding RNAs (ncRNAs) involved in DNA/histone acetylation, methylation, ubiquitination, phosphorylation, and RNAi. This machinery was active and differentially thermosensitive in TSD versus GSD (ZZ/ZW) turtles. Methylation and histone acetylation genes responded the strongest. The results suggest these working hypotheses: (i) TSD might be mediated by epigenetically controlled hormonal pathways (via acetylation, methylation, and ncRNAs), or by (ii) hormonally controlled epigenetic processes, and (iii) key epigenetic events prior to the canonical thermosensitive period may explain differences between TSD and GSD. Novel epigenetic candidate regulators other than methylation were identified, including previously unknown ncRNAs that could potentially mediate gonadogenesis. These findings illuminate the molecular ecology of reptilian sex determination and permitted hypothesis building to help guide future functional studies on the epigenetic transduction of external cues in TSD versus GSD systems.

MeDIP-seq and nCpG analyses illuminate sexually dimorphic methylation of gonadal development genes with high historic methylation in turtle hatchlings with temperature-dependent sex determination

Background

DNA methylation alters gene expression but not DNA sequence and mediates some cases of phenotypic plasticity. Temperature-dependent sex determination (TSD) epitomizes phenotypic plasticity where environmental temperature drives embryonic sexual fate, as occurs commonly in turtles. Importantly, the temperature-specific transcription of two genes underlying gonadal differentiation is known to be induced by differential methylation in TSD fish, turtle and alligator. Yet, how extensive is the link between DNA methylation and TSD remains unclear. Here we test for broad differences in genome-wide DNA methylation between male and female hatchling gonads of the TSD painted turtle Chrysemys picta using methyl DNA immunoprecipitation sequencing, to identify differentially methylated candidates for future study. We also examine the genome-wide nCpG distribution (which affects DNA methylation) in painted turtles and test for historic methylation in genes regulating vertebrate gonadogenesis.

Results

Turtle global methylation was consistent with other vertebrates (57% of the genome, 78% of all CpG dinucleotides). Numerous genes predicted to regulate turtle gonadogenesis exhibited sex-specific methylation and were proximal to methylated repeats. nCpG distribution predicted actual turtle DNA methylation and was bimodal in gene promoters (as other vertebrates) and introns (unlike other vertebrates). Differentially methylated genes, including regulators of sexual development, had lower nCpG content indicative of higher historic methylation.

Conclusions

Ours is the first evidence suggesting that sexually dimorphic DNA methylation is pervasive in turtle gonads (perhaps mediated by repeat methylation) and that it targets numerous regulators of gonadal development, consistent with the hypothesis that it may regulate thermosensitive transcription in TSD vertebrates. However, further research during embryogenesis will help test this hypothesis and the alternative that instead, most differential methylation observed in hatchlings is the by-product of sexual differentiation and not its cause.

Electronic supplementary material

The online version of this article (doi:10.1186/s13072-017-0136-2) contains supplementary material, which is available to authorized users.

Dmrt1 induces the male pathway in a turtle species with temperature-dependent sex determination

The molecular mechanism underlying temperature-dependent sex determination (TSD) has been a long-standing mystery; in particular, the thermosensitive genetic triggers for gonadal sex differentiation are largely unknown. Here, we have characterized a conserved DM domain gene, Dmrt1, in the red-eared slider turtle Trachemys scripta (T. scripta), which exhibits TSD. We found that Dmrt1 has a temperature-dependent, sexually dimorphic expression pattern, preceding gonadal sex differentiation, and is capable of responding rapidly to temperature shifts and aromatase inhibitor treatment. Most importantly, loss- and gain-of-function analyses provide solid evidence that Dmrt1 is both necessary and sufficient to initiate male development in T. scripta Furthermore, the DNA methylation dynamics of the Dmrt1 promoter are tightly correlated with temperature and could mediate the impact of temperature on sex determination. Collectively, our findings demonstrate that Dmrt1 is a candidate master male sex-determining gene in this TSD species, consistent with the idea that DM domain genes are conserved during the evolution of sex determination mechanisms.

Transcriptomic responses to environmental temperature by turtles with temperature-dependent and genotypic sex determination assessed by RNAseq inform the genetic architecture of embryonic gonadal development

Vertebrate sexual fate is decided primarily by the individual's genotype (GSD), by the environmental temperature during development (TSD), or both. Turtles exhibit TSD and GSD, making them ideal to study the evolution of sex determination. Here we analyze temperature-specific gonadal transcriptomes (RNA-sequencing validated by qPCR) of painted turtles (Chrysemys picta TSD) before and during the thermosensitive period, and at equivalent stages in soft-shell turtles (Apalone spinifera-GSD), to test whether TSD's and GSD's transcriptional circuitry is identical but deployed differently between mechanisms. Our data show that most elements of the mammalian urogenital network are active during turtle gonadogenesis, but their transcription is generally more thermoresponsive in TSD than GSD, and concordant with their sex-specific function in mammals [e.g., upregulation of Amh, Ar, Esr1, Fog2, Gata4, Igf1r, Insr, and Lhx9 at male-producing temperature, and of β-catenin, Foxl2, Aromatase (Cyp19a1), Fst, Nf-kb, Crabp2 at female-producing temperature in Chrysemys]. Notably, antagonistic elements in gonadogenesis (e.g., β-catenin and Insr) were thermosensitive only in TSD early-embryos. Cirbp showed warm-temperature upregulation in both turtles disputing its purported key TSD role. Genes that may convert thermal inputs into sex-specific development (e.g., signaling and hormonal pathways, RNA-binding and heat-shock) were differentially regulated. Jak-Stat, Nf-κB, retinoic-acid, Wnt, and Mapk-signaling (not Akt and Ras-signaling) potentially mediate TSD thermosensitivity. Numerous species-specific ncRNAs (including Xist) were differentially-expressed, mostly upregulated at colder temperatures, as were unannotated loci that constitute novel TSD candidates. Cirbp showed warm-temperature upregulation in both turtles. Consistent transcription between turtles and alligator revealed putatively-critical reptilian TSD elements for male (Sf1, Amh, Amhr2) and female (Crabp2 and Hspb1) gonadogenesis. In conclusion, while preliminary, our data helps illuminate the regulation and evolution of vertebrate sex determination, and contribute genomic resources to guide further research into this fundamental biological process.

Cytogenetic Insights into the Evolution of Chromosomes and Sex Determination Reveal Striking Homology of Turtle Sex Chromosomes to Amphibian Autosomes

Turtle karyotypes are highly conserved compared to other vertebrates; yet, variation in diploid number (2n = 26-68) reflects profound genomic reorganization, which correlates with evolutionary turnovers in sex determination. We evaluate the published literature and newly collected comparative cytogenetic data (G- and C-banding, 18S-NOR, and telomere-FISH mapping) from 13 species spanning 2n = 28-68 to revisit turtle genome evolution and sex determination. Interstitial telomeric sites were detected in multiple lineages that underwent diploid number and sex determination turnovers, suggesting chromosomal rearrangements. C-banding revealed potential interspecific variation in centromere composition and interstitial heterochromatin at secondary constrictions. 18S-NORs were detected in secondary constrictions in a single chromosomal pair per species, refuting previous reports of multiple NORs in turtles. 18S-NORs are linked to ZW chromosomes in Apalone and Pelodiscus and to X (not Y) in Staurotypus. Notably, comparative genomics across amniotes revealed that the sex chromosomes of several turtles, as well as mammals and some lizards, are homologous to components of Xenopus tropicalis XTR1 (carrying Dmrt1). Other turtle sex chromosomes are homologous to XTR4 (carrying Wt1). Interestingly, all known turtle sex chromosomes, except in Trionychidae, evolved via inversions around Dmrt1 or Wt1. Thus, XTR1 appears to represent an amniote proto-sex chromosome (perhaps linked ancestrally to XTR4) that gave rise to turtle and other amniote sex chromosomes.

Physical Mapping and Refinement of the Painted Turtle Genome (Chrysemys picta) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation

Comparative genomics continues illuminating amniote genome evolution, but for many lineages our understanding remains incomplete. Here, we refine the assembly (CPI 3.0.3 NCBI AHGY00000000.2) and develop a cytogenetic map of the painted turtle (Chrysemys picta-CPI) genome, the first in turtles and in vertebrates with temperature-dependent sex determination. A comparison of turtle genomes with those of chicken, selected nonavian reptiles, and human revealed shared and novel genomic features, such as numerous chromosomal rearrangements. The largest conserved syntenic blocks between birds and turtles exist in four macrochromosomes, whereas rearrangements were evident in these and other chromosomes, disproving that turtles and birds retain fully conserved macrochromosomes for greater than 300 Myr. C-banding revealed large heterochromatic blocks in the centromeric region of only few chromosomes. The nucleolar-organizing region (NOR) mapped to a single CPI microchromosome, whereas in some turtles and lizards the NOR maps to nonhomologous sex-chromosomes, thus revealing independent translocations of the NOR in various reptilian lineages. There was no evidence for recent chromosomal fusions as interstitial telomeric-DNA was absent. Some repeat elements (CR1-like, Gypsy) were enriched in the centromeres of five chromosomes, whereas others were widespread in the CPI genome. Bacterial artificial chromosome (BAC) clones were hybridized to 18 of the 25 CPI chromosomes and anchored to a G-banded ideogram. Several CPI sex-determining genes mapped to five chromosomes, and homology was detected between yet other CPI autosomes and the globally nonhomologous sex chromosomes of chicken, other turtles, and squamates, underscoring the independent evolution of vertebrate sex-determining mechanisms.

Molecular and morphological differentiation of testes and ovaries in relation to the thermosensitive period of gonad development in the snapping turtle, Chelydra serpentina

Ambient temperatures during embryonic development determine gonadal sex in many reptiles. The temperature sensitive period for sex determination has been defined by shifting eggs between female- and male-producing temperatures in a few species. This phase spans 20-35% of embryogenesis in most species, which makes it difficult to define the mechanisms that transduce temperature into a signal for ovarian versus testicular development. We present an extensive set of studies that define a brief period when high temperature specifies, and then determines, ovarian fate in a northern population of snapping turtles, Chelydra serpentina. We shifted embryos from male to female temperatures, or vice versa, at various stages of development. Gonads in embryos incubated at female temperatures commit to ovarian fate earlier (by stage 18) than gonads in embryos incubated at male temperatures commit to testicular fate (by stages 19-21). In double shift studies, embryos were incubated at a female temperature, exposed to a male temperature for set times, and shifted back to the original temperature, or vice versa. The time required to induce ovarian development (≤6 days at female temperatures) was much shorter than the time required to induce testicular formation (>20 days at male temperatures). Differentiation of the gonads at the histological level occurred after the sex-determining period. Nevertheless, we found that a change in temperature rapidly (within 24h) influenced expression and splicing of WT1 mRNA: the absolute abundance of WT1 mRNA, the relative abundance of +KTS versus -KTS isoforms, as well as the ratio of +KTS:-KTS isoforms was higher in gonads at a male versus a female temperature. In conclusion, ovarian fate is more readily determined than testicular fate in snapping turtle embryos. The short sex-determining period in this species (6-8% of embryogenesis) will facilitate studies of molecular mechanisms for specification and determination of gonad fate by temperature.

Molecular players involved in temperature-dependent sex determination and sex differentiation in Teleost fish

The molecular mechanisms that underlie sex determination and differentiation are conserved and diversified. In fish species, temperature-dependent sex determination and differentiation seem to be ubiquitous and molecular players involved in these mechanisms may be conserved. Although how the ambient temperature transduces signals to the undifferentiated gonads remains to be elucidated, the genes downstream in the sex differentiation pathway are shared between sex-determining mechanisms. In this paper, we review recent advances on the molecular players that participate in the sex determination and differentiation in fish species, by putting emphasis on temperature-dependent sex determination and differentiation, which include temperature-dependent sex determination and genetic sex determination plus temperature effects. Application of temperature-dependent sex differentiation in farmed fish and the consequences of temperature-induced sex reversal are discussed.

An unbiased approach to identify genes involved in development in a turtle with temperature-dependent sex determination

BACKGROUND

Many reptiles exhibit temperature-dependent sex determination (TSD). The initial cue in TSD is incubation temperature, unlike genotypic sex determination (GSD) where it is determined by the presence of specific alleles (or genetic loci). We used patterns of gene expression to identify candidates for genes with a role in TSD and other developmental processes without making a priori assumptions about the identity of these genes (ortholog-based approach). We identified genes with sexually dimorphic mRNA accumulation during the temperature sensitive period of development in the Red-eared slider turtle (Trachemys scripta), a turtle with TSD. Genes with differential mRNA accumulation in response to estrogen (estradiol-17β; E(2)) exposure and developmental stages were also identified.

RESULTS

Sequencing 767 clones from three suppression-subtractive hybridization libraries yielded a total of 581 unique sequences. Screening a macroarray with a subset of those sequences revealed a total of 26 genes that exhibited differential mRNA accumulation: 16 female biased and 10 male biased. Additional analyses revealed that C16ORF62 (an unknown gene) and MALAT1 (a long noncoding RNA) exhibited increased mRNA accumulation at the male producing temperature relative to the female producing temperature during embryonic sexual development. Finally, we identified four genes (C16ORF62, CCT3, MMP2, and NFIB) that exhibited a stage effect and five genes (C16ORF62, CCT3, MMP2, NFIB and NOTCH2) showed a response to E(2) exposure.

CONCLUSIONS

Here we report a survey of genes identified using patterns of mRNA accumulation during embryonic development in a turtle with TSD. Many previous studies have focused on examining the turtle orthologs of genes involved in mammalian development. Although valuable, the limitations of this approach are exemplified by our identification of two genes (MALAT1 and C16ORF62) that are sexually dimorphic during embryonic development. MALAT1 is a noncoding RNA that has not been implicated in sexual differentiation in other vertebrates and C16ORF62 has an unknown function. Our results revealed genes that are candidates for having roles in turtle embryonic development, including TSD, and highlight the need to expand our search parameters beyond protein-coding genes.

The origin and differentiation process of X and Y chromosomes of the black marsh turtle (Siebenrockiella crassicollis, Geoemydidae, Testudines)

The black marsh turtle (Siebenrockiella crassicollis) has morphologically differentiated X and Y sex chromosomes. To elucidate the origin and evolutionary process of S. crassicollis X and Y chromosomes, we performed cross-species chromosome painting with chromosome-specific DNA from Chinese soft-shelled turtle (Pelodiscus sinensis) and chromosome mapping of the sex-linked genes of S. crassicollis using FISH. The X and Y chromosomes of S. crassicollis were hybridized with DNA probe of P. sinensis chromosome 5, which is homologous to chicken chromosome 5. S. crassicollis homologues of 14 chicken chromosome 5-linked genes were all localized to the X long arm, whereas two genes were mapped to the Y short arm and the other 12 genes were localized to the Y long arm in the same order as the X chromosome. This result suggests that extensive linkage homology has been retained between chicken chromosome 5 and S. crassicollis X and Y chromosomes and that S. crassicollis X and Y chromosomes are at an early stage of sex chromosome differentiation. Comparison of the locations of two site-specific repetitive DNA sequences on the X and Y chromosomes demonstrated that the centromere shift was the result of centromere repositioning, not of pericentric inversion.

From the origin of sex-determining factors to the evolution of sex-determining systems

Sex determination is typically classified as either genotypic or environmental. However, this dichotomy obscures the developmental origin and evolutionary modification of determinants of sex, and therefore hinders an understanding of the processes that generates diversity in sex-determining systems. Recent research on reptiles and fish emphasizes that sex determination is a multifactorial regulatory process that is best understood as a threshold dichotomy rather than as the result of genetically inherited triggers of development. Here we critically assess the relationship between the developmental origin of sex-determining factors and evolutionary transitions in sex-determining systems. Our perspective emphasizes the importance of both genetic and nongenetic causes in evolution of sex determination and may help to generate predictions with respect to the evolutionary patterns of sex-determining systems and the underlying diversity of developmental and genetic regulatory networks.

Differential gene expression in male and female rainbow trout embryos prior to the onset of gross morphological differentiation of the gonads

BACKGROUND

There are large differences between the sexes at the genetic level; these differences include heterogametic sex chromosomes and/or differences in expression of genes between the sexes. In rainbow trout (Oncorhynchus mykiss) qRT-PCR studies have found significant differences in expression of several candidate sex determining genes. However, these genes represent a very small fraction of the genome and research in other species suggests there are large portions of the transcriptome that are differentially expressed between the sexes. These differences are especially noticeable once gonad differentiation and maturation has occurred, but less is known at earlier stages of development. Here we use data from a microarray and qRT-PCR to identify genes differentially expressed between the sexes at three time points in pre-hatch embryos, prior to the known timing of sexual differentiation in this species.

RESULTS

The microarray study revealed 883 differentially expressed features between the sexes with roughly equal numbers of male and female upregulated features across time points. Most of the differentially expressed genes on the microarray were not related to sex function, suggesting large scale differences in gene expression between the sexes are present early in development. Candidate gene analysis revealed sox9, DMRT1, Nr5a1 and wt1 were upregulated in males at some time points and foxl2, ovol1, fst and cyp19a1a were upregulated in females at some time points.

CONCLUSION

This is the first study to identify sexual dimorphism in expression of the genome during embryogenesis in any fish and demonstrates that transcriptional differences are present before the completion of gonadogenesis.

A review of sex determining mechanisms in geckos (Gekkota: Squamata)

Geckos are a species-rich clade of reptiles possessing diverse sex determining mechanisms. Some species possess genetic sex determination, with both male and female heterogamety, while other species have temperature-dependent sex determination. I compiled information from the literature on the taxonomic distribution of these sex determining mechanisms in geckos. Using phylogenetic data from the literature, I reconstructed the minimum number of transitions among these sex determining mechanisms with parsimony-based ancestral state reconstruction. While only a small number of gecko species have been characterized, numerous changes among sex determining mechanisms were inferred. This diversity, coupled with the high frequency of transitions, makes geckos excellent candidates as a model clade for the study of vertebrate sex determination and evolution.

Molecular mechanisms of sex determination in reptiles

Charles Darwin first provided a lucid explanation of how gender differences evolve nearly 140 years ago. Yet, a disconnect remains between his theory of sexual selection and the mechanisms that underlie the development of males and females. In particular, comparisons between representatives of different phyla (i.e., flies and mice) reveal distinct genetic mechanisms for sexual differentiation. Such differences are hard to comprehend unless we study organisms that bridge the phylogenetic gap. Analysis of variation within monophyletic groups (i.e., amniotes) is just as important if we hope to elucidate the evolution of mechanisms underlying sexual differentiation. Here we review the molecular, cellular, morphological, and physiological changes associated with sex determination in reptiles. Most research on the molecular biology of sex determination in reptiles describes expression patterns for orthologs of mammalian sex-determining genes. Many of these genes have evolutionarily conserved expression profiles (i.e., DMRT1 and SOX9 are expressed at a higher level in developing testes vs. developing ovaries in all species), which suggests functional conservation. However, expression profiling alone does not test gene function and will not identify novel sex-determining genes or gene interactions. For that reason, we provide a prospectus on various techniques that promise to reveal new sex-determining genes and regulatory interactions among these genes. We offer specific examples of novel candidate genes and a new signaling pathway in support of these techniques.

Expression profiles of sex differentiation-related genes during ontogenesis in the European sea bass acclimated to two different temperatures

The European sea bass is a teleost fish that lacks sex chromosomes and for which temperature influences sex ratios. However, correlation between temperature, developmental stage at a given age and sex-specific gene expression is hampered by the lack of sex markers. To study this correlation, fish were exposed to feminizing (15 degrees C) or masculinizing temperature (21 degrees C) from 0-120 days post fertilization, throughout the thermosensitive period (TSP). Aromatase (cyp19a1a), 11beta-hydroxylase (cyp11b), androgen receptor (arb) and estrogen receptors (era, erb1 and erb2) were assessed by qPCR prior and during sex differentiation. Canonical discriminant analysis (CDA), with length--as proxy for developmental stage--and cyp19a1a expression as predictors, was validated and used to reliably assign gonadal sex to fish sampled within and outside the TSP. Differences in cyp19a1a and cyp11b expression could be detected 1-month before the first signs of histological sex differentiation. Cyp19a1a and cyp11b were significantly higher in future females and males, respectively, and revealed as robust molecular markers to predict future ovarian and testicular differentiation. In contrast, no association between phenotypic sex and arb, era, erb1 and erb2 expression was found, suggesting that these genes do not contribute to the differentiation of a particular sex. The CDA-based approach implemented here could be used to sex undifferentiated animals in species where genetic sex cannot be known owing to the lack of simple sex determining systems, as it is the case of many fish and reptiles with or without temperature-dependent sex determination, and provide a useful tool to relate gene expression and phenotypic sex.

The painted turtle, Chrysemys picta: a model system for vertebrate evolution, ecology, and human health

Painted turtles (Chrysemys picta) are representatives of a vertebrate clade whose biology and phylogenetic position hold a key to our understanding of fundamental aspects of vertebrate evolution. These features make them an ideal emerging model system. Extensive ecological and physiological research provide the context in which to place new research advances in evolutionary genetics, genomics, evolutionary developmental biology, and ecological developmental biology which are enabled by current resources, such as a bacterial artificial chromosome (BAC) library of C. picta, and the imminent development of additional ones such as genome sequences and cDNA and expressed sequence tag (EST) libraries. This integrative approach will allow the research community to continue making advances to provide functional and evolutionary explanations for the lability of biological traits found not only among reptiles but vertebrates in general. Moreover, because humans and reptiles share a common ancestor, and given the ease of using nonplacental vertebrates in experimental biology compared with mammalian embryos, painted turtles are also an emerging model system for biomedical research. For example, painted turtles have been studied to understand many biological responses to overwintering and anoxia, as potential sentinels for environmental xenobiotics, and as a model to decipher the ecology and evolution of sexual development and reproduction. Thus, painted turtles are an excellent reptilian model system for studies with human health, environmental, ecological, and evolutionary significance.

Blurring the edges in vertebrate sex determination

Sex in vertebrates is determined by genetically or environmentally based signals. These signals initiate molecular cascades and cell-cell interactions within the gonad that lead to the adoption of the male or female fate. Previously, genetically and environmentally based mechanisms were thought to be distinct, but this idea is fading as a result of the unexpected discovery of coincident genetic and thermal influences within single species. Together with accumulating phylogenetic evidence of frequent transitions between sex-determining mechanisms, these findings suggest that genetic and environmental sex determination actually represent points on a continuum rather than discrete categories, and that populations may shift in one direction or the other in response to mutations or changing ecological conditions. Elucidation of the underlying molecular basis of sex determination in mice has yielded a bistable model of mutually antagonistic signaling pathways and feedback regulatory loops. This system would be highly responsive to changes in the upstream primary signal and may provide a basis for the rapid evolution of and transitions between different methods of sex determination.

Analyzing the coordinated gene network underlying temperature-dependent sex determination in reptiles

Although gonadogenesis has been extensively studied in vertebrates with genetic sex determination, investigations at the molecular level in nontraditional model organisms with temperature-dependent sex determination are relatively new areas of research. Results show that while the key players of the molecular network underlying gonad development appear to be retained, their functions range from conserved to novel roles. In this review, we summarize experiments investigating candidate molecular players underlying temperature-dependent sex determination. We discuss some of the problems encountered unraveling this network, pose potential solutions, and suggest rewarding future directions of research.

New resources inform study of genome size, content, and organization in nonavian reptiles

Genomic resources for studies of nonavian reptiles have recently improved and will reach a new level of access once the genomes of the painted turtle (Chrysemys picta) and the green anole (Anolis carolinensis) have been published. Eleven speakers gathered for a symposium on reptilian genomics and evolutionary genetics at the 2008 meeting of the Society for Integrative and Comparative Biology in San Antonio, Texas. Presentations described results of reptilian genetic studies concerning molecular evolution, chromosomal evolution, genomic architecture, population dynamics, endocrinology and endocrine disruption, and the evolution of developmental mechanisms. The presented studies took advantage of the recent generation of genetic and genomic tools and resources. Novel findings demonstrated the positive impact made by the improved availability of resources like genome annotations and bacterial artificial chromosomes (BACs). The symposium was timely and important because it provided a vehicle for the dissemination of novel findings that advance the field. Moreover, this meeting fostered the synergistic interaction of the participants as a group, which is anticipated to encourage the funding and creation of further resources such as additional BAC libraries and genomic projects. Novel data have already been collected and studies like those presented in this symposium promise to shape and improve our understanding of overall amniote evolution. Additional reptilian taxa such as the American alligator (Alligator mississippiensis), tuatara (Sphenodon punctatus), and garter snake (Thamnophis sirtalis) should be the foci of future genomic projects. We hope that the following articles in this volume will help promote these efforts by describing the conclusions and the potential that the improvement of genomic resources for nonavian reptiles can continue having in this important area of integrative and comparative biology.