Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data

Background

For anurans, knowledge of 5S rDNA is scarce. For Engystomops species, chromosomal homeologies are difficult to recognize due to the high level of inter- and intraspecific cytogenetic variation. In an attempt to better compare the karyotypes of the Amazonian species Engystomops freibergi and Engystomops petersi, and to extend the knowledge of 5S rDNA organization in anurans, the 5S rDNA sequences of Amazonian Engystomops species were isolated, characterized, and mapped.

Results

Two types of 5S rDNA, which were readily differentiated by their NTS (non-transcribed spacer) sizes and compositions, were isolated from specimens of E. freibergi from Brazil and E. petersi from two Ecuadorian localities (Puyo and Yasuní). In the E. freibergi karyotypes, the entire type I 5S rDNA repeating unit hybridized to the pericentromeric region of 3p, whereas the entire type II 5S rDNA repeating unit mapped to the distal region of 6q, suggesting a differential localization of these sequences. The type I NTS probe clearly detected the 3p pericentromeric region in the karyotypes of E. freibergi and E. petersi from Puyo and the 5p pericentromeric region in the karyotype of E. petersi from Yasuní, but no distal or interstitial signals were observed. Interestingly, this probe also detected many centromeric regions in the three karyotypes, suggesting the presence of a satellite DNA family derived from 5S rDNA. The type II NTS probe detected only distal 6q regions in the three karyotypes, corroborating the differential distribution of the two types of 5S rDNA.

Conclusions

Because the 5S rDNA types found in Engystomops are related to those of Physalaemus with respect to their nucleotide sequences and chromosomal locations, their origin likely preceded the evolutionary divergence of these genera. In addition, our data indicated homeology between Chromosome 5 in E. petersi from Yasuní and Chromosomes 3 in E. freibergi and E. petersi from Puyo. In addition, the chromosomal location of the type II 5S rDNA corroborates the hypothesis that the Chromosomes 6 of E. petersi and E. freibergi are homeologous despite the great differences observed between the karyotypes of the Yasuní specimens and the others.     

Further evidence for early sex chromosome differentiation of anuran species

Chromosome banding and meiotic evidence show that XX/XY systems found in two Eupsophus species (Amphibia-Leptodactylidae) represent early stages of sex chromosome differentiation. Pair 14 is heteromorphic in E. migueli males and represents the heterochromosomes. In E. roseus this pair is metacentric and does not show heteromorphism. Paracentromeric constitutive heterochromatin is present in all chromosomes except in the E. migueli and E. roseus metacentric Y chromosomes. Constitutive heterochromatin loss is the structural modification responsible for Y chromosome differentiation. Pericentric inversions may have modified the morphology of the X chromosome of Eupsophus species.     

Further evidence for early sex chromosome differentiation of Anuran species

Chromosome banding and meiotic evidence show that XX/XY systems found in two Eupsophus species (Amphibia-Leptodactylidae) represent early stages of sex chromosome differentiation. Pair 14 is heteromorphic in E. migueli males and represents the heterochromosomes. In E. roseus this pair is metacentric and does not show heteromorphism. Paracentromeric constitutive heterochromatin is present in all chromosomes except in the E. migueli and E. roseus metacentric Y chromosomes. Constitutive heterochromatin loss is the structural modification responsible for Y chromosome differentiation. Pericentric inversions may have modified the morphology of the X chromosome of Eupsophus species.Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de ChileDepartamento de Biología Celular y Genética, Facultad de Medicina, Universidad de Chile     

Evidence for a highly differentiated sex chromosome heteromorphism in the salamander Necturus maculosus (Rafinesque)

The mitotic chromosomes of the neotenic (sensu Gould, 1977, and Alberch et al., 1979) salamander Necturus maculosus (Rafinesque) have been examined using a C-band technique to demonstrate the distribution of heterochromatin. The C-banded mitotic chromosomes provide evidence of a highly differentiated XY male/XX female sex chromosome heteromorphism, in which the X and Y chromosomes differ greatly in size and morphology, and in the amount and distribution of C-band heterochromatin. The X chromosome represents one of the largest biarmed chromosomes in the karyotype and is indistinguishable from similar sized autosomes on the basis of C-band heterochromatin. The Y chromosome, on the other hand, is diminutive, morphologically distinct from all other chromosomes of the karyotype, and is composed almost entirely of C-band heterochromatin. The discovery of an X/Y chromosome heteromorphism in this species is consistent with the observation by King (1912) of a heteromorphic spermatogenic bivalent. Karyological and phylogenetic implications are discussed.     

Interchromosomal duplications on the Bactrocera oleae Y chromosome imply a distinct evolutionary origin of the sex chromosomes compared to Drosophila

Background

Diptera have an extraordinary variety of sex determination mechanisms, and Drosophila melanogaster is the paradigm for this group. However, the Drosophila sex determination pathway is only partially conserved and the family Tephritidae affords an interesting example. The tephritid Y chromosome is postulated to be necessary to determine male development. Characterization of Y sequences, apart from elucidating the nature of the male determining factor, is also important to understand the evolutionary history of sex chromosomes within the Tephritidae. We studied the Y sequences from the olive fly, Bactrocera oleae. Its Y chromosome is minute and highly heterochromatic, and displays high heteromorphism with the X chromosome.

Methodology/Principal Findings

A combined Representational Difference Analysis (RDA) and fluorescence in-situ hybridization (FISH) approach was used to investigate the Y chromosome to derive information on its sequence content. The Y chromosome is strewn with repetitive DNA sequences, the majority of which are also interdispersed in the pericentromeric regions of the autosomes. The Y chromosome appears to have accumulated small and large repetitive interchromosomal duplications. The large interchromosomal duplications harbour an importin-4-like gene fragment. Apart from these importin-4-like sequences, the other Y repetitive sequences are not shared with the X chromosome, suggesting molecular differentiation of these two chromosomes. Moreover, as the identified Y sequences were not detected on the Y chromosomes of closely related tephritids, we can infer divergence in the repetitive nature of their sequence contents.

Conclusions/Significance

The identification of Y-linked sequences may tell us much about the repetitive nature, the origin and the evolution of Y chromosomes. We hypothesize how these repetitive sequences accumulated and were maintained on the Y chromosome during its evolutionary history. Our data reinforce the idea that the sex chromosomes of the Tephritidae may have distinct evolutionary origins with respect to those of the Drosophilidae and other Dipteran families.     

X1X1X2X2/X1X2Y sex chromosome systems in the Neotropical Gymnotiformes electric fish of the genus Brachyhypopomus

Several types of sex chromosome systems have been recorded among Gymnotiformes, including male and female heterogamety, simple and multiple sex chromosomes, and different mechanisms of origin and evolution. The X₁X₁X₂X₂/X₁X₂Y systems identified in three species of this order are considered homoplasic for the group. In the genus Brachyhypopomus, only B. gauderio presented this type of system. Herein we describe the karyotypes of Brachyhypopomus pinnicaudatus and B. n. sp. FLAV, which have an X₁X₁X₂X₂/X₁X₂Y sex chromosome system that evolved via fusion between an autosome and the Y chromosome. The morphology of the chromosomes and the meiotic pairing suggest that the sex chromosomes of B. gauderio and B. pinnicaudatus have a common origin, whereas in B . n. sp. FLAV the sex chromosome system evolved independently. However, we cannot discard the possibility of common origin followed by distinct processes of differentiation. The identification of two new karyotypes with an X₁X₁X₂X₂/X₁X₂Y sex chromosome system in Gymnotiformes makes it the most common among the karyotyped species of the group. Comparisons of these karyotypes and the evolutionary history of the taxa indicate independent origins for their sex chromosomes systems. The recurrent emergence of the X₁X₁X₂X₂/X₁X₂Y system may represent sex chromosomes turnover events in Gymnotiformes.     

Cytogenetic contributions for the study of the Amazonian Engystomops (Anura; Leiuperidae) assessed in the light of phylogenetic relationships

Genetic divergence and speciation mechanisms of the Amazonian Engystomops frog have been inferred mainly from mtDNA sequences, microsatellite and male advertisement call. Although many aspects of this divergence remain unclear, cytogenetic analyses of Amazonian Engystomops populations are described and are compared to the relationships inferred from mitochondrial and nuclear DNA sequence data. High cytogenetic variation distinguished karyotypic patterns among the populations, even between populations which had no prezygotic isolation previously inferred from mating call analysis. Interestingly, the Puyo and Acre populations, which are in different clades, showed heteromorphic sex chromosomes (XX/XY), not identified in the other Ecuatorian populations analyzed. The analysis of a specimen collected in a site near Yasuní (Ecuador) which was cytogenetically related to the specimens from Puyo (Ecuador), was also phylogenetically closely related these specimens. In the rhodopsin nucleotide sequences, six polymorphic sites were identified and various specimens were heterozygous for them. All the data presented herein, in conjunction with those previously reported, corroborate the hypothesis that Engystomops petersi is a complex of distinct species. It also indicates that karyotypic evolution patterns may have played a substantial role in the Engystomops speciation and the occurrence of sporadic mating events between divergent evolutive lineages is discussed.     

Effects of sex chromosome dosage on corpus callosum morphology in supernumerary sex chromosome aneuploidies

Background

Supernumerary sex chromosome aneuploidies (sSCA) are characterized by the presence of one or more additional sex chromosomes in an individual’s karyotype; they affect around 1 in 400 individuals. Although there is high variability, each sSCA subtype has a characteristic set of cognitive and physical phenotypes. Here, we investigated the differences in the morphometry of the human corpus callosum (CC) between sex-matched controls 46,XY (N =99), 46,XX (N =93), and six unique sSCA karyotypes: 47,XYY (N =29), 47,XXY (N =58), 48,XXYY (N =20), 47,XXX (N =30), 48,XXXY (N =5), and 49,XXXXY (N =6).

Methods

We investigated CC morphometry using local and global area, local curvature of the CC boundary, and between-landmark distance analysis (BLDA). We hypothesized that CC morphometry would vary differentially along a proposed spectrum of Y:X chromosome ratio with supernumerary Y karyotypes having the largest CC areas and supernumerary X karyotypes having significantly smaller CC areas. To investigate this, we defined an sSCA spectrum based on a descending Y:X karyotype ratio: 47,XYY, 46,XY, 48,XXYY, 47,XXY, 48,XXXY, 49,XXXXY, 46,XX, 47,XXX. We similarly explored the effects of both X and Y chromosome numbers within sex. Results of shape-based metrics were analyzed using permutation tests consisting of 5,000 iterations.

Results

Several subregional areas, local curvature, and BLDs differed between groups.Moderate associations were found between area and curvature in relation to the spectrum and X and Y chromosome counts. BLD was strongly associated with X chromosome count in both male and female groups.

Conclusions

Our results suggest that X- and Y-linked genes have differential effects on CC morphometry. To our knowledge, this is the first study to compare CC morphometry across these extremely rare groups.

     

Evidence for Emergence of Sex-Determining Gene(s) in a Centromeric Region in Vasconcellea parviflora

Sex chromosomes have been studied in many plant and animal species. However, few species are suitable as models to study the evolutionary histories of sex chromosomes. We previously demonstrated that papaya (Carica papaya) (2n = 2x = 18), a fruit tree in the family Caricaceae, contains recently emerged but cytologically heteromorphic X/Y chromosomes. We have been intrigued by the possible presence and evolution of sex chromosomes in other dioecious Caricaceae species. We selected a set of 22 bacterial artificial chromosome (BAC) clones that are distributed along the papaya X/Y chromosomes. These BACs were mapped to the meiotic pachytene chromosomes of Vasconcellea parviflora (2n = 2x = 18), a species that diverged from papaya ∼27 million years ago. We demonstrate that V. parviflora contains a pair of heteromorphic X/Y chromosomes that are homologous to the papaya X/Y chromosomes. The comparative mapping results revealed that the male-specific regions of the Y chromosomes (MSYs) probably initiated near the centromere of the Y chromosomes in both species. The two MSYs, however, shared only a small chromosomal domain near the centromere in otherwise rearranged chromosomes. The V. parviflora MSY expanded toward the short arm of the chromosome, whereas the papaya MSY expanded in the opposite direction. Most BACs mapped to papaya MSY were not located in V. parviflora MSY, revealing different DNA compositions in the two MSYs. These results suggest that mutation of gene(s) in the centromeric region may have triggered sex chromosome evolution in these plant species.     

Sex chromosome pairing during male meiosis in marsupials

The pairing of the sex chromosomes at pachytene has been examined in twenty-two species of Australian marsupials, including four with complex sex chromosome systems. The axial elements of the sex chromosomes associate in all but one species. However, no synaptonemal complex has been observed between the axes of the X and Y chromosome in any of the examined species. Both the type of association between the sex chromosome axes, and the structural modifications of these axes are conserved within taxonomic groupings. In three species with complex sex chromosome systems, the t(XA), Y, A trivalents do not have a favoured relative orientation of the axes of the Y and A chromosomes, whereas in a fourth species with a t(XA₁), t(A₂YA₂), A₂ system the t(XA₁) and A₂ axes are in a cis arrangement with each other.     

Sex chromosome differentiation in Belostoma (Insecta: Heteroptera: Belostomatidae)

Belostoma, a genus of the family Belostomatidae, includes species of great ecological importance as biocontrol agents. Few species of these species have been the subject of cytogenetic analyses. Karyotypic evolution in this genus involves agmatoploidy and simploidy; there are also different sex chromosome systems. We examined two Belostoma species (B. dilatatum and B. candidulum) collected from the Paranapanema River Basin (Brazil). Mitotic and meiotic analysis revealed 2n(♂) = 26 + X(1)X(2)X(3)Y for B. dilatatum and 2n(♂) = 14 + XY for B. candidulum; both karyotypes have holokinetic chromosomes. Differences in heterochromatin distribution were also observed between the species, besides variation in the localization of CMA(3)(+)/DAPI(-) blocks. The existence of different types of sex chromosome systems in these species was confirmed based on arrangements of the chromosomes in different meiotic stages. We identified a new sex system in B. dilatatum, and make the first cytogenetic report on B. candidulum.     

Sex chromosome polymorphism in guppies

Sex chromosomes differ from autosomes by dissimilar gene content and, at a more advanced stage of their evolution, also in structure and size. This is driven by the divergence of the Y or W from their counterparts, X and Z, due to reduced recombination and the resulting degeneration as well as the accumulation of sex-specific and sexually antagonistic genes. A paradigmatic example for Y-chromosome evolution is found in guppies. In these fishes, conflicting data exist for a morphological and molecular differentiation of sex chromosomes. Using molecular probes and the previously established linkage map, we performed a cytogenetic analysis of sex chromosomes. We show that the Y chromosome has a very large pseudoautosomal region, which is followed by a heterochromatin block (HCY) separating the subtelomeric male-specific region from the rest of the chromosome. Interestingly, the size of the HCY is highly variable between individuals from different population. The largest HCY was found in one population of Poecilia wingei, making the Y almost double the size of the X and the largest chromosome of the complement. Comparative analysis revealed that the Y chromosomes of different guppy species are homologous and share the same structure and organization. The observed size differences are explained by an expansion of the HCY, which is due to increased amounts of repetitive DNA. In one population, we observed also a polymorphism of the X chromosome. We suggest that sex chromosome-linked color patterns and other sexually selected genes are important for maintaining the observed structural polymorphism of sex chromosomes.     

Sex chromosomal dimorphisms narrated by X-chromosome translocation in a spiny frog (<Emphasis Type="Italic">Quasipaa boulengeri</Emphasis>)

Background

In the general model of sex chromosome evolution for diploid dioecious organisms, the Y (or W) chromosome is derived, while the homogametic sex presumably represents the ancestral condition. However, in the frog species Quasipaa boulengeri, heteromorphisms caused by a translocation between chromosomes 1 and 6 are not related to sex, because the same heteromorphic chromosomes are found both in males and females at the cytological level. To confirm whether those heteromorphisms are unrelated to sex, a sex-linked locus was mapped at the chromosomal level and sequenced to identify any haplotype difference between sexes.

Results

Chromosome 1 was assigned to the sex chromosome pair by mapping the sex-linked locus. X-chromosome translocation was demonstrated and confirmed by the karyotypes of the progeny. Translocation heteromorphisms were involved in normal and translocated X chromosomes in the rearranged populations. Based on phylogenetic inference using both male and female sex-linked haplotypes, recombination was suppressed not only between the Y and normal X chromosomes, respectively the Y and translocated X chromosomes, but also between the normal and translocated X chromosomes. Both males and females shared not only the same translocation heteromorphisms but also the X chromosomal dimorphisms in this frog.

Conclusions

The reverse of the typical situation, in which the X is derived and the Y has remained unchanged, is known to be very rare. In the present study, X-chromosome translocation has been known to cause sex chromosomal dimorphisms. The X chromosome has gone processes of genetic differentiation and/or structural changes by chance, which may facilitate sex chromosome differentiation. These sex chromosomal dimorphisms presenting in both sexes may represent the early stages of sex chromosome differentiation and aid in understanding sex chromosome evolution.

     

XX/XY sex chromosome system and chromosome markers in the snake eel Ophisurus serpens (Anguilliformes: Ophichtidae)

We report evidence of an XX/XY sex chromosome system in the snake eel Ophisurus serpens (Anguilliformes: Ophichthidae). We characterized the male and female karyotypes by C-, replication- and HaeIII-bandings. The 45S and 5S ribosomal gene families were located using dual fluorescence in situ hybridization, which showed that the 5S rDNA sites were present on the X chromosome, beside an autosome pair. FISH with a telomeric peptide nucleic acid probe enabled recognition of Interstitial Telomeric Sequences (ITSs), likely remnants of chromosomal rearrangements, in five chromosome pairs, including the rDNA-bearing ones. Possible mechanisms of the origin of sex chromosomes in this species are discussed, considering the presence of a sex-linked marker and ITSs.     

Molecular and evolutionary analysis of a plant Y chromosome.

Plants have evolved a great diversity of sex determination systems. Among these, the XY system, also found in mammals, is one of the most exciting since it gives the opportunity to compare the evolution of sex chromosomes in two different kingdoms. Whereas genetic and molecular mechanisms controlling sex determination in drosophila and mammals, have been well studied, very little is known about such processes in plants. White campion (Silene latifolia) is an example of plant with X and Y chromosomes. What is the origin of the X and Y chromosomes? How did they evolve from a pair of autosomes? In our laboratory, we have isolated the first active genes located on a plant Y chromosome. We are using them as markers to trace the origin and evolution of sex chromosomes in the Silene genus.     

Highly Differentiated ZW Sex Microchromosomes in the Australian Varanus Species Evolved through Rapid Amplification of Repetitive Sequences

Transitions between sex determination systems have occurred in many lineages of squamates and it follows that novel sex chromosomes will also have arisen multiple times. The formation of sex chromosomes may be reinforced by inhibition of recombination and the accumulation of repetitive DNA sequences. The karyotypes of monitor lizards are known to be highly conserved yet the sex chromosomes in this family have not been fully investigated. Here, we compare male and female karyotypes of three Australian monitor lizards, Varanus acanthurus, V. gouldii and V. rosenbergi, from two different clades. V. acanthurus belongs to the acanthurus clade and the other two belong to the gouldii clade. We applied C-banding and comparative genomic hybridization to reveal that these species have ZZ/ZW sex micro-chromosomes in which the W chromosome is highly differentiated from the Z chromosome. In combination with previous reports, all six Varanus species in which sex chromosomes have been identified have ZZ/ZW sex chromosomes, spanning several clades on the varanid phylogeny, making it likely that the ZZ/ZW sex chromosome is ancestral for this family. However, repetitive sequences of these ZW chromosome pairs differed among species. In particular, an (AAT)n microsatellite repeat motif mapped by fluorescence in situ hybridization on part of W chromosome in V. acanthurus only, whereas a (CGG)n motif mapped onto the W chromosomes of V. gouldii and V. rosenbergi. Furthermore, the W chromosome probe for V. acanthurus produced hybridization signals only on the centromeric regions of W chromosomes of the other two species. These results suggest that the W chromosome sequences were not conserved between gouldii and acanthurus clades and that these repetitive sequences have been amplified rapidly and independently on the W chromosome of the two clades after their divergence.     

Amplification of a long terminal repeat-like element on the Y chromosome of the platyfish, Xiphophorus maculatus

The platyfish (Xiphophorus maculatus), in which sex chromosomes are evident from stable and predictable inheritance of sex, is one of the best-studied lower vertebrates with respect to sex determination. In order to identify the structural equivalent for this in the karyotype, which does not contain heteromorphic pairs of chromosomes, two sex-linked molecular probes were used for fluorescent in situ hybridization analysis. One probe, derived from the melanoma oncogene locus ONC-Xmrk, stained both the X and the Y chromosome. This cytogenetic analysis mapped the sex-determining locus to the subtelomeric region of a medium-sized telocentric chromosome. Another probe, a repetitive element (XIR), specifically labeled the Y chromosome in metaphase spreads and in interphase nuclei. The sex chromosomes of X. maculatus can be considered to be at an early stage of evolution of gonosomes. Expansion of the XIR repeat is obviously one of the earliest of the molecular events that lead to divergence of the Y chromosome and recombinational isolation of the sex-determining locus. Received: 10 December 1999; in revised form: 20 January 2000 / Accepted: 24 January 2000     

Dynamic gene order on the <Emphasis Type="Italic">Silene latifolia</Emphasis> Y chromosome

Dioecious Silene latifolia evolved heteromorphic sex chromosomes within the last ten million years, making it a species of choice for studies of the early stages of sex chromosome evolution in plants. About a dozen genes have been isolated from its sex chromosomes and basic genetic and deletion maps exist for the X and Y chromosomes. However, discrepancies between Y chromosome maps led to the proposal that individual Y chromosomes may differ in gene order. Here, we use an alternative approach, with fluorescence in situ hybridization (FISH), to locate individual genes on S. latifolia sex chromosomes. We demonstrate that gene order on the Y chromosome differs between plants from two populations. We suggest that dynamic gene order may be a general property of Y chromosomes in species with XY systems, in view of recent work demonstrating that the gene order on the Y chromosomes of humans and chimpanzees are dramatically different.     

黄鳝体内寄生胃瘤线虫的染色体核型及G-带分析

采用常规空气干燥法制片,对寄生于黄鳝(Monopterus albus)体腔内的胃瘤线虫(Eustrongylidesignotus)染色体核型进行分析。结果表明:胃瘤线虫体细胞有12条染色体,为二倍体,核型公式为2n=12=10 m+2 sm。由5对常染色体和1对性染色体组成,性别决定模式为XX-XY,其中X、Y和1～4号染色体都为中着丝粒染色体,5号为亚中着丝粒染色体。每对染色体都有特定的G-带带型。