Chromosome Research最新文献

{"title":"A single species, different repeatomes? Genomic plasticity in Passiflora foetida L. complex and comparative insights across the subgenus Passiflora.","authors":"Arthur Monteiro, Mariela A Sader, Jéssica Nascimento, Gustavo Luna, Daniela Cristina Imig, Andrea Pedrosa-Harand","doi":"10.1007/s10577-026-09804-7","DOIUrl":"10.1007/s10577-026-09804-7","url":null,"abstract":"<p><p>The genus Passiflora L. comprises approximately 650 species, and exhibits high diversity in the Neotropics, especially the subgenus Passiflora. Several species of this subgenus have an abundant repetitive fraction, consistent with their increased genome sizes. However, the repetitive DNA fraction of Passiflora foetida (n = 10), sister to the other species of the subgenus (n = 9) and the species with the smallest genome, has not yet been described in detail. In addition, this species comprises a complex of morphological varieties with a wide geographical distribution. The aim of this study was to characterize its repeatome variability in comparison to other species in section Dysosmia and other sections in the same subgenus, and to investigate whether it may reflect the high variability reported for this species complex. The results showed that P. foetida has a proportion of repetitive DNA fraction in part consistent with its small genome size, but with marked intraspecific variation. The LTR Ty1/copia retrotransposons were the most abundant, as in the other species of the subgenus, but Ty3/gypsy represented a much smaller fraction compared to the others. The variation observed within P. foetida was greater than that detected among Dysosmia species. Satellite DNAs were partly unique and partly similar to species from different subgenera, supporting its phylogenetic position. In addition, one Dysosmia-specific satellite showed a proximal chromosomal location, making it the first candidate of a centromeric repeat for the genus, despite its variation in abundance among chromosomes.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"34 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13429553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148664944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Satellite DNA evolution in two holocentric species of Edessa true bugs (Hemiptera: Pentatomidae) with unusually high heterochromatin abundance.","authors":"Letícia M Calegari, Diogo Milani, Vanessa B Bardella, Frederico Hickmann, Diogo C Cabral-de-Mello","doi":"10.1007/s10577-026-09809-2","DOIUrl":"10.1007/s10577-026-09809-2","url":null,"abstract":"<p><p>Satellite DNAs (satDNAs) are a major component of eukaryotic genomes, playing key roles in chromosome organization, heterochromatin formation, and genome evolution. Although satellitomes have been increasingly characterized in insects, most studies focus on monocentric species, leaving holocentric systems comparatively understudied. Here, we investigate the satellitomes of two pentatomid bugs, Edessa meditabunda and Edessa loxdalii, which exhibit unusually large heterochromatin blocks for holocentric chromosomes. Using an integrative approach combining genome analysis and molecular cytogenetics, we identified 31 satDNA families shared between species. E. loxdalii shows higher satDNA abundance and lower sequence divergence, consistent with recent amplification and homogenization, whereas E. meditabunda exhibits lower abundance and higher divergence, suggesting more advanced sequence degeneration. SatDNA landscape analyses indicate distinct evolutionary trajectories, with evidence of multiple amplification waves and differential repeat turnover. Despite these differences, both species share a conserved set of satDNAs, including highly abundant families that dominate their satellitomes, supporting the library hypothesis. Compared to other Pentatomidae species with low heterochromatin content, there is no overall increase in satDNA abundance in Edessa, but rather amplification of specific families. Chromosomal mapping revealed that these amplified satDNAs are major components of terminal heterochromatin blocks, while less abundant families show chromosome-specific distributions, including accumulation on the Y chromosome, with signs of evolutionary differentiation between species. Overall, this study provides new insights into satellitome organization and evolution in Pentatomidae, highlighting the role of satDNAs in shaping chromosome architecture in holocentric systems.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"34 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13427858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148632651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Meiotic telomeres of vole B chromosomes: shelterin and associated proteins provide a link to the nuclear envelope.","authors":"Sergey N Matveevsky, Tatyana V Petrova, Svetlana V Pavlova","doi":"10.1007/s10577-026-09808-3","DOIUrl":"10.1007/s10577-026-09808-3","url":null,"abstract":"<p><p>Meiotic telomeres play a critical role in chromosome dynamics, facilitating homolog pairing and synapsis through attachment to the nuclear envelope (NE). While these mechanisms are well-documented for standard A-set chromosomes, the molecular composition of supernumerary (or B) chromosome telomeres remains poorly understood. In this study, for the first time we investigated the distribution of key telomeric and NE-attachment proteins in Bs. Using immunocytochemistry and immuno-FISH on spermatocytes of the narrow-headed vole, Lasiopodomys gregalis (Rodentia, Mammalia), we identified the presence of the shelterin components RAP1, POT1 and TIN2; the LINC complex proteins SUN1 and KASH5; a major component of the nuclear lamina, Lamin B1; the regulatory kinase CDK2; and telomeric DNA specifically at the termini of meiotic supernumeraries. Our results demonstrate that despite their univalent nature and involvement in meiotic inactivation, Bs of this mammalian species possess a telomeric protein architecture that is highly similar, if even not identical, to that of A-set and sex chromosomes. These findings suggest that Bs are integrated into the meiotic machinery, utilizing standard protective and anchoring mechanisms to ensure genomic stability during prophase I.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"34 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148537415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ring chromosomes uncovered by optical genome mapping: impact of telomeric-associated regions and reference genome selection on structural variant interpretation.","authors":"Bruna Burssed, André R C P Oliveira, Fernanda Teixeira Bellucco, Maria Isabel Melaragno","doi":"10.1007/s10577-026-09806-5","DOIUrl":"10.1007/s10577-026-09806-5","url":null,"abstract":"<p><p>Ring chromosomes (RCs) are rare structural variants usually formed by fusion of both chromosome arm extremities, frequently associated with terminal deletions. RCs are investigated through karyotype, fluorescence in situ hybridization, chromosomal microarray analysis, and, more recently, optical genome mapping (OGM), which enables genome-wide structural variant detection; however, its accuracy depends on alignment to a reference genome and proper filtering of SVs. Here, two patients with previously characterized ring chromosomes 3 and 18, each with a terminal deletion in only one chromosome arm (3p and 18q), were analyzed by OGM after aligning the data against two reference genomes (GRCh38/hg38 and T2T-CHM13) and compared with long-read sequencing (LRS) results stemming from a parallel study that included both patients. Patient 1's RC3 was misinterpreted as a translocation between chromosomes 3 and 19 when analyzed with GRCh38/hg38. Reanalysis with T2T-CHM13 correctly identified the RC3 and demonstrated retention of the full 3q arm, including telomeric-associated regions, which was confirmed by LRS. Patient 2's ring chromosome 18 was identified with GRCh38/hg38 only after lowering the confidence score filter, whereas T2T-CHM13 detected the RC18 immediately without involvement of 18p telomeric-associated regions. LRS diverged from this analysis by showing the presence of these regions in the RC18 due to its nucleotide-level resolution. Only eight out of ~ 3,000 RCs have been reported in the literature as resolved using OGM, and here we add two more cases analyzed with different reference genomes and highlight the techniques' advantages and limitations for RC characterization. Since the T2T-CHM13 analysis outperformed GRCh38/hg38 because it resolves previously inaccessible telomeric regions, we included an investigation into which other chromosomes could also benefit more from this approach.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"34 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13384989/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148521396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary relationship between yeast telomeric protein Cdc13 and Pot1.","authors":"Ion Udroiu","doi":"10.1007/s10577-026-09807-4","DOIUrl":"10.1007/s10577-026-09807-4","url":null,"abstract":"<p><p>The CST complex protects the ss-overhang of telomeres. In animals, it is composed of CTC1, STN1 and TEN1. In Schizosaccharomyces pombe, CTC1 is absent, while in Saccharomyces cerevisiae it is substituted by Cdc13. Pot1 is the only Shelterin protein that binds ssDNA, and is absent in Saccharomyces cerevisiae. In this study, I looked for homologues of CTC1, Cdc13 and Pot1 in Fungi. I found that CTC1 has been lost in Dikarya (yeasts and mushrooms), with its function probably being taken by Pot1. Furthermore, my analyses show that Cdc13 probably evolved from Pot1, by the loss of its third domain, which is responsible for binding Tpz1. In this way, Est3 (the orthologue of Tpz1 in Saccharomyces cerevisiae) became part of the telomerase complex. Cdc13 further evolved by gene duplication in some budding yeasts, giving rise to two paralogues in Serinales, Ascoideales, Phaffomycetales, Saccharomycetales and Saccharomycodales: in these latter two orders, the two paralogues fused to give rise to a \"long\" Cdc13. Beyond their evolutionary interest, these results could be useful for researchers using new species of yeasts as model organisms.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"34 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148498321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Combining ultrastructure expansion microscopy with immunofluorescence and Oligopaint DNA FISH.","authors":"Lorielle M Raab, Clio B Hockens, Ling Sze Lee, Rose K Runyan, Emma E Burns, Nasser M Rusan, Leah F Rosin","doi":"10.1007/s10577-026-09805-6","DOIUrl":"10.1007/s10577-026-09805-6","url":null,"abstract":"","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"34 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13372861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148457625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combining ultrastructure expansion microscopy with immunofluorescence and Oligopaint DNA FISH.","authors":"Lorielle M Raab, Clio B Hockens, Ling Sze Lee, Rose K Runyan, Emma E Burns, Nasser M Rusan, Leah F Rosin","doi":"10.1007/s10577-026-09802-9","DOIUrl":"10.1007/s10577-026-09802-9","url":null,"abstract":"<p><p>Expansion microscopy (ExM) enlarges biological samples by embedding them in a swellable hydrogel, enabling nanoscale imaging of subcellular structures with standard light microscopes. This offers an accessible alternative to super-resolution methods. ExM has yet to be combined with the Oligopaint DNA fluorescence in situ hybridization (FISH) technology. We present an optimized ExM workflow for simultaneous Oligopaint DNA FISH and immunofluorescence (IF) in intact Drosophila ovaries. The protocol incorporates nucleic-acid anchoring, reliable protein retention, and digestion conditions that preserve chromatin while maintaining probe accessibility. Our approach achieves ~ 5 × expansion and strong signal retention, enabling high-resolution studies of nuclear organization.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"34 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13220437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147984291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bridging methodological gaps in avian cytogenetics: comprehensive and optimized protocols for chromosomal preparation in birds.","authors":"Marcelo de Bello Cioffi, Gustavo Akira Toma, Princia Grejo Setti, Jhon Alex Dziechciarz Vidal, Guilherme Mota-Souza, Marie Altmanová, Edivaldo Herculano Correa de Oliveira, Rafael Kretschmer","doi":"10.1007/s10577-026-09803-8","DOIUrl":"10.1007/s10577-026-09803-8","url":null,"abstract":"<p><p>This methodological study outlines effective and standardized procedures for obtaining high-quality chromosomal preparations in birds, which display complex karyotypes with a large number of microchromosomes. We describe every stage from sample obtaining and culture setup to the successful acquisition of metaphase chromosomes appropriate for in-depth analysis by combining three main methodologies (fibroblast, lymphocyte, and bone marrow cultures) into a coherent and methodical workflow. Furthermore, we offer thorough troubleshooting instructions to tackle typical problems, such as low mitotic indices, poor chromosome spreading, contamination, and suboptimal chromosomal morphology. We also focused on repeatability and adaptation across several bird taxa, taking into consideration species-specific differences in their body sizes, cell development, and chromosomal behavior, extending beyond standard procedure improvement. The incorporation of diverse methodologies into a unified framework offers avian cytogenetics researchers a readily available and practical workflow. Ultimately, our approach enhances the integration of cytogenetic data with novel genomic resources, facilitates the re-evaluation of chromosomal counts, and enables more precise karyotype characterization. This integration is crucial for advancing our understanding of chromosomal evolution, avian genome architecture, and the broader mechanisms underlying avian speciation and diversification.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"34 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13180766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147965378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of satellite DNA-enriched heterochromatic variants in reproductive disorders: Insights from standardized cytogenetic analysis.","authors":"Sílvia Pires, Isaltina França, Pedro Oliveira, Paula Jorge, Thomas Liehr, Natália Oliva-Teles","doi":"10.1007/s10577-026-09800-x","DOIUrl":"10.1007/s10577-026-09800-x","url":null,"abstract":"<p><p>Non-coding DNA, long considered \"junk\", is now recognized as a central regulator of genome architecture. Highly repetitive satellite DNA sequences shape heterochromatin and are essential for chromosome stability, segregation, and gene regulation. Pericentromeric heterochromatic variants, or chromosomal heteromorphisms (CHs), have emerged as modulators of human fertility, potentially affecting gametogenesis and early embryonic development. Despite their ubiquity, the functional and clinical significance of CHs remains largely enigmatic. Molecular reference genomes fail to fully capture these repetitive domains, and cytogenetic assessment has shown critical inconsistencies due to the lack of standardized evaluation criteria. To address this gap, we proposed a comparison-based scoring system to reliably identify and characterize CHs. By applying this framework to 300 individuals with idiopathic reproductive disorders and 155 fertile controls, we observed a significantly higher CH frequency in the infertile cohort (2.4-fold increase; p < 0.001). Chromosome 9 variants were the most prevalent (5.3%; p = 0.036), with 1qh+ and 16qh+ as the most common type-specific variants. Cases of recurrent pregnancy loss exhibited the highest CH burden. These results support a significant association between CHs and adverse reproductive outcomes, suggesting that heterochromatic variants may act as predisposing factors for infertility. Importantly, the proposed scoring system addresses critical cytogenetic inconsistencies and provides a comprehensive, reproducible framework that will enhance cross-study comparability and enable future investigations into the structural, functional, evolutionary, and clinical relevance of satellite DNA-enriched heterochromatic regions.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"34 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13156139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147845596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cytogenomics of Myloplus tiete reveals conserved satellite DNAs since the Late Eocene in Serrasalmidae (Teleostei, Characiformes).","authors":"Francisco de Menezes Cavalcante Sassi, Giovanna Igepi, Beatriz Lopes Torgan, Caio Augusto Gomes Goes, Rodrigo Zeni Dos Santos, Maria Eduarda Gisloti-Ribeiro, Diogo Teruo Hashimoto, Fábio Porto-Foresti, Ricardo Utsunomia","doi":"10.1007/s10577-026-09801-w","DOIUrl":"10.1007/s10577-026-09801-w","url":null,"abstract":"<p><p>The Neotropical family Serrasalmidae (pacus and piranhas) exhibits remarkable karyotype conservation, yet cytogenetic data remain limited for several genera, particularly Myloplus. Here we present the first integrative cytogenomic characterization of Myloplus tiete, an endemic and near-threatened species from the upper Paraná River basin, combining classical cytogenetics with satellitome analysis. Karyotyping of 12 specimens collected from Rio Grande, Frutal-MG, Brazil, revealed a consistent diploid number of 2n = 58 chromosomes with karyotype formula 16m + 20sm + 22a, while C-banding identified heterochromatic blocks predominantly in pericentromeric and subtelomeric regions. Genome sequencing and iterative satDNA mining identified 32 satellite DNA families, with repeat lengths ranging from 24 to 2,265 bp and a predominance of AT-rich sequences. Comparative analysis with the Colossomatinae species Colossoma macropomum and Piaractus mesopotamicus revealed 12 conserved satDNAs across ~ 40 million years of divergence, with moderate consensus turnover rates. FISH mapping of the ten most abundant satDNAs revealed diverse chromosomal distributions, including pericentromeric, subtelomeric, and dispersed patterns, highlighting the diverse genomic integration of conserved repeats. These findings provide evidence for long-term evolutionary conservation of both karyotype architecture and satDNA repertoires across Serrasalmidae subfamilies and suggest that structural or functional constraints may contribute to shaping the evolution of repetitive DNA in this ecologically and aquaculturally important fish group.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"34 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13156159/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147845565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}