Search Results (78)

Satellite DNA is a dynamic component of plant genomes and a valuable source of cytogenetic markers, but its diversity and chromosomal distribution in polyploid Triticeae remain insufficiently studied. Here, low-coverage whole-genome sequencing, graph-based repeat clustering, quantitative PCR, multivariate statistics and fluorescence in situ hybridization (FISH) were used to identify and characterize satellite repeats in Elymus and related Triticeae species. Sixteen repeat clusters (E1–E16), with monomer lengths of 118–667 bp, showed distinct taxonomic distributions and copy-number profiles across 14 species. Correlation analysis, principal component analysis and hierarchical clustering revealed concerted variation among repeats and separated the perennial taxa Elymus and Pseudoroegneria from Triticum, Secale, Hordeum and Dasypyrum. Spearman correlation analysis identified E7 and E9 as putative candidates associated with St/StY genomic backgrounds, whereas E10 was identified as a putative candidate associated with the H genome. These statistical associations require independent cytogenetic validation. Contrasting copy numbers of E6 and E11 in bread wheat cv. Chinese Spring versus Dasypyrum villosum (L.) Candargy identified them as V-genome candidates. FISH localized E6 to the terminal regions of chromosomes 3VL, 4VS and 7VS, and E11 to 4VL. Karyotyping further revealed that two lines previously considered as wheat-D. villosum addition lines were in fact substitution lines: W3 was identified as a 3V(3D) substitution line and W4 as a 4V(4B) substitution line, whereas W7 retained its 7V addition status. These results expand the set of chromosomal markers for comparative genomics and introgression analysis in wheat. Full article

Background: Bone and soft-tissue sarcomas are rare, heterogeneous malignancies whose surveillance remains dominated by imaging despite substantial molecular diversity and variable patterns of relapse. Circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) offer minimally invasive approaches for monitoring tumor biology, but their performance in sarcoma depends strongly on subtype, disease burden, assay design, and biological shedding. Methods: This narrative review synthesizes evidence published from 2015 to 2026 on ctDNA and CTCs for baseline risk assessment, treatment-response monitoring, minimal residual disease (MRD) detection, molecular relapse, and integration with imaging-based surveillance in bone and soft-tissue sarcomas. Results: Current evidence supports a genomics-guided framework in which liquid-biopsy strategy is selected according to sarcoma subtype, molecular architecture, and clinical purpose. ctDNA is the most mature analyte, with best-supported evidence in osteosarcoma, where tumor-informed assays predict postoperative relapse, and in translocation-associated sarcomas, where breakpoint-guided assays enable highly specific longitudinal monitoring. Copy-number-based approaches are relevant for complex-karyotype tumors, while mutation-, methylation-, fragmentomic-, and RNA-based strategies may be useful in selected contexts. However, detection rates vary, false-negative results occur in low-shedding or low-volume disease, and clinical utility for changing treatment remains incompletely established. CTCs provide complementary cellular and prognostic information, particularly in osteosarcoma, but remain limited by platform heterogeneity and incomplete standardization. Conclusion: Liquid biopsy may refine risk stratification, support treatment-response assessment, clarify indeterminate imaging findings, and identify molecular relapse in selected sarcoma patients. At present, it should be interpreted as an adjunct to imaging and specialist multidisciplinary care rather than as a replacement for standard radiologic surveillance. Full article

The systematics of white-tailed deer (Odocoileus virginianus) has been controversial. Some mammalogists consider the white-tailed deer to be a single species, whereas others consider it to consist of multiple species. To help resolve the controversy, we sequenced mitochondrial cytochrome B (mtCyt-b) in samples collected from 83 Neotropical white-tailed deer. Furthermore, we analyzed mitogenomes of samples collected from 19 white-tailed deer. There were five main results, as follows: (1) Phylogenetic analyses with the mtCyt-b dataset showed the existence of eight groups of O. virginianus, three in North and Central America and five in South America. It was hypothesized from different analyses that a Central American O. virginianus population generated the white-tailed deer populations in South America. (2) The haplotype temporal diversification within O. virginianus occurred during the Pleistocene. With the mitogenome dataset, it was dated to have occurred approximately 2.2 mya, using both Bayesian inference and haplotype networks. (3) All of these O. virginianus groups showed elevated levels of mitochondrial genetic diversity for the mtCyt-b dataset, with the exception of the Ecuadorian population (4) Some groups of O. virginianus yielded significant evidence of female population expansions with the mtCyt-b dataset. (5) Although the genetic heterogeneity among these O. virginianus groups was significant, the genetic distances were relatively small. Provisionally, the karyotypic differences between North American and Colombian specimens were very small; therefore, until further karyotypic studies demonstrate otherwise, we consider the existence of a single species of O. virginianus. Because mtDNA genomes have only one quarter of the effective number of autosomal nuclear genes, this generates relatively rapid coalescence times, which can inflate estimates of divergence among populations. Therefore, it is very important to soon sequence the nuclear genes for the different geographic assemblages of O. virginianus found. Full article

Background: Meningiomas, the most common primary intracranial tumors, are predominantly benign, but high-grade variants show marked aggressiveness, histo-molecular heterogeneity, and treatment resistance. Although the 2021 WHO CNS classification integrates molecular and histopathologic criteria, substantial inter- and intratumoral variability still limits prognostic accuracy and treatment effectiveness. The goal was to provide insight regarding the histo-molecular intratumoral heterogeneity (ITH) of meningioma and examine its clinical implications. Methods: A narrative review was performed in accordance with PRISMA guidelines. PubMed and Google Scholar were screened for studies on “meningioma” and “intratumoral heterogeneity” published up to 28 July 2025. Eligible studies included original human research reporting histological or molecular heterogeneity with clinical relevance. Results: Eighteen studies comprising 2952 meningioma patients (mean age 59.4 ± 14.8 years, range 16–85) were included. Integrated cytogenetic, molecular, and spatial analyses, including FISH, karyotyping, scRNA-seq, CNV profiling, and spatial transcriptomics, revealed multilayered histo-molecular heterogeneity. Histologically, regional variations in morphology and proliferative index increased with tumor grade. Genomic diversity, marked by recurrent losses of 1p, 14q, and 22q and transcriptionally distinct subclones, defined a complex tumor architecture. Spatial and temporal analyses demonstrated subclonal expansion, stepwise clonal evolution, and therapy resistance, particularly in recurrent tumors. Functionally, SULT1E1⁺ subclones and COL6A3-mediated macrophage–tumor interactions emerged as potential key drivers of malignancy, recurrence, and radioresistance. Conclusions: Histo-molecular diversity underlies meningioma progression, recurrence, and therapeutic resistance. Standardization of ITH assessment, integration of AI-based spatial analytics, and the development of subclone-specific therapies are essential next steps toward advancing precision neuro-oncology. Full article

Background: Advances in genome-wide DNA-based technologies have fundamentally transformed prenatal genetic diagnostics, enabling detection of clinically significant submicroscopic chromosomal abnormalities that are not identifiable by conventional cytogenetic methods. These developments have important implications for the diagnosis and management of pregnancies complicated by fetal structural abnormalities, as they enable more accurate etiological diagnosis, improved prognostic assessment, and more informed clinical decision-making and reproductive counselling. Methods: This narrative review synthesizes contemporary international evidence on prenatal genetic diagnostic approaches, including conventional karyotyping, chromosomal microarray analysis (CMA), and genome-wide sequencing technologies. The review focuses on diagnostic performance, clinical utility, ethical considerations, and implementation within diverse healthcare systems. Results: Accumulating evidence demonstrates that genome-wide approaches—particularly CMA and sequencing-based methods—provide a higher diagnostic yield in fetuses with structural anomalies, with an incremental yield of approximately 3–5% over conventional karyotyping. This is mainly due to their ability to detect pathogenic copy number variants below the cytogenetic resolution of karyotyping. These technologies improve etiological insight, enhance genotype–phenotype correlation, and support more precise prognostication and reproductive counselling, especially in pregnancies with fetal structural anomalies. Emerging sequencing platforms further expand the diagnostic spectrum by integrating copy number and sequence-level variant detection. Conclusions: Genome-wide Copy Number Variation (CNV) analysis represents a critical component of contemporary prenatal diagnostics and should be integrated into invasive prenatal testing pathways in accordance with international recommendations. Genome-wide approaches need robust counselling frameworks and equitable health policy implementation to spread. The expense, lack of required experience, and variation in healthcare infrastructure across locations make widespread deployment difficult. Full article

Background/Objectives: Flea beetles (Coleoptera, Chrysomelidae: Alticinae) show extensive karyotypic diversity, yet cytogenetic and genomic data remain scarce for many taxa. Species of the genus Podagrica are characterized by unusually high chromosome numbers compared with the modal condition in Alticinae, suggesting a history of chromosomal fissions. This study aimed to characterize the karyotype and repetitive DNA composition of Podagrica fuscicornis, with special emphasis on the satellitome and its contribution to chromosome organization. Methods: Male specimens of P. fuscicornis collected in southern Spain were analyzed using conventional cytogenetic techniques, including Giemsa staining, DAPI staining, and C-banding. Fluorescence in situ hybridization was employed to map nucleolar organizer regions (NORs), telomeric repeats, and major satellite DNA (satDNA) families. The satellitome was characterized using Illumina short-read sequencing and analyzed with the RepeatExplorer2/TAREAN pipeline to identify satDNA families and estimate their genomic abundance and divergence. Results: The male karyotype of P. fuscicornis was 2n = 40 (38 + XY), with an Xy_p sex chromosome system. Constitutive heterochromatin was mainly pericentromeric, and the Y chromosome was largely heterochromatic. NORs were located on a single autosomal pair, and the ancestral insect telomeric motif (TTAGG)_n was detected at chromosome ends. The satellitome comprised at least 70 different satDNA families, representing 9.51% of the genome, some of them related to transposable elements. Ten of these 70 satDNAs are shared in other Alticinae species. The most abundant families were primarily localized in pericentromeric regions and showed differential distribution between autosomes and sex chromosomes. Conclusions: These results indicate that extensive chromosomal fissions and high satDNA dynamics could drive the high chromosome number and heterogeneous genome organization in P. fuscicornis, highlighting the role of repetitive DNA in karyotype evolution within Chrysomelidae. Full article

Aleppo oak (Quercus infectoria) is among the most industrially and ecologically significant oak species, valued for its medicinal properties and considerable genetic importance. Cytogenetic analysis provides critical insight into evolutionary history, interspecific relationships, and karyotypic differentiation. This study investigated the chromosomal architecture and karyotypic diversity of five natural populations of this species in western Iran (Sardasht, Oramanat, Baneh, Paveh, and Marivan) using actively dividing root meristems and a high-resolution image-based cytogenetic system. All examined cells displayed a basic chromosome number of x = 12 and a diploid condition, and chromosome lengths ranged from 0.90 to 2.12 µm. ANOVA and mean comparisons of five chromosomal parameters (Long Arm, Short Arm and Total Length, Arm Ratio, and Centromeric Index) revealed significant interpopulation differences in chromosome length and arm dimensions. All populations shared the karyotype formula 12 m and were classified into Stebbins’ Category B, indicating a moderately symmetrical, relatively primitive cytogenetic structure. Principal component analysis reduced the dataset to two major axes explaining 99.93% of the total variance, predominantly influenced by SA and TL on PC1 and by LA, AR, and CI on PC2. Hierarchical clustering grouped the populations into three distinct lineages, with Sardasht–Oramanat–Baneh showing the greatest divergence. Biplot vector patterns further clarified trait correlations, highlighting genomic structuring and potential breeding utility. Full article

Complex genetic syndromes represent a diagnostic challenge due to their diverse phenotypic presentations, which often evolve over time and may not be fully evident at birth. Disorders of sex development (DSD) comprise congenital conditions with discordance between chromosomal, gonadal, and/or genital sex. In 46,XY gonadal dysgenesis, undervirilisation or female-appearing genitalia may occur despite a normal karyotype, and diagnosis increasingly relies on genomic approaches. Prenatal and postnatal growth failure has been described in patients with syndromic 46,XY DSD. We report a male patient with SGA, lack of postnatal catch-up growth, and syndromic dysgenetic 46,XY DSD followed longitudinally from infancy to 11 years, in whom whole-exome sequencing (WES) reanalysis revealed a pathogenic 2.7 Mb microdeletion at 3q27.1q27.2. Systematic review of previously reported 3q27.1 deletions identified overlapping phenotypes but limited documentation of gonadal dysfunction. Curation of 71 genes within the deleted region highlighted DVL3 and CLCN2 as potential contributors to the gonadal phenotype, although functional evidence remains lacking. This case expands the phenotypic spectrum of 3q27.1 microdeletion syndrome, suggesting that 46,XY gonadal dysgenesis may represent an under-recognised feature. It also underscores the importance of copy number variant (CNV) analysis and periodic re-evaluation of sequencing data to increase diagnostic yield. Full article

Polemonium L. (Polemoniaceae) is a widespread genus native to subarctic and arctic regions of the Northern Hemisphere. The taxonomy and genome relationships within Polemonium are still unclear. We analyzed genomes of three species from each Polemonium caeruleum and Polemonium pulcherrimum complex using bioinformatic analysis by RepeatExplorer2/TAREAN pipelines of next-generation sequencing data. The repeatomes of all studied species were similar in type and number of repeats. Satellite DNAs (satDNAs) demonstrated high sequence identity within the studied species. FISH chromosome mapping of 45S rDNA, 5S rDNA, and two satDNAs Pol_C 33 and Pol_C 46 allowed us to construct the species karyograms and assess the genome diversity within the P. caeruleum complex and P. pulcherrimum complex, and also confirm the taxonomic status of P. kiushianum as an independent species. Our findings demonstrate a close genomic relationship among the species from P. caeruleum and P. pulcherrimum complexes, indicating the presence of a common ancestral genome; additionally, our results provide cytogenetic evidence for the monophyletic origin of these sections and also complex evolutionary history of the genus Polemonium. The developed approach may be a valuable framework for further investigation of the chromosomal organization of karyotypes in other species of the genus Polemonium. Full article

Background/Objectives: Sites of ribosomal RNA genes are the most widely documented regions of chromosomes in various groups of eukaryotes, including insects. Data on the number and chromosomal location of 45S rDNAs (25S, 5.8S, and 18S rDNA) are actively used to study the diversity of karyotypes, the organization of individual chromosomes, and the evolution of entire genomes. In true bugs (suborder Heteroptera), the number and chromosomal distribution of 18S rDNA loci are currently known for less than 0.5% of described species. Although some patterns of rDNA distribution can already be identified both in individual taxa of true bugs and in the suborder as a whole, there are still negligible data. In order to expand our understanding of the diversity of rDNA distribution in Heteroptera, we studied for the first time the location of 18S rDNA in 13 species from 13 genera (seven families) of the infraorders Cimicomorpha and Pentatomomorpha (=Terheteroptera, the terminal group of Heteroptera). Methods: Fluorescence in situ hybridization (FISH) with an 18S rDNA probe was used in our study. Results: In total, we have identified three main types of rDNA arrangement: (1) on autosomes, (2) on the X chromosome, and (3) on autosomes and on the X chromosome simultaneously. In most of the studied species, 18S rDNA loci were detected in the terminal position on one pair of autosomes. Conclusions: This study contributed to the understanding of the chromosomal distribution of rDNA loci in the infraorders Cimicomorpha and Pentatomomorpha and confirmed the importance of rDNA in the reorganization of the genomes of Heteroptera as a whole. Full article

Psalidodon rivularis, a fish endemic to the São Francisco River Basin and known as “piaba do córrego,” has long been regarded as a widely distributed species complex, exhibiting remarkable morphological and cytogenetic variation, even in sympatry. This study aims to determine whether P. rivularis represents a single polymorphic species or a group of cryptic species. We analyzed meristic, morphometric, and karyotypic data from 419 specimens identified as P. rivularis, as well as from the related species Astyanax turmalinensis and Hyphessobrycon santae. Additionally, we inferred the phylogeny of the group using NGS data from 25 individuals, incorporating both mitochondrial and nuclear genomic sequences. Our integrative results support the recognition of at least five distinct species within the P. rivularis complex. The true P. rivularis (called morphotype 1) has 46 chromosomes, while the others have 50 and differ in both morphology and distribution. One of these corresponds to Psalidodon santae comb. nov.—which includes A. turmalinensis as a junior synonym—and three others are newly described species. These findings clarify the diversity of fishes in the São Francisco River Basin and highlight the importance of conserving its unique freshwater ecosystems. Full article

Madagascar is one of the world’s most prominent biodiversity hotspots and is characterized by exceptionally high amphibian diversity, with 429 currently described, mostly endemic species. However, cytogenetic research on Malagasy amphibians has been conducted only intermittently over the years. Previous studies, mostly using conventional staining and banding methods and often confined to single taxa or isolated families, have provided only partial insights into the karyotype evolution and genome organization of the major Malagasy clades. In this contribution, we present the first comprehensive synthesis of all available cytogenetic data on Malagasy anurans, including chromosome number and morphology, heterochromatin distribution, and chromosomal markers across the major endemic Malagasy families. By integrating and comparing results from decades of scattered studies, this review reveals consistent patterns of chromosomal diversification and identifies evolutionary trends associated with speciation and adaptive radiation in Malagasy amphibians. Overall, native Malagasy amphibian species can be subdivided into two main karyotype groups: the first includes karyotypes with only biarmed chromosomes (Heterixalus, Ptychadena, Boophis, Mantella, and Guibemantis), while the second comprises karyotypes with one or more uniarmed elements (Gephyromantis, Mantidactylus, and Microhylidae). The localization of NORs follows a diverse pattern, often varying even among closely related species. Heterochromatin distribution and composition also appear to be species-specific and thus taxonomically informative. Beyond summarizing existing knowledge, this work establishes a unified framework for interpreting chromosome evolution within the unique biogeography and evolutionary history of Madagascar. Our synthesis provides essential baseline data for future molecular, genomic, and conservation studies, thereby enhancing our understanding of the mechanisms that have generated and maintained the island’s extraordinary amphibian diversity. Full article

Amaranthus L. includes valuable and promising crops of multi-purpose use, having high morphological diversity and complicated taxonomy. Their karyotypes and genomic relationships remain insufficiently studied. For the first time, a comparative repeatome analysis of Amaranthus tricolor L., Amaranthus cruentus L., and Amaranthus hypochondriacus L. was performed based on the high-throughput sequencing data obtained via bioinformatic analyses using the RepeatExplorer2/TAREAN/DANTE_LTR pipelines. Interspecific variations in the abundance of Ty1 Copia and Ty3 Gypsy retroelements, DNA transposons, and ribosomal and satellite DNA (satDNA) were detected. Based on fluorescence in situ hybridization (FISH), chromosome mapping of 45S rDNA, 5S rDNA, and satDNAs AmC9 and AmC70, and unique karyograms of A. tricolor, A. cruentus, Amaranthus paniculatus L., and A. hypochondriacus were constructed. The analysis of the interspecies genome diversity/similarity in DNA repeat contents, sequences of the identified satDNAs, and chromosome distribution patterns of the studied molecular markers indicated that these species might also share a common evolutionary ancestor. However, the genomes of A. cruentus, A. paniculatus, and A. hypochondriacus were more similar compared to A. tricolor, which aligns with the previous phylogenetic data. Our results demonstrate that cytogenomic studies might provide important data on Amaranthus species relationships elucidating taxonomy and evolution of these valuable crops. Full article

Structural variation (SV) serves as a fundamental driver of phenotypic diversity and environmental adaptation in plants and animals, significantly influencing key agronomic traits in crops. Common wheat (Triticum aestivum L.), an allohexaploid species, harbors extensive chromosomal SVs and distant hybridization-induced recombination events that provide critical resources for genetic improvement. This study utilizes non-denaturing fluorescence in situ hybridization (ND-FISH) and oligonucleotide multiplex probe-based FISH (ONPM-FISH) to analyze the karyotypes of 153 BC₁F₄–BC₁F₆ lines derived from the hybrid line Xiaoyan 7430 and common wheat Yannong 1212. The results revealed that Xiaoyan 7430 carries 8 alien chromosome pairs and 20 wheat chromosome pairs (lacking 6B), and Yannong 1212 contains 21 pairs of wheat chromosomes. The parental lines exhibited presence/absence variations (PAVs) on chromosomes 2A, 6A, 5B, 1D, and 2D. Chromosomal variations, including numerical chromosomal variation (NCV), structural chromosomal variation (SCV), and complex chromosomal variation (CCV), were detected in the progeny lines through ONPM-FISH analysis. The tracking of alien chromosomes over three consecutive generations revealed a significant decrease in transmission frequency, declining from 61.82% in BC₁F₄ to 26.83% in BC₁F₆. Telosomes were also lost during transmission, declining from 21.82% in BC₁F₄ to 9.76% in BC₁F₆. Alien chromosome 1J^S, 4J, and 6J exhibited the highest transmission stability and were detected across all three generations. Association analysis showed that YN-PAV.2A significantly affected the length/width ratio (LWR) and grain diameter (GD); YN-PAV.6A, XY-PAV.6A, and PAV.5B increased six grain traits (+2.25%~15.36%); YN-PAV.1D negatively affected grain length (GL) and grain circumference (GC); and XY-PAV.2D exerted positive effects on thousand-grain weight (TGW). Alien chromosomes differentially modulated grain characteristics: 1J^S and 6J both reduced grain length and grain circumference; 1J^S increased LWR; and 4J negatively impacted TGW, grain width (GW), GD, and grain area (GA). Meanwhile, increasing alien chromosome numbers correlated with progressively stronger negative effects on grain traits. These findings elucidate the genetic mechanisms underlying wheat chromosomal variations induced by distant hybridization and their impact on wheat grain traits, and provide critical intermediate materials for genome design breeding and marker-assisted selection in wheat improvement. Full article

Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition often associated with genetic syndromes. Structural variants on the long arm of chromosome 15 (15q) are recurrently implicated in syndromic ASD, yet their phenotypic spectrum remains insufficiently characterized in diverse populations. We retrospectively analyzed clinical and molecular data from three patients with ASD treated at a Brazilian public reference center who also presented neurological and systemic comorbidities. Genetic investigations included G-banded karyotyping, chromosomal microarray analysis (CMA), methylation assays, and multiplex ligation-dependent probe amplification (MLPA) when indicated. Variants were classified according to ACMG guidelines and correlated with individual phenotypes. Case 1 showed an 8.4 Mb triplication at 15q11.2–q13.1 encompassing SNRPN, UBE3A, and GABRB3, which are associated with epilepsy, delayed neuropsychomotor development, and dysmorphic traits. Case 2 presented a 418 kb duplication at 15q13.3 involving CHRNA7 and OTUD7A, a variant of uncertain significance correlated with intellectual disability, speech apraxia, and self-injurious behavior. Case 3 demonstrated extensive loss of heterozygosity at 15q11.2–q13.1 and 15q21.3–q26.2, which is compatible with maternal uniparental disomy and Prader–Willi syndrome, manifesting hypotonia, seizures, and global delay. These findings underscore the potential involvement of the 15q region in syndromic ASD and related neurological comorbidities, highlighting the diverse pathogenic mechanisms and the importance of comprehensive genomic profiling for diagnosis, counseling, and individualized care. Full article