Search Results (131)

Satellite DNAs (satDNAs) play a crucial role in understanding chromosomal evolution and the differentiation of sex chromosomes across diverse taxa, particularly when high karyotypic diversity occurs. The Physalaemus cuvieri–Physalaemus ephippifer species complex comprises at least seven divergent lineages, each exhibiting specific karyotypic signatures. The group composed of Ph. ephippifer, Lineage 1B of ‘Ph. cuvieri’ (L1B), and a lineage resulting from their secondary contact is especially intriguing due to varying degrees of sex chromosome heteromorphism. In this study, we characterized the satellitome of Ph. ephippifer in order to identify novel satDNAs that may provide insights into chromosomal evolution, particularly concerning sex chromosomes. We identified 62 satDNAs in Ph. ephippifer, collectively accounting for approximately 10% of the genome. Notably, nine satDNA families were shared with species from distantly related clades, raising questions about their potential roles in anurans genomes. Among the seven satDNAs mapped via fluorescent in situ hybridization, PepSat3 emerged as a strong candidate for the centromeric sequence in this group. Additionally, PepSat11 and PepSat24 provided evidence supporting a translocation involving both arms of the W chromosome in Ph. ephippifer. Furthermore, a syntenic block composed of PepSat3, PcP190, and PepSat11 suggested an inversion event during the divergence of Ph. ephippifer and L1B. The variation in signal patterns of satDNAs associated with nucleolar organizer regions (NORs) highlights the complexity of NOR evolution in this species complex, which exhibits substantial diversity in this genomic region. Additionally, our findings for PepSat30-350 emphasize the importance of validating the sex-biased abundance of satDNAs. Full article

Background: The order Suliformes exhibits significant karyotype diversity, with Sula species showing a Z₁Z₁Z₂Z₂/Z₁Z₂W multiple-sex chromosome system, an uncommon occurrence in avians. Satellite DNAs (satDNAs), which consist of tandemly repeated sequences, often vary considerably even among closely related species, making them valuable markers for studying karyotypic evolution, particularly that of sex chromosome evolution. This study aims to characterize and investigate the potential role of these sequences in the karyotypic evolution of the group, with special attention to the sex chromosomes. Methods: Through characterizing satDNAs in two Suliformes species (Sula leucogaster and Nannopterum brasilianum) using BGISEQ-500 platform and bioinformatics analysis. Their chromosomal distribution was mapped by fluorescence in situ hybridization (FISH) within their own karyotypes and in three additional Suliformes species (S. sula, S. dactylatra, and Fregata magnificens). Results: Five satDNAs were identified in S. leucogaster and eight in N. brasilianum. Within the genus Sula, three species shared specific satDNA sequences, although with different hybridization patterns. In contrast, the satDNAs of N. brasilianum were species-specific. Additionally, the Z chromosome, including Z₂ in Sula species, showed reduced accumulation of repetitive DNAs. Conclusions: These results suggest that differential accumulation of repetitive sequences may have contributed to the diversification of karyotypes in this group, particularly influencing the structure and differentiation of sex chromosomes. Full article

Snakes are cytogenetically dynamic, characterized by largely conserved diploid chromosome numbers although displaying varied variable evolutionary stages of their sex chromosomes. This study examined four snakes, with a special focus on the genus Ptyas, to provide evolutionary insights into the evolution of ZW sex chromosomes. We performed an extensive karyotype characterization using conventional and molecular cytogenetic approaches, described for the first time the karyotype of Ptyas korros, and revisited the karyotype descriptions of P. mucosa, Chrysopelea ornata, and Fowlea flavipunctatus. We found that all species except F. flavipunctatus have highly heterochromatic W chromosomes enriched in satDNAs or microsatellite repeats. Repetitive sequences accumulate with the heterochromatinization of the W chromosome but are not necessarily associated with this process, demonstrating the dynamic makeup of snake sex chromosomes. Autosomal locus-specific and sex chromosome probes from Pogona vitticeps and Varanus acanthurus did not show hybridization signals in Ptyas snakes, suggesting divergent evolutionary pathways. This finding highlighted the dynamic nature of sex chromosome evolution in snakes, which occurred independently in lizards. Full article

The Lauraceae family, a keystone group in subtropical evergreen broad-leaved forest ecosystems, exhibits exceptional diversity in sexual systems (including hermaphroditic flowers, functionally unisexual flowers, and pseudo-dioecy), serving as a natural model for studying plant sexual differentiation mechanisms. This review synthesizes advances in the evolutionary mechanisms and genomic studies of sexual differentiation in Lauraceae, focusing on three key areas: (1) the evolution of taxonomic classification and floral morphology, (2) molecular trajectories of sexual differentiation, and (3) challenges and future directions in sex determination research (e.g., sex-linked marker development and gene-editing-assisted breeding). Morphological and phylogenetic analyses suggest that ancestral Lauraceae species were late Cretaceous hermaphroditic trees, with recent radiation of unisexual lineages (e.g., Cinnamomum and Laurus) linked to pollinator pressure, genome duplication events (WGD), and incipient sex chromosome evolution. Despite progress, critical challenges remain, including unresolved thresholds for sex chromosome origination, unquantified molecular pathways integrating environmental signals (e.g., photoperiod, temperature) with genetic networks, and the lack of efficient sex-specific markers and genetic transformation systems. Future studies should integrate single-cell omics, epigenetic profiling, and cross-species comparative genomics to elucidate spatiotemporal dynamics and evolutionary drivers of sexual differentiation. These efforts will advance genetic improvement and ecological restoration strategies. This review provides a systematic framework for advancing plant sexual evolution theory and promoting sustainable utilization of Lauraceae resources. Full article

Anseriformes represent a basal order in the phylogeny of neognath birds and are of particular interest in cytogenetic research due to their distinctive chromosomal features. However, aspects of their chromosomal evolution, such as the distribution and organization of microsatellite sequences, remain poorly understood. Given the role of these dynamic repetitive sequences in chromosome organization, differentiation, and evolution, we analyzed microsatellite distribution in three Anatidae species, each representing a different subfamily: Amazonetta brasiliensis-Brazilian Teal (Anatinae), Coscoroba coscoroba-Coscoroba Swan (Anserinae), and Dendrocygna viduata-White-faced Whistling Duck (Dendrocygninae). This is the first karyotypic description for White-faced Whistling Duck (2n = 78) and Brazilian Teal (2n = 80), whereas Coscoroba Swan, previously analyzed, exhibits a notably high diploid number (2n = 98). Despite sharing a similar macrochromosome morphology, the three showed differences in diploid numbers and microsatellite distribution. Extensive microsatellite accumulation was found in both autosomal and sex chromosomes (Z and W) of Brazilian Teal and Coscoroba Swan, while White-faced Whistling Duck displays minimal hybridization signals and an absence of microsatellites on the sex chromosomes. The accumulation of specific microsatellites, such as (CAC)₁₀ and (GAG)₁₀, in centromeric and pericentromeric regions suggests an association with transposable elements, potentially driving chromosomal evolution. Notably, the substantial accumulation of these sequences on the Z and W chromosomes of Brazilian Teal and Coscoroba Swan, but not White-faced Whistling Duck, supports the hypothesis that repetitive sequence expansion occurs in a species-specific manner, contributing to sex chromosome differentiation. These findings highlight microsatellite mapping as a valuable tool for understanding chromosomal evolution and genomic differentiation in Anseriformes. Full article

The canonical model of vertebrate sex chromosome evolution predicts a one-way trend toward degradation. However, most sex chromosomes in lower vertebrates are homomorphic. Recent progress in studies of sex determination has resulted in the discovery of more than 30 master sex determination (MSD) genes, most of which are from teleost fish. An analysis of MSD gene acquisition, recombination suppression, and sex chromosome-specific sequences revealed correlations in the modes of MSD gene acquisition and the evolution of sex chromosomes. Sex chromosomes remain homomorphic with MSD genes acquired by simple mutations, gene duplications, allelic variations, or neofunctionalization; in contrast, they become heteromorphic with MSD genes acquired by chromosomal inversion, fusion, and fission. There is no recombination suppression with sex chromosomes carrying MSD genes gained through simple mutations. In contrast, there is extensive recombination suppression with sex chromosomes carrying MSD genes gained through chromosome inversion. There is limited recombination suppression with sex chromosomes carrying MSD genes gained through transposition or translocation. We propose a cause–effect model that predicts sex chromosome evolution as a consequence of the acquisition modes of MSD genes, which explains the evolution of sex chromosomes in various vertebrates. A key factor determining the trend of sex chromosome evolution is whether non-homologous regions are created during the acquisition of MSD genes. Chromosome inversion creates inversely homologous but directly non-homologous sequences, which lead to recombination suppression but retain recombination potential. Over time, recurrent recombination in the inverted regions leads to the formation of strata and may cause the degradation of sex chromosomes. Depending on the nature of deletions in the inverted regions, sex chromosomes may evolve with dosage compensation, or the selective retention of haplo-insufficient genes may be used as an alternative strategy. Full article

Probasin protein was originally identified as a basic protein present in rat prostate epithelium. So far, its physiological role, its origin, and its presence in other species including humans remain largely elusive. With the ever-growing number of genome assemblies, thus far, probasin genes (Pbsn/PBSN) have only been predicted in a subset of rodent genomes. In this study, we addressed the phylogeny of probasin genes and found them to be exclusively present in members of the superfamily Muroidea. It first emerged in the so-called pseudoautosomal region, a subtelomeric gene cluster of both mammalian sex chromosomes. During evolution of the Muroidea lineages, probasin recombined to the X-specific region of the X-chromosome in mice and hamster species. This event likely saved the gene from events that other pseudoautosomal genes suffered, namely displaying an increase in G and C nucleotide composition or accumulation of repetitive elements. We observed changes to its coding region, e.g., sequence insertions in exon 6, which challenge the current understanding of rodent phylogeny, in particular regarding the evolutionary history of tribe formation within the subfamily Murinae. Analyzing the evolution of probasin genes in Muroidea allows fostering understanding of phylogenetic relationships in one of the largest groups of mammalian species. Full article

Background/Objectives: Arachnids are a megadiverse arthropod group. The present study investigated the chromosomes of pedipalpid tetrapulmonates (orders Amblypygi, Thelyphonida, Schizomida) and two arachnid orders of uncertain phylogenetic placement, Ricinulei and Solifugae, to reconstruct their karyotype evolution. Except for amblypygids, the cytogenetics of these arachnid orders was almost unknown prior to the present study. Methods: Chromosomes were investigated using methods of standard (Giemsa-stained preparations, banding techniques) and molecular cytogenetics (fluorescence in situ hybridization, comparative genomic hybridization). Results and Conclusions: New data for 38 species, combined with previously published data, suggest that ancestral arachnids possessed low to moderate 2n (22–40), monocentric chromosomes, one nucleolus organizer region (NOR), low levels of heterochromatin and recombinations, and no or homomorphic sex chromosomes. Karyotypes of Pedipalpi and Solifugae diversified via centric fusions, pericentric inversions, and changes in the pattern of NORs and, in solifuges, also through tandem fusions. Some solifuges display an enormous amount of constitutive heterochromatin and high NOR number. It is hypothesized that the common ancestor of amblypygids, thelyphonids, and spiders exhibited a homomorphic XY system, and that telomeric heterochromatin and NORs were involved in the evolution of amblypygid sex chromosomes. The new findings support the Cephalosomata clade (acariforms, palpigrades, and solifuges). Hypotheses concerning the origin of acariform holocentric chromosomes are presented. Unlike current phylogenetic hypotheses, the results suggest a sister relationship between Schizomida and a clade comprising other tetrapulmonates as well as a polyploidization in the common ancestor of the clade comprising Araneae, Amblypygi, and Thelyphonida. Full article

Background: Argyrosomus japonicus, a member of the Sciaenidae family, is widely distributed across the sea areas near China, Japan, Australia, and South Africa. The aim of this study is to provide a high-quality genome with new technology and to understand the sex determination mechanism of this species. Methods: We generated a high-quality chromosome-level genome for Argyrosomus japonicus using PacBio HiFi and Hi-C sequencing technologies. To map the sex determination region, we employed re-sequencing data from 38 A. japonicus and conducted genome-wide association studies (GWASs) on sex phenotypes. Results: Utilizing Hifiasm, we assembled a 708.8 Mb genome with a contig N50 length of 30 Mb. Based on Hi-C data, these contigs were organized into 24 chromosomes. The completeness of the assembly was assessed to be 99% using BUSCO, and over 98% according to Merqury. We identified a total of 174.57 Mb of repetitive elements and annotated 24,726 protein-coding genes in the genome. We mapped a 2.8 Mb sex determination region on chromosome 9, within which we found two sex-linked markers. Furthermore, we confirmed that the XX-XY sex determination system is adopted in A. japonicus. Conclusions: The findings of this study provide significant insights into genetic breeding, genome evolution research, and sex control breeding in A. japonicus. Full article

The Northern snakehead (Channa argus) is a significant economic aquaculture species in China. Exhibiting sexual dimorphism in the growth rate between females and males, mono-sex breeding holds substantial value for aquaculture. This study employed GWAS and transcriptome analysis were applied to identify sex determination genomic regions and develop sex-specific markers. A total of 270 single-nucleotide polymorphisms (SNPs) and 31 insertion-deletions (InDels) were identified as being sexually dimorphic through GWAS and fixation index (Fst) scanning. Based on GWAS results, two sex-specific InDel markers were developed, effectively distinguishing genetic sex for XX females, XY males, and YY super-males via (polymerase chain reaction) PCR amplification. A major genomic segment of approximately 115 kb on chromosome 3 (Chr 03) was identified as the sex-determination region. A comparative transcriptome analysis of gonads for three sexes identified 158 overlapping differentially expressed genes (DEGs). Additionally, three sex-related candidate genes were identified near the sex determination region, including id2, sox11, and rnf144a. Further studies are required to elucidate the functions of these genes. Overall, two sex-specific InDel markers support a male heterogametic XX/XY sex-determination system in Northern snakeheads and three candidate genes offer new insights into sex determination and the evolution of sex chromosomes in teleost fish. Full article

Eukaryotic genomes exhibit a dynamic interplay between single-copy sequences and repetitive DNA elements, with satellite DNA (satDNA) representing a substantial portion, mainly situated at telomeric and centromeric chromosomal regions. We utilized Illumina next-generation sequencing data from Adalia bipunctata to investigate its satellitome. Cytogenetic mapping via fluorescence in situ hybridization was performed for the most abundant satDNA families. In silico localization of satDNAs was carried out using the CHRISMAPP (Chromosome In Silico Mapping) pipeline on the high-fidelity chromosome-level assembly already available for this species, enabling a meticulous characterization and localization of multiple satDNA families. Additionally, we analyzed the conservation of the satellitome at an interspecific scale. Specifically, we employed the CHRISMAPP pipeline to map the satDNAs of A. bipunctata onto the genome of Adalia decempunctata, which has also been sequenced and assembled at the chromosome level. This analysis, along with the creation of a synteny map between the two species, suggests a rapid turnover of centromeric satDNA between these species and the potential occurrence of chromosomal rearrangements, despite the considerable conservation of their satellitomes. Specific satDNA families in the sex chromosomes of both species suggest a role in sex chromosome differentiation. Our interspecific comparative study can provide a significant advance in the understanding of the repeat genome organization and evolution in beetles. Full article

Sex determination is remarkably diverse, with frequent transitions between sex chromosomes, in amphibians. Under these transitions, some chromosomes are more likely to be recurrently co-opted as sex chromosomes, as they are often observed across deeply divergent taxa. However, little is known about the pattern of sex chromosome evolution among closely related groups. Here, we examined sex chromosome and sex determination in two spiny frogs, Nanorana quadranus and Quasipaa yei. We conducted an analysis of genotyping-by-sequencing (GBS) data from a total of 34 individuals to identify sex-specific makers, with the results verified by PCR. The results suggest that chromosome 1 is a homologous sex chromosome with an XY pattern in both species. This chromosome has been evolutionarily conserved across these closely related groups within a period of time. The DMRT1 gene is proposed to be implicated in homology across two distantly related spiny frog species as a putative candidate sex-determining gene. Harboring the DMRT1 gene, chromosome 1 would have been independently co-opted for sex determination in deeply divergent groups of anurans. Full article

We present a comparative chromosome study of several taxa of the Malagasy ground geckos of the Paroedura bastardi and P. picta species groups. We employed a preliminary molecular analysis using a trait of the mitochondrial 16S rRNA gene (of about 570 bp) to assess the taxonomic status of the samples studied and a cytogenetic analysis with standard karyotyping (5% Giemsa solution), silver staining (Ag–NOR staining) and sequential C-banding (C-banding + Giemsa and + fluorochromes). Our results show that all the taxa studied of the P. bastardi group (P. ibityensis, P. rennerae and P. cf. guibeae) have a similar karyotype composed of 2n = 34 chromosomes, with two metacentric pairs (1 and 3) and all other pairs being acrocentric. Chromosome diversification in the P. bastardi group was mainly linked to the diversification of heteromorphic sex chromosome systems (ZZ/ZW) in P. ibityensis and P. rennerae, while no heteromorphic sex chromosome pair was found in P. cf. guibeae. The two taxa investigated of the P. picta species group (here named P. picta and P. cf. picta based on molecular data) showed the same chromosome number of 2n = 36, mostly acrocentric elements, but differed in the number of metacentric elements, probably as a result of an inversion at chromosome pair 2. We highlight that the genus Paroedura is characterized by the independent diversification of heterogametic sex chromosomes in different evolutionary lineages and, similarly to other phylogenetically related gecko genera, by a progressive formation of a biarmed element by means of tandem fusions and inversions of distinct pairs. Full article

Karyotype diversification represents an important, yet poorly understood, driver of evolution. Squamate reptiles are characterized by a high taxonomic diversity which is reflected at the karyotype level in terms of general structure, chromosome number and morphology, and insurgence of differentiated simple or multiple-sex-chromosome systems with either male or female heterogamety. The potential of squamate reptiles as unique model organisms in evolutionary cytogenetics has been recognised in recent years in several studies, which have provided novel insights into the chromosome evolutionary dynamics of different taxonomic groups. Here, we review and summarize the resulting complex, but promising, general picture from a systematic perspective, mapping some of the main squamate karyological characteristics onto their phylogenetic relationships. We highlight how all the major categories of balanced chromosome rearrangements contributed to the karyotype evolution in different taxonomic groups. We show that distinct karyotype evolutionary trends may occur, and coexist, with different frequencies in different clades. Finally, in light of the known squamate chromosome diversity and recent research advances, we discuss traditional and novel hypotheses on karyotype evolution and propose a scenario of circular karyotype evolution. Full article

Vanellus (Charadriidae; Charadriiformes) comprises around 20 species commonly referred to as lapwings. In this study, by integrating cytogenetic and genomic approaches, we assessed the satellite DNA (satDNA) composition of one typical species, Vanellus chilensis, with a highly conserved karyotype. We additionally underlined its role in the evolution, structure, and differentiation process of the present ZW sex chromosome system. Seven distinct satellite DNA families were identified within its genome, accumulating on the centromeres, microchromosomes, and the W chromosome. However, these identified satellite DNA families were not found in two other Charadriiformes members, namely Jacana jacana and Calidris canutus. The hybridization of microsatellite sequences revealed the presence of a few repetitive sequences in V. chilensis, with only two out of sixteen displaying positive hybridization signals. Overall, our results contribute to understanding the genomic organization and satDNA evolution in Charadriiform birds. Full article