Chromosome banding in Amphibia. XVI. High-resolution replication banding patterns in Xenopus laevis

Understanding the role of environmental temperature on sex determination through comparative studies in reptiles and amphibians

In vertebrates, species exhibit phenotypic plasticity of sex determination that the sex can plastically be determined by the external environmental temperature through a mechanism, temperature-dependent sex determination (TSD). Temperature exerts influence over the direction of sexual differentiation pathways, resulting in distinct primary sex ratios in a temperature-dependent manner. This review provides a summary of the thermal sensitivities associated with sex determination in reptiles and amphibians, with a focus on the pattern of TSD, gonadal differentiation, temperature sensing, and the molecular basis underlying thermal sensitivity in sex determination. Comparative studies across diverse lineages offer valuable insights into comprehending the evolution of sex determination as a phenotypic plasticity. While evidence of molecular mechanisms governing sexual differentiation pathways continues to accumulate, the intracellular signaling linking temperature sensing and sexual differentiation pathways remains elusive. We emphasize that uncovering these links is a key for understanding species-specific thermal sensitivities in TSD and will contribute to a more comprehensive understanding of ecosystem and biodiversity conservations.

Heterogeneity in conservation of multifunctional partner enzymes with meiotic importance, CDK2 kinase and BRCA1 ubiquitin ligase

The evolution of proteins can be accompanied by changes not only to their amino acid sequences, but also their structural and spatial molecular organization. Comparison of the protein conservation within different taxonomic groups (multifunctional, or highly specific) allows to clarify their specificity and the direction of evolution. Two multifunctional enzymes, cyclin-dependent kinase 2 (CDK2) and BRCA1 ubiquitin ligase, that are partners in some mitotic and meiotic processes were investigated in the present work. Two research methods, bioinformatics and immunocytochemical, were combined to examine the conservation levels of the two enzymes. It has been established that CDK2 is a highly conserved protein in different taxonomic lineages of the eukaryotic tree. Immunocytochemically, a conserved CDK2 pattern was revealed in the meiotic autosomes of five rodent species and partially in domestic turkey and clawed frog. Nevertheless, variable CDK2 distribution was detected at the unsynapsed segments of the rodent X chromosomes. BRCA1 was shown to be highly conserved only within certain mammalian taxa. It was also noted that in those rodent nuclei, where BRCA1 specifically binds to antigens, asynaptic regions of sex chromosomes were positive. BRCA1 staining was not always accompanied by specific binding, and a high nonspecificity in the nucleoplasm was observed. Thus, the studies revealed different conservation of the two enzymes at the level of protein structure as well as at the level of chromosome behavior. This suggests variable rates of evolution due to both size and configuration of the protein molecules and their multifunctionality.

Comparative Distribution of Repetitive Sequences in the Karyotypes of Xenopus tropicalis and Xenopus laevis (Anura, Pipidae)

Xenopus laevis and its diploid relative, Xenopus tropicalis, are the most used amphibian models. Their genomes have been sequenced, and they are emerging as model organisms for research into disease mechanisms. Despite the growing knowledge on their genomes based on data obtained from massive genome sequencing, basic research on repetitive sequences in these species is lacking. This study conducted a comparative analysis of repetitive sequences in X. laevis and X. tropicalis. Genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) with Cot DNA of both species revealed a conserved enrichment of repetitive sequences at the ends of the chromosomes in these Xenopus species. The repeated sequences located on the short arm of chromosome 3 from X. tropicalis were not related to the sequences on the short arm of chromosomes 3L and 3S from X. laevis, although these chromosomes were homoeologous, indicating that these regions evolved independently in these species. Furthermore, all the other repetitive sequences in X. tropicalis and X. laevis may be species-specific, as they were not revealed in cross-species hybridizations. Painting experiments in X. laevis with chromosome 7 from X. tropicalis revealed shared sequences with the short arm of chromosome 3L. These regions could be related by the presence of the nucleolus organizer region (NOR) in both chromosomes, although the region revealed by chromosome painting in the short arm of chromosome 3L in X. laevis did not correspond to 18S + 28S rDNA sequences, as they did not colocalize. The identification of these repeated sequences is of interest as they provide an explanation to some problems already described in the genome assemblies of these species. Furthermore, the distribution of repetitive DNA in the genomes of X. laevis and X. tropicalis might be a valuable marker to assist us in understanding the genome evolution in a group characterized by numerous polyploidization events coupled with hybridizations.

Chromosome divergence during evolution of the tetraploid clawed frogs, Xenopus mellotropicalis and Xenopus epitropicalis as revealed by Zoo-FISH

Whole genome duplication (WGD) generates new species and genomic redundancy. In African clawed frogs of the genus Xenopus, this phenomenon has been especially important in that (i) all but one extant species are polyploid and (ii) whole genome sequences of some species provide an evidence for genomic rearrangements prior to or after WGD. Within Xenopus in the subgenus Silurana, at least one allotetraploidization event gave rise to three extant tetraploid (2n = 4x = 40) species–Xenopus mellotropicalis, X. epitropicalis, and X. calcaratus–but it is not yet clear the degree to which these tetraploid genomes experienced rearrangements prior to or after allotetraploidization. To explore genome evolution during diversification of these species, we performed cytogenetic analyses of X. mellotropicalis, including assessment of the localization of nucleolar organizer region, chromosome banding, and determination of the p/q arm ratios for each chromosome pair. We compared these data to a previously characterized karyotype of X. epitropicalis. Morphometric, C-banding and Zoo-FISH data support a previously hypothesized common allotetraploid predecessor of these species. Zoo-FISH with whole chromosome painting (WCP) probes derived from the closely related diploid species X. tropicalis confirmed the existence of ten chromosomal quartets in X. mellotropicalis somatic cells, as expected by its ploidy level and tetraploid ancestry. The p/q arm ratio of chromosome 2a was found to be substantially different between X. mellotropicalis (0.81) and X. epitropicalis (0.67), but no substantial difference between these two species was detected in this ratio for the homoeologous chromosome pair 2b, or for other chromosome pairs. Additionally, we identified variation between these two species in the locations of a heterochromatic block on chromosome pair 2a. These results are consistent with a dynamic history of genomic rearrangements before and/or after genome duplication, a surprising finding given the otherwise relatively conserved genomic structure of most frogs.

Sex Reversal in Amphibians

Amphibians have been widely used to study developmental biology due to the fact that embryo development takes place independently of the maternal organism and that observations and experimental approaches are easy. Some amphibians like Xenopus became model organisms in this field. In the first part of this article, the differentiation of the gonads in amphibians and the mechanisms governing this process are reviewed. In the second part, the state of the art about sex reversal, which can be induced by steroid hormones in general and by temperature in some species, is presented. Also information about pollutants found in the environment that could interfere with the development of the amphibian reproductive apparatus or with their reproductive physiology is given. Such compounds could play a part in the amphibian decline, since in the wild, many amphibians are endangered species.

Coexistence of Y, W, and Z sex chromosomes in Xenopus tropicalis

Homomorphic sex chromosomes and rapid turnover of sex-determining genes can complicate establishing the sex chromosome system operating in a given species. This difficulty exists in Xenopus tropicalis, an anuran quickly becoming a relevant model for genetic, genomic, biochemical, and ecotoxicological research. Despite the recent interest attracted by this species, little is known about its sex chromosome system. Direct evidence that females are the heterogametic sex, as in the related species Xenopus laevis, has yet to be presented. Furthermore, X. laevis' sex-determining gene, DM-W, does not exist in X. tropicalis, and the sex chromosomes in the two species are not homologous. Here we identify X. tropicalis' sex chromosome system by integrating data from (i) breeding sex-reversed individuals, (ii) gynogenesis, (iii) triploids, and (iv) crosses among several strains. Our results indicate that at least three different types of sex chromosomes exist: Y, W, and Z, observed in YZ, YW, and ZZ males and in ZW and WW females. Because some combinations of parental sex chromosomes produce unisex offspring and other distorted sex ratios, understanding the sex-determination systems in X. tropicalis is critical for developing this flexible animal model for genetics and ecotoxicology.

Chromosome Banding in Amphibia. XXXII. The Genus Xenopus (Anura, Pipidae)

Mitotic chromosomes of 16 species of the frog genus Xenopus were prepared from kidney and lung cell cultures. In the chromosomes of 7 species, high-resolution replication banding patterns could be induced by treating the cultures with 5-bromodeoxyuridine (BrdU) and deoxythymidine (dT) in succession, and in 6 of these species the BrdU/dT-banded chromosomes could be arranged into karyotypes. In the 3 species of the clade with 2n = 20 and 4n = 40 chromosomes (X. tropicalis, X. epitropicalis, X. new tetraploid 1), as well as in the 3 species with 4n = 36 chromosomes (X. laevis, X. borealis, X. muelleri), the BrdU/dT-banded karyotypes show a high degree of homoeology, though differences were detected between these groups. Translocations, inversions, insertions or sex-specific replication bands were not observed. Minor replication asynchronies found between chromosomes probably involve heterochromatic regions. BrdU/dT replication banding of Xenopus chromosomes provides the landmarks necessary for the exact physical mapping of genes and repetitive sequences. FISH with an X. laevis 5S rDNA probe detected multiple hybridization sites at or near the long-arm telomeric regions in most chromosomes of X. laevis and X. borealis, whereas in X. muelleri, the 5S rDNA sequences are located exclusively at the long-arm telomeres of a single chromosome pair. Staining with the AT base pair-specific fluorochrome quinacrine mustard revealed brightly fluorescing heterochromatic regions in the majority of X. borealis chromosomes which are absent in other Xenopus species.

Xenopus Cytogenetics and Chromosomal Evolution

The genus Xenopus represents important model organisms in the field of developmental biology and chromosomal evolution. Developmental processes are tightly coupled with the analysis of gene function via genetic linkage and mapping. Cytogenetic techniques such as chromosome banding or FISH are essential tools for the determination of gene position and subsequently for the construction of linkage and physical maps. Here, we present a summary of key achievements in X. tropicalis and X. laevis cytogenetics with emphasis on the gene localization to chromosomes. The second part of this review is focused on the chromosomal evolution regarding both above-mentioned species. With respect to methodology, hybridization techniques such as FISH and chromosome-specific painting FISH are highlighted.

A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis

Xenopus laevis (XLA) is an allotetraploid species which appears to have undergone whole-genome duplication after the interspecific hybridization of 2 diploid species closely related to Silurana/Xenopus tropicalis (XTR). Previous cDNA fluorescence in situ hybridization (FISH) experiments have identified 9 sets of homoeologous chromosomes in X. laevis, in which 8 sets correspond to chromosomes 1-8 of X. tropicalis (XTR1-XTR8), and the last set corresponds to a fusion of XTR9 and XTR10. In addition, recent X. laevis genome sequencing and BAC-FISH experiments support this physiological relationship and show no gross chromosome translocation in the X. laevis karyotype. Therefore, for the benefit of both comparative cytogenetics and genome research, we here propose a new chromosome nomenclature for X. laevis based on the phylogenetic relationship and chromosome length, i.e. XLA1L, XLA1S, XLA2L, XLA2S, and so on, in which the numbering of XLA chromosomes corresponds to that in X. tropicalis and the postfixes 'L' and 'S' stand for 'long' and 'short' chromosomes in the homoeologous pairs, which can be distinguished cytologically by their relative size. The last chromosome set is named XLA9L and XLA9S, in which XLA9 corresponds to both XTR9 and XTR10, and hence, to emphasize the phylogenetic relationship to X. tropicalis, XLA9_10L and XLA9_10S are also used as synonyms.

Homoeologous chromosomes of Xenopus laevis are highly conserved after whole-genome duplication

It has been suggested that whole-genome duplication (WGD) occurred twice during the evolutionary process of vertebrates around 450 and 500 million years ago, which contributed to an increase in the genomic and phenotypic complexities of vertebrates. However, little is still known about the evolutionary process of homoeologous chromosomes after WGD because many duplicate genes have been lost. Therefore, Xenopus laevis (2n=36) and Xenopus (Silurana) tropicalis (2n=20) are good animal models for studying the process of genomic and chromosomal reorganization after WGD because X. laevis is an allotetraploid species that resulted from WGD after the interspecific hybridization of diploid species closely related to X. tropicalis. We constructed a comparative cytogenetic map of X. laevis using 60 complimentary DNA clones that covered the entire chromosomal regions of 10 pairs of X. tropicalis chromosomes. We consequently identified all nine homoeologous chromosome groups of X. laevis. Hybridization signals on two pairs of X. laevis homoeologous chromosomes were detected for 50 of 60 (83%) genes, and the genetic linkage is highly conserved between X. tropicalis and X. laevis chromosomes except for one fusion and one inversion and also between X. laevis homoeologous chromosomes except for two inversions. These results indicate that the loss of duplicated genes and inter- and/or intrachromosomal rearrangements occurred much less frequently in this lineage, suggesting that these events were not essential for diploidization of the allotetraploid genome in X. laevis after WGD.

Genetic and genomic interactions of animals with different ploidy levels

Polyploid animals have independently evolved from diploids in diverse taxa across the tree of life. We review a few polyploid animal species or biotypes where recently developed molecular and cytogenetic methods have significantly improved our understanding of their genetics, reproduction and evolution. Mitochondrial sequences that target the maternal ancestor of a polyploid show that polyploids may have single (e.g. unisexual salamanders in the genus Ambystoma) or multiple (e.g. parthenogenetic polyploid lizards in the genus Aspidoscelis) origins. Microsatellites are nuclear markers that can be used to analyze genetic recombinations, reproductive modes (e.g. Ambystoma) and recombination events (e.g. polyploid frogs such as Pelophylax esculentus). Hom(e)ologous chromosomes and rare intergenomic exchanges in allopolyploids have been distinguished by applying genome-specific fluorescent probes to chromosome spreads. Polyploids arise, and are maintained, through perturbations of the 'normal' meiotic program that would include pre-meiotic chromosome replication and genomic integrity of homologs. When possible, asexual, unisexual and bisexual polyploid species or biotypes interact with diploid relatives, and genes are passed from diploid to polyploid gene pools, which increase genetic diversity and ultimately evolutionary flexibility in the polyploid. When diploid relatives do not exist, polyploids can interact with another polyploid (e.g. species of African Clawed Frogs in the genus Xenopus). Some polyploid fish (e.g. salmonids) and frogs (Xenopus) represent independent lineages whose ancestors experienced whole genome duplication events. Some tetraploid frogs (P. esculentus) and fish (Squaliusalburnoides) may be in the process of becoming independent species, but diploid and triploid forms of these 'species' continue to genetically interact with the comparatively few tetraploid populations. Genetic and genomic interaction between polyploids and diploids is a complex and dynamic process that likely plays a crucial role for the evolution and persistence of polyploid animals. See also other articles in this themed issue.

Efficient high-throughput sequencing of a laser microdissected chromosome arm

BACKGROUND

Genomic sequence assemblies are key tools for a broad range of gene function and evolutionary studies. The diploid amphibian Xenopus tropicalis plays a pivotal role in these fields due to its combination of experimental flexibility, diploid genome, and early-branching tetrapod taxonomic position, having diverged from the amniote lineage ~360 million years ago. A genome assembly and a genetic linkage map have recently been made available. Unfortunately, large gaps in the linkage map attenuate long-range integrity of the genome assembly.

RESULTS

We laser dissected the short arm of X. tropicalis chromosome 7 for next generation sequencing and computational mapping to the reference genome. This arm is of particular interest as it encodes the sex determination locus, but its genetic map contains large gaps which undermine available genome assemblies. Whole genome amplification of 15 laser-microdissected 7p arms followed by next generation sequencing yielded ~35 million reads, over four million of which uniquely mapped to the X. tropicalis genome. Our analysis placed more than 200 previously unmapped scaffolds on the analyzed chromosome arm, providing valuable low-resolution physical map information for de novo genome assembly.

CONCLUSION

We present a new approach for improving and validating genetic maps and sequence assemblies. Whole genome amplification of 15 microdissected chromosome arms provided sufficient high-quality material for localizing previously unmapped scaffolds and genes as well as recognizing mislocalized scaffolds.

Effects of 17α-ethynylestradiol on sexual differentiation and development of the African clawed frog (Xenopus laevis)

Several studies have shown that exposure of amphibians, including the African clawed frog (Xenopus laevis), to potent estrogens at critical times during development results in feminization and/or demasculinization. However, genotyping of X. laevis has only recently become possible, so studies performed in the past were rarely able to make explicit linkages between genetic and phenotypic sex. Therefore, to further characterize this relationship, X. laevis tadpoles were exposed during development to 0.09, 0.84, or 8.81 μg/L 17α-ethynylestradiol (EE2), which is the estrogen analog commonly used in oral contraceptives. Exposure to all concentrations of EE2 tested resulted in significant delays in time to metamorphosis. Genotyping showed that genetic sex ratios were similar among treatments. However, morphological evaluation revealed that a significant number of individuals with a male genotype displayed mixed sex and abnormal phenotypes. Additionally, both genetic males and females exposed to EE2 exhibited greater presence of vitellogenin protein relative to the respective controls. Since estrogens function downstream of the initial molecular signals of sexual differentiation, it is likely that genetic male animals received mixed endogenous male and exogenous female signals that caused disordered sexual development. The production of vitellogenin was probably temporally separated and independent from primary effects on sexual differentiation, and might have contributed to delays in metamorphosis observed in individuals exposed to EE2.

Identification and expression analysis of GPAT family genes during early development of Xenopus laevis

Production of lysophosphatidic acid (LPA) is the first step in the de novo pathway for glycerolipid biosynthesis, which is mainly catalyzed by the glycerol-3-phosphate acyltransferases (GPATs; EC2.3.1.15). DHAPAT (EC2.3.1.42) also contributes in a minor way, using dihydroxyacetone phosphate as substrate. Final products and intermediates of the glycerolipid synthesis pathway are the main structural components of cellular membranes, and provide signalling molecules that regulate diverse biological processes, including cell proliferation, differentiation and growth. Here we identified the four orthologs of the mammalian GPATs (1-4) and DHAPAT in Xenopus, including a novel, short variant of GPAT2, and analyzed their expression pattern during embryonic development. Xenopus GPAT1/2 localized to mitochondria, while GPAT3/4 associated with the endoplasmic reticulum. All are similarly expressed in the early embryonic nervous system. A more tissue specific pattern emerges during organogenesis, including liver expression for GPAT1/4, and testis expression for GPAT2. All acyltransferases were expressed in kidney, though GPAT3 was excluded from the pronephric ducts. Our results suggest important roles of GPATs and DHAPAT during early organogenesis.

Preparation of Xenopus tropicalis whole chromosome painting probes using laser microdissection and reconstruction of X. laevis tetraploid karyotype by Zoo-FISH

Laser microdissection was used for the preparation of whole chromosome painting probes in Silurana (Xenopus) tropicalis. Subsequent cross-species fluorescence in situ hybridization (Zoo-FISH) on its tetraploid relative Xenopus laevis revealed persistence of chromosomal quartets even after 50-65 million years of separate evolution. Their arrangement is in a partial concordance with previous experiments based on similarity of a high-resolution replication banding pattern. Further support for an allotetraploid origin of X. laevis was given by hybridization with a probe derived from the smallest X. tropicalis chromosome (Xt10). Here, pericentric areas of both arms of Xl 14 and 18 were stained, indicating intrachromosomal rearrangements. The positions of signals were not in agreement with the chromosomal quartets revealed by painting probes Xt 8 and 9 (Xl 11 + 14 and Xl 15 + 18, respectively). This suggests that both X. tropicalis chromosomes underwent non-reciprocal translocation of Xt10 separately in at least two different ancient ancestors. In addition, the observed translocation events could explain the origin of individuals with 18 chromosomes in diploid karyotypes, probably extinct after the genesis of the allotetraploid X. laevis (2n = 36).

Effects of 17 beta-estradiol exposure on Xenopus laevis gonadal histopathology

The natural estrogen 17 beta-estradiol (E2) is a potential environmental contaminant commonly employed as a positive control substance in bioassays involving estrogenic effects. The aquatic anuran Xenopus laevis is a frequent subject of reproductive endocrine disruptor research; however, histopathological investigations have tended to be less than comprehensive. Consequently, a study was designed to characterize gross and microscopic changes in the gonads of X. laevis as a result of E2 exposure. Additional goals of this study, which consisted of three separate experiments, included the standardization of diagnostic terminology and criteria, the validation of statistical methodology, and the establishment of a half maximal effective concentration (EC50) for E2 as defined by an approximately 50% conversion of presumptive genotypic males to phenotypic females. In the first experiment, frogs were exposed to nominal concentrations of 0, 0.2, 1.5, or 6.0 microg/L E2. From these experimental results and those of a subsequent range finding trial, the EC50 for E2 was determined to be approximately 0.2 microg/L. This E2 concentration was utilized in the other two experiments, which were performed at different facilities to confirm the reproducibility of results. Experiments were conducted according to Good Laboratory Practice guidelines, and the histopathologic evaluations were peer reviewed by an independent pathologist. Among the three trials, the histopathological findings that were strongly associated with E2-exposure (p<0.001 to 0.0001) included an increase in the proportion of phenotypic females, mixed sex, dilated testis tubules, dividing gonocytes in the testis, and dilated ovarian cavities in phenotypic ovaries. A comparison of the gross and microscopic evaluations suggested that some morphologic changes in the gonads may potentially be missed if studies rely entirely on macroscopic assessment.

Automated identification of conserved synteny after whole-genome duplication

An important objective for inferring the evolutionary history of gene families is the determination of orthologies and paralogies. Lineage-specific paralog loss following whole-genome duplication events can cause anciently related homologs to appear in some assays as orthologs. Conserved synteny-the tendency of neighboring genes to retain their relative positions and orders on chromosomes over evolutionary time-can help resolve such errors. Several previous studies examined genome-wide syntenic conservation to infer the contents of ancestral chromosomes and provided insights into the architecture of ancestral genomes, but did not provide methods or tools applicable to the study of the evolution of individual gene families. We developed an automated system to identify conserved syntenic regions in a primary genome using as outgroup a genome that diverged from the investigated lineage before a whole-genome duplication event. The product of this automated analysis, the Synteny Database, allows a user to examine fully or partially assembled genomes. The Synteny Database is optimized for the investigation of individual gene families in multiple lineages and can detect chromosomal inversions and translocations as well as ohnologs (paralogs derived by whole-genome duplication) gone missing. To demonstrate the utility of the system, we present a case study of gene family evolution, investigating the ARNTL gene family in the genomes of Ciona intestinalis, amphioxus, zebrafish, and human.

A W-linked DM-domain gene, DM-W, participates in primary ovary development in Xenopus laevis

In the XX/XY sex-determining system, the Y-linked SRY genes of most mammals and the DMY/Dmrt1bY genes of the teleost fish medaka have been characterized as sex-determining genes that trigger formation of the testis. However, the molecular mechanism of the ZZ/ZW-type system in vertebrates, including the clawed frog Xenopus laevis, is unknown. Here, we isolated an X. laevis female genome-specific DM-domain gene, DM-W, and obtained molecular evidence of a W-chromosome in this species. The DNA-binding domain of DM-W showed a strikingly high identity (89%) with that of DMRT1, but it had no significant sequence similarity with the transactivation domain of DMRT1. In nonmammalian vertebrates, DMRT1 expression is connected to testis formation. We found DMRT1 or DM-W to be expressed exclusively in the primordial gonads of both ZZ and ZW or ZW tadpoles, respectively. Although DMRT1 showed continued expression after sex determination, DM-W was expressed transiently during sex determination. Interestingly, DM-W mRNA was more abundant than DMRT1 mRNA in the primordial gonads of ZW tadpoles early in sex determination. To assess the role of DM-W, we produced transgenic tadpoles carrying a DM-W expression vector driven by approximately 3 kb of the 5'-flanking sequence of DM-W or by the cytomegalovirus promoter. Importantly, some developing gonads of ZZ transgenic tadpoles showed ovarian cavities and primary oocytes with both drivers, suggesting that DM-W is crucial for primary ovary formation. Taken together, these results suggest that DM-W is a likely sex (ovary)-determining gene in X. laevis.

Sterility and gene expression in hybrid males of Xenopus laevis and X. muelleri

BACKGROUND

Reproductive isolation is a defining characteristic of populations that represent unique biological species, yet we know very little about the gene expression basis for reproductive isolation. The advent of powerful molecular biology tools provides the ability to identify genes involved in reproductive isolation and focuses attention on the molecular mechanisms that separate biological species. Herein we quantify the sterility pattern of hybrid males in African Clawed Frogs (Xenopus) and apply microarray analysis of the expression pattern found in testes to identify genes that are misexpressed in hybrid males relative to their two parental species (Xenopus laevis and X. muelleri).

METHODOLOGY/PRINCIPAL FINDINGS

Phenotypic characteristics of spermatogenesis in sterile male hybrids (X. laevis x X. muelleri) were examined using a novel sperm assay that allowed quantification of live, dead, and undifferentiated sperm cells, the number of motile vs. immotile sperm, and sperm morphology. Hybrids exhibited a dramatically lower abundance of mature sperm relative to the parental species. Hybrid spermatozoa were larger in size and accompanied by numerous undifferentiated sperm cells. Microarray analysis of gene expression in testes was combined with a correction for sequence divergence derived from genomic hybridizations to identify candidate genes involved in the sterility phenotype. Analysis of the transcriptome revealed a striking asymmetric pattern of misexpression. There were only about 140 genes misexpressed in hybrids compared to X. laevis but nearly 4,000 genes misexpressed in hybrids compared to X. muelleri.

CONCLUSIONS/SIGNIFICANCE

Our results provide an important correlation between phenotypic characteristics of sperm and gene expression in sterile hybrid males. The broad pattern of gene misexpression suggests intriguing mechanisms creating the dominance pattern of the X. laevis genome in hybrids. These findings significantly contribute to growing evidence for allelic dominance in hybrids and have implications for the mechanism of species differentiation at the transcriptome level.

Localization of the single copy gene Mdh2 on Xenopus tropicalis chromosomes by FISH-TSA

A single copy gene, mitochondrial malate dehydrogenase 2 (Mdh2), was localized on Xenopus tropicalis chromosomes by fluorescence in situ hybridization coupled with tyramide signal amplification (FISH-TSA). The respective cDNA was cloned and sequenced. The labeled probe hybridized with a subcentromeric region of the long arms of homologous chromosomes 3. Results of comparison of the gene localization with previously mapped X. laevis paralogs strongly suggest a common evolutionary origin of chromosomes 3 and 8 in X. laevis and chromosome 3 in X. tropicalis. This is the first time that a single copy gene has been visualized on X. tropicalis chromosomes. The FISH-TSA method gives a strong signal with a 1-kb labeled probe.

Sex-biased gene expression in a ZW sex determination system

Studies of the transcriptome have shown that a substantial fraction of interspecific differences in gene expression is the result of sex-biased gene expression. These results suggest that sex-dependent selection may be an important force in generating differences between species but to date all studies have focused on Drosophila. We examined a sample of the transcriptome in the gonads of two species of Xenopus to provide an additional test of how sex-biased gene expression may contribute to differences in gene expression between species. In contrast to Drosophila, Xenopus provides an example of a ZW system with morphologically indistinguishable sex chromosomes. About 81% of the transcriptome was differentially expressed between X. laevis and X. muelleri and there were more genes that were male-biased compared to the number of genes that were female-biased or non-sex-biased. While there were more genes up-regulated in males of Xenopus, the largest magnitude difference in expression between species occurred in female-biased genes, and male-biased genes were proportionally more abundant for the smallest changes in expression between species. Our results suggest that more genes have a role in the function of the testis compared to the ovary and female-biased genes play a principle role in expression divergence between species. These results differ from those in the Drosophila XY system in that more female-biased genes had >4-fold difference of expression between species than male-biased genes, suggesting that ZW sex chromosomes may facilitate enhanced gene expression divergence between species.

Cytogenetics of the bleak (Alburnus alburnus), with special emphasis on the B chromosomes

Some of the largest B chromosomes so far discovered in vertebrates are present in the cyprinid fish Alburnus alburnus. Previous cytogenetic analyses revealed a diploid chromosome number of 2n = 50. In addition, in some individuals one or two unusually large B chromosomes are present. Two morphologically different types of B chromosomes were observed. The frequency of animals bearing a supernumerary chromosome was found to vary considerably between different populations. A more detailed analysis of the A and B chromosomes of A. alburnus by conventional banding techniques, as well as fluorescence in-situ hybridization (FISH) with the telomeric DNA repeats (GGGTTA)7/(TAACCC)7, 18S + 28S rDNA and 5S rDNA were performed in the present study. Furthermore, a B chromosome-specific DNA probe obtained by amplified length polymorphism (AFLP) was hybridized on metaphases of A. alburnus carrying supernumerary B chromosomes. The banding analyses showed that the B chromosomes are completely heterochromatic, consist of GC-rich DNA sequences, replicate their DNA in the very late S-phase of the cell cycle and are composed mainly of a specific retrotransposable DNA element. Finally, blood probes from A. alburnus were collected for DNA-flow cytometric measurements. It could be shown that the huge supernumerary chromosomes represent nearly 10% of the total genome size of A. alburnus.

Localization, structure and polymorphism of two paralogous Xenopus laevis mitochondrial malate dehydrogenase genes

Two paralogous mitochondrial malate dehydrogenase 2 (Mdh2) genes of Xenopus laevis have been cloned and sequenced, revealing 95% identity. Fluorescence in-situ hybridization (FISH) combined with tyramide amplification discriminates both genes; Mdh2a was localized into chromosome q3 and Mdh2b into chromosome q8. One kb cDNA probes detect both genes with 85% accuracy. The remaining signals were on the paralogous counterpart. Introns interrupt coding sequences at the same nucleotide as defined for mouse. Restriction polymorphism has been detected in the first intron of Mdh2a, while the individual variability in intron 6 of Mdh2b gene is represented by an insertion of incomplete retrotransposon L1Xl. Rates of nucleotide substitutions indicate that both genes are under similar evolutionary constraints. X. laevis Mdh2 genes can be used as markers for physical mapping and linkage analysis.

Multiple origins of tetraploid taxa in the Eurasian Bufo viridis subgroup

We used Q-banding and analyzed nucleolar organizing regions (NORs) to study the cytogenetic evolution of tetraploids within the Palearctic Bufo viridis subgroup, the only known amphibian complex comprising di-, tri- and tetraploid bisexually reproducing taxa. We examined three diploid (2n) nominal taxa (Bufo viridis viridis, B. v. turanensis, B. v. kermanensis) from five Eurasian localities and six tetraploid (4n) nominal taxa (B. oblongus, B. o. danatensis, B. pewzowi pewzowi, B. p. taxkorensis, B. p. unicolor, B. p. strauchi) from eight Central Asian localities. Homeologous chromosomes of 2n and 4n toads exhibit a similar morphology. Silver-staining and in situ hybridization revealed terminal NORs in the long arms of chromosomes 6 in all 2n but in only two out of four chromosomes 6 in all 4n taxa. Q-banding and a rapidly evolving mitochondrial marker suggest at least two origination events for Asian 4n toads: "Western Central Asian tetraploids" (B. oblongus Nikolsky, 1896) exhibit distinct differences within some chromosome quartets, which are divisible into pairs of chromosomes and may be allopolyploid. In contrast, "Central Asian tetraploids" (B. pewzowi Bedriaga, 1898) showed homogenous Q-banding patterns within each quartet, suggesting autopolyploidy. In Northeastern Iran, we discovered a zone of either common ancestry or hybridization of 2n and Western Central Asian 4n toads. This raises intriguing questions about how diploid and tetraploid taxa may evolve by exchanging genetic material.

A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution

The African clawed frogs (Silurana and Xenopus), model organisms for scientific inquiry, are unusual in that allopolyploidization has occurred on multiple occasions, giving rise to tetraploid, octoploid, and dodecaploid species. To better understand their evolution, here we estimate a mitochondrial DNA phylogeny from all described and some undescribed species. We examine the timing and location of diversification, and test hypotheses concerning the frequency of polyploid speciation and taxonomy. Using a relaxed molecular clock, we estimate that extant clawed frog lineages originated well after the breakup of Gondwana, about 63.7 million years ago, with a 95% confidence interval from 50.4 to 81.3 million years ago. Silurana and two major lineages of Xenopus have overlapping distributions in sub-Saharan Africa, and dispersal-vicariance analysis suggests that clawed frogs originated in central and/or eastern equatorial Africa. Most or all extant species originated before the Pleistocene; recent rainforest refugia probably acted as "lifeboats" that preserved existing species, rather than "species pumps" where many new successful lineages originated. We estimate that polyploidization occurred at least six times in clawed frogs.

Amphibians as a model for the study of endocrine disruptors

Evidence shows that environmental compounds can interfere with the endocrine systems of wildlife and humans. The main sink of such substances, called endocrine disruptors (EDs), which are mainly of anthropogenic origin, is surface water; thus, aquatic vertebrates such as fishes and amphibians are most endangered. Despite numerous reports on EDs in fishes, information about EDs in amphibians is scarce, and this paucity of information is of particular concern in view of the worldwide decline of amphibians. EDs could contribute to changes of amphibian populations via adverse effects on reproduction and the thyroid system. In amphibians, EDs can affect reproduction by (anti)estrogenic and (anti)androgenic modes of action that produce severe effects including abnormal sexual differentiation. ED actions on the thyroid system cause acceleration or retardation of metamorphosis, which may also affect population levels. Our broad knowledge of amphibian biology and endocrinology indicates that amphibians are very suitable models for the study of EDs. In particular, effects of EDs on the thyroid system triggering metamorphosis can be determined easily and most sensitively in amphibians compared to other vertebrates. A new classification of EDs according to their biological modes of action is proposed because EDs have quite heterogeneous chemical structures, which do not allow prediction of their biological effects. Methods and strategies are proposed for identification and risk assessment of EDs, whether as pure test substances or as mixtures from environmental samples. Effects of EDs on the thyroid system of amphibians can be assessed by a single animal model (Xenopus laevis), whereas the various types of reproduction need comparative studies to investigate whether general endocrine principles do exist among several species of anurans and urodeles. Thus, at least one anuran and one urodelean model are needed to determine ED interference with reproduction.

Techniques and probes for the study of Xenopus tropicalis development

The frog Xenopus laevis has provided significant insights into developmental and cellular processes. However, X. laevis has an allotetraploid genome precluding its use in forward genetic analysis. Genetic analysis may be applicable to Xenopus (Silurana) tropicalis, which has a diploid genome and a shorter generation time. Here, we show that many tools for the study of X. laevis development can be applied to X. tropicalis. By using the developmental staging system of Nieuwkoop and Faber, we find that X. tropicalis embryos develop at similar rates to X. laevis, although they tolerate a narrower range of temperatures. We also show that many of the analytical reagents available for X. laevis can be effectively transferred to X. tropicalis. The X. laevis protocol for whole-mount in situ hybridization to mRNA transcripts can be successfully applied to X. tropicalis without alteration. Additionally, X. laevis probes often work in X. tropicalis--alleviating the immediate need to clone the X. tropicalis orthologs before initiating developmental studies. Antibodies that react against X. laevis proteins can effectively detect the X. tropicalis protein by using established immunohistochemistry procedures. Antisense morpholino oligonucleotides (MOs) offer a new alternative to study loss of gene activity during development. We show that MOs function in X. tropicalis. Finally, X. tropicalis offers the possibility for forward genetics and genomic analysis.

Xenopus, the next generation: X. tropicalis genetics and genomics

A small, fast-breeding, diploid relative of the frog Xenopus laevis, Xenopus tropicalis, has recently been adopted for research in developmental genetics and functional genomics. X. tropicalis shares advantages of X. laevis as a classic embryologic system, but its simpler genome and shorter generation time make it more convenient for multigenerational genetic, genomic, and transgenic approaches. Its embryos closely resemble those of X. laevis, except for their smaller size, and assays and molecular probes developed in X. laevis can be readily adapted for use in X. tropicalis. Genomic manipulation techniques such as gynogenesis facilitate genetic screens, because they permit the identification of recessive phenotypes after only one generation. Stable transgenic lines can be used both as in vivo reporters to streamline a variety of embryologic and molecular assays, or to experimentally manipulate gene expression through the use of binary constructs such as the GAL4/UAS system. Several mutations have been identified in wild-caught animals and during the course of generating inbred lines. A variety of strategies are discussed for conducting and managing genetic screens, obtaining mutations in specific sequences, achieving homologous recombination, and in developing and taking advantage of the genomic resources for Xenopus tropicalis.

Functional genomics and sexual differentiation in amphibians

In Xenopus laevis the basic mechanisms underlying sexual differentiation were investigated by determining time courses of sexual steroids and their corresponding receptors during complete larval development from egg to juveniles. Androgens as well as estradiol (E2) are derived from maternal origin and accumulate in hatching tadpoles. Sexual steroid contents decreased rapidly after hatching and rose again at the end of metamorphosis indicating endogenous production. In parallel the mRNA expression for corresponding androgen (AR) and estrogen receptors (ER) was measured by means of semiquantitative RT-PCR. Both receptor mRNAs increased dramatically just after hatching and decreased only moderately until end of metamorphosis. In female juveniles E2 and ER-mRNA levels were higher compared with males. Treatment by exogenous E2 elevated both, ER- and AR-mRNA, indicating stimulatory functions of E2 for gene expression of both receptors. Effects on sexual differentiation during larval development were achieved by treatment with E2 and the antiandrogen cyproterone acetate both causing feminization, the antiestrogen tamoxifen resulting in neutralization, and the androgens, methyltestosterone and dihydrotestosterone, but not testosterone, leading to masculinization. The data presented are in accordance with further recent findings and suggest a new hypothesis for functional genomics in sexual differentiation of amphibians.

Chromosome mapping of Xenopus tropicalis using the G- and Ag-bands: tandem duplication and polyploidization of larvae heads

Developmental cytogenetic analyses of Xenopus tropicalis larvae from two origins were performed on stage 27-34 heads treated with colchicine. Standard G-band karyotyping using trypsin and chromosome mapping of 184 bands were examined. Although the main karyotype was 2n = 20, polyploidy (3n = 30 or 4n = 40) and aneuploidy were detected in each individual treated with colchicine, even those treated for only 1 h. The percentage of polyploid karyotypes was 10-20% across the total of measured metaphases. The mean mitotic index was 0.10. Chromosomal breaks and exchanges were detected at the secondary constriction of chromosomes 5 or 6. Ag-band detection showed clearly positive staining at the secondary constriction of chromosome 5, which corresponds to the nucleolar organizer region. Tandem duplication of negative G-bands at the secondary constriction of chromosome 6 and the short arm of chromosome 10 was suggested by this study. X. tropicalis thus provides a good model to study the mechanism and effects of chromosomal abnormalities, gene mapping and tissue specific gene expression in the developmental process.

Sex chromosomes, sex-linked genes, and sex determination in the vertebrate class amphibia

In this chapter the different categories of homomorphic and heteromorphic sex chromosomes, types of sex-determining mechanisms, known sex-linked genes, and data about sex-determining genes in the Amphibia have been compiled. Thorough cytogenetic analyses have shown that both XY/XX and ZW/ZZ sex chromosomes exist in the order Anura and Urodela. In some species quite unusual systems of sex determination have evolved (e.g. 0W-females/00-males or the co-existence of XY/XX and ZW/ZZ sex chromosomes within the same species). In the third order of the Amphibia, the Gymnophiona (or Apoda) there is still no information regarding any aspect of sex determination. Whereas most species of Anura and Urodela present undifferentiated, homomorphic sex chromosomes, there is also a considerable number of species in which an increasing structural complexity of the Y and W chromosomes exists. In various cases, the morphological differentiation of the sex chromosomes occurred as a result of quantitative and/or qualitative changes to the repetitive DNA sequences in the constitutive heterochromatin of the Y and W chromosomes. The greater the structural differences between the sex chromosomes, the lesser the extent of pairing in meiosis. No dosage compensation of the sex-linked genes in the somatic cells of the homogametic (XX or ZZ) individuals have been detected. The genes located to date on the amphibian sex chromosomes lead to the conclusion that there is no common ancestral or conserved sex-linkage group. In all amphibians, genetic sex determination (GSD) seems to operate, although environmental factors may influence sex determination and differentiation. Despite the accumulated evidence that GSD is operating in Anura and Urodela, there is little substantial information about how it functions. Although several DNA sequences homologous to the mammalian ZFY, SRY and SOX genes have been detected in the Anura or Urodela, none of these genes is an appropriate candidate to explain sex determination in these vertebrates.

Major histocompatibility complex and immunoglobulin loci visualized by in situ hybridization on Xenopus chromosomes

A technique for fluorescent in situ hybridization (FISH) on chromosomes of the amphibian Xenopus laevis is described. Positive results were obtained with cDNA probes of about 1kb when at least three adjacent copies of the gene are present. The immunoglobulin heavy chain locus is in the centre of the long arm of chromosome 1. Previously, family studies showed that bona fide MHC class Ib genes segregated independently. Now we show that MHC class II alpha and beta genes and class Ib genes are on the same acrocentric chromosome, with MHC in the middle of the long arm, the class Ib complex (XNC) at the tip or the same arm. Each locus or complex is found on only one pair of chromosomes confirming the diploidization of these genes in the pseudotetraploid X. laevis.

A ribosomal orphon sequence from Xenopus laevis flanked by novel low copy number repetitive elements

We have used a differential cloning approach to isolate ribosomal/non-ribosomal frontier sequences from Xenopus laevis. A ribosomal intergenic spacer sequence (IGS) was cloned and shown not to be physically linked with the ribosomal locus. This ribosomal orphon contained the IGS sequences found immediately downstream of the 28S gene and included an array of enhancer repetitions and a non-functional spacer promoter. The orphon sequence was flanked by a member of the novel 'Frt' low copy repetitive element family. Three individual Frt repeats were sequenced and all members of this family were shown to lie clustered at two chromosomal sites, one of which contained the ribosomal orphon. One of the Frt elements contained an insertion of 297 bp that showed extensive homology to sequences within at least three other Xenopus genes. Each homology region was flanked by members of the T2 family of short interspersed repetitive elements, (SINEs), and by its target insertion sequence, suggesting multiple translocation events. The data are discussed in terms of the evolution of the ribosomal gene locus.

Chromosomal locations of major tRNA gene clusters of Xenopus laevis

In Xenopus laevis eight tRNA genes are located in a 3.18 kb tandemly repeated unit. There are 150 copies of the unit at a single locus near the long arm telomere of one of the acrocentric chromosomes in the 14-17 group. Two additional classes of tRNA gene-containing repeats have been isolated (defined by clones p3.1 and p3.2) that have structures related to that of the 3.18 kb unit. Using in situ hybridization at the electron microscopic level, the p3.2 repeats are found clustered at a single locus in the subtelomeric region on one of the submetacentric chromosomes, whereas the p3.1 repeats are clustered at a locus indistinguishable from that containing the 3.18 kb repeats. This suggests that these tDNA tandem repeats can diverge in sequence from each other without being at distantly separated loci.

Patterns of DNase sensitivity in the chromosomes of Rana perezi (Amphibia: Anura)

We have analyzed the patterns of DNase I/nick translation in the chromosomes of Rana perezi. The results show a nonuniform DNase sensitivity in different chromosome domains; the hypersensitivity appears to be concentrated at both the NOR and the distal regions. The resemblance to the situation in mammals, where active genes are DNase I hypersensitive, is discussed.Key words: DNase sensitivity, chromosomes, Rana perezi.

The late replication banding patterns of chromosomes are highly conserved in the genera Rana, Hyla, and Bufo (Amphibia: Anura)

Late replication banding and C-banding analyses were performed on the metaphase chromosomes of six species and one subspecies of Palearctic water frogs, genus Rana. Although C-banding patterns showed interspecific or intersubspecific variation, late replication banding patterns of all 13 chromosome pairs of these species were homologous. Minor differences of banding patterns were observed only in chromosomes 2, 7 and 13. Close comparison of the late replication banding patterns with those of three non-water frog species of Rana, and one each of Hyla and Bufo, provided important information on interspecific and intergeneric variability. In the Rana species, the banding patterns of all 13 pairs were homologous except for those some regions of 8 pairs. In one species each of Hyla and Bufo that was examined, the six large chromosome pairs (Nos. 1-6) showed banding homologies. Furthermore, among the Rana, Hyla and Bufo species the four large chromosome pairs (Nos. 1-3, 5 of Rana and Hyla, and Nos. 1, 3-5 of Bufo) shared banding homologies. These results show that the large chromosomes have been highly conserved in the evolutionary history of the three genera.