Cytogenetic and Genome Research最新文献

{"title":"Spaghetti Connections: Synaptonemal Complexes as a Tool to Explore Chromosome Structure, Evolution, and Meiotic Behavior in Fish.","authors":"Artem Lisachov, Dmitrij Dedukh, Sergey Simanovsky, Thitipong Panthum, Worapong Singchat, Kornsorn Srikulnath","doi":"10.1159/000538238","DOIUrl":"10.1159/000538238","url":null,"abstract":"<p><strong>Background: </strong>The synaptonemal complex (SC) is a protein axis formed along chromosomes during meiotic prophase to ensure proper pairing and crossing over. SC analysis has been widely used to study the chromosomes of mammals and less frequently of birds, reptiles, and fish. It is a promising method to investigate the evolution of fish genomes and chromosomes as a part of complex approach.</p><p><strong>Summary: </strong>Compared with conventional metaphase chromosomes, pachytene chromosomes are less condensed and exhibit pairing between homologous chromosomes. These features of SCs facilitate the study of the small chromosomes that are typical in fish. Moreover, it allows the study of heteromorphisms in sex chromosomes and supernumerary chromosomes. In addition, it enables the investigation of the pairing between orthologous chromosomes in hybrids, which is crucial for uncovering the causes of hybrid sterility and asexual reproduction, such as gynogenesis or hybridogenesis. However, the application of SC analysis to fish chromosomes is limited by the associated complications. First, in most fish, meiosis does not occur during every season and life stage. Second, different SC preparation methods are optimal for different fish species. Third, commercial antibodies targeting meiotic proteins have been primarily developed against mammalian antigens, and not all of them are suitable for fish chromosomes.</p><p><strong>Key messages: </strong>In the present review, we provide an overview of the methods for preparing fish SCs and highlight important studies using SC analysis in fish. This study will be valuable for planning and designing research that applies SC analysis to fish cytogenetics and genomics.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140058914","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":"Whole-Genome Sequencing Reveals a Novel Pathogenic GRIN2B Variant in a Patient with Neurodevelopmental Disorder and an inv(6)(p24p11.2)pat.","authors":"Carlos Córdova-Fletes, Horacio Rivera, Ma Guadalupe Domínguez-Quezada, Thania Alejandra Aguayo-Orozco, Elvira Garza-González, Luis A Núñez-García, Francisco Miguel Mercado-Silvae, Mónica Alejandra Rosales-Reynoso, Patricio Barros-Núñez","doi":"10.1159/000539975","DOIUrl":"10.1159/000539975","url":null,"abstract":"<p><strong>Introduction: </strong>Neurodevelopmental disorders (NDDs) are diverse and can be explained by either genomic aberrations or single nucleotide variants. Most likely due to methodological approaches and/or disadvantages, the concurrence of both genetic events in a single patient has hardly been reported and even more rarely the pathogenic variant has been regarded as the cause of the phenotype when a chromosomal alteration is initially identified.</p><p><strong>Case presentation: </strong>Here, we describe a NDD patient with a 6p nonpathogenic paracentric inversion paternally transmitted and a de novo pathogenic variant in the GRIN2B gene. Molecular-cytogenetic studies characterized the familial 6p inversion and revealed a paternal 9q inversion not transmitted to the patient. Subsequent whole-genome sequencing in the patient-father dyad corroborated the previous findings, discarded inversions-related cryptic genomic rearrangements as causative of the patient's phenotype, and unveiled a novel heterozygous GRIN2B variant (p.(Ser570Pro)) only in the proband. In addition, Sanger sequencing ruled out such a variant in her mother and thereby confirmed its de novo origin. Due to predicted disturbances in the local secondary structure, this variant may alter the ion channel function of the M1 transmembrane domain. Other pathogenic variants in GRIN2B have been related to the autosomal dominant neurodevelopmental disorder MRD6 (intellectual developmental disorder, autosomal dominant 6, with or without seizures), which presents with a high variability ranging from mild intellectual disability (ID) without seizures to a more severe encephalopathy. In comparison, our patient's clinical manifestations include, among others, mild ID and brain anomalies previously documented in subjects with MRD6.</p><p><strong>Conclusion: </strong>Occasionally, gross chromosomal abnormalities can be coincidental findings rather than a prime cause of a clinical phenotype (even though they appear to be the causal agent). In brief, this case underscores the importance of comprehensive genomic analysis in unraveling the wide-ranging genetic causes of NDDs and may bring new insights into the MRD6 variability.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141455834","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":"New Karyotype Information for Ctenomys (Rodentia: Ctenomyidae) from Midwest and Northern Brazil.","authors":"Thays Duarte de Oliveira, Natasha A Bertocchi, Bruno Busnello Kubiak, Daniel Galiano, Sérgio Luiz Althoff, Thales R O de Freitas","doi":"10.1159/000538014","DOIUrl":"10.1159/000538014","url":null,"abstract":"<p><strong>Introduction: </strong>Its wide karyotypic variation characterizes the genus Ctenomys, and in Brazil, the genus is distributed in the country's southern, Midwest, and northern regions. Recently, populations of Ctenomys have been found in the Midwest and northern Brazil, with two new lineages named C. sp. \"xingu\" and C. sp. \"central.\"</p><p><strong>Methods: </strong>This work combines classical cytogenetic and molecular analyses to provide new chromosomal information on the boliviensis group distributed in northern and Midwestern Brazil. This includes the validation of the karyotype of C. bicolor and C. nattereri and the description of the karyotype of C. sp. \"xingu\" and C. sp. \"central.\"</p><p><strong>Results: </strong>We found three different karyotypes: 2n = 40 for C. bicolor; 2n = 36 for C. nattereri, and specimens from a locality belonging to C. sp. \"central\"; 2n = 34 for the lineage C. sp. \"xingu\" and specimens from a locality belonging to C. sp. \"central.\" Furthermore, GTG banding revealed homologous chromosomes between species/lineages and allowed the identification of the rearrangements that occurred, which proved the occurrence of fissions.</p><p><strong>Conclusion: </strong>Considering our results on the variation of 2n in the boliviensis group, we found two possibilities: the first, deduced by parsimony, is that 2n = 36 appeared initially, and two fissions produced gave rise to 2n = 40, and an independent fusion gave rise to 2n = 34 from 2n = 36; moreover, the second explanation is that all karyotypes arose independently.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139971276","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":"Molecular Cytogenetic Characterization of Rare but Repeatedly Observed Inversions in German Population.","authors":"Joana Seixas, Niklas Padutsch, Stefanie Kankel, Thomas Liehr, Alody Sy","doi":"10.1159/000539447","DOIUrl":"10.1159/000539447","url":null,"abstract":"<p><strong>Introduction: </strong>The term inversion refers to an aberration caused by two breakage and fusion events found in one or both arms of a chromosome. The presence of such aberrations can but must not be associated with infertility or unbalanced products of conception. Normally, inversions are not associated with phenotypic alterations for the carrier. Despite the fact that most such inversions are de novo and unique, recurrent breakpoints have also been reported.</p><p><strong>Methods: </strong>Here two recurrent paracentric inversions in the long arm of chromosomes 11 and 12 and a pericentric one in chromosome 10 were studied in at least 10 unrelated (infertile) patients, each. Breakpoints were narrowed down by fluorescence in situ hybridization applying locus-specific bacterial artificial chromosome-derived probes.</p><p><strong>Results: </strong>Molecular cytogenetically identical breakpoints could be characterized for all three studied inversions. Pericentric inversion inv(10)(p11.21q21.2), previously reported to be of single origin and distributed mainly in Northern Europe, could be found to be present all over Germany, too. In the studied cases with paracentric inversion inv(11)(q21q23.3), recurrent breakpoints were found in all parts of Germany, as well; however, additional 2 cases with slightly different breakpoints were characterized besides. Most interestingly, inversion inv(12)(q14.1∼14.2q24.11∼24.13) had always the same recurrent breakpoints and presented an exclusive occurrence in North-Western part of Germany.</p><p><strong>Conclusion: </strong>Overall, (at least) three different cytogenetically detectable recurrent inversions were characterized here. This highlights that such events may be more frequent in human population than yet suggested. Accordingly, such events might even spread in (middle European) human population. Specific impact on reproduction and fitness of inversion carriers characterized here seems to be negligible. Nonetheless, such recurrent rearrangements need more attention as they may provide valuable information for genetic counseling in future.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141155091","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":"Karyotypic Reshuffling in the Genus Rhipidomys (Rodentia: Cricetidae: Sigmodontinae) Revealed by Zoo-FISH.","authors":"Camila N Moreira, Fernanda G Pricoli, Malcolm A Ferguson-Smith, Yatiyo Yonenaga-Yassuda, Karen Ventura","doi":"10.1159/000539476","DOIUrl":"10.1159/000539476","url":null,"abstract":"<p><strong>Introduction: </strong>Rhipidomys is the second most specious and the most widespread genus of the tribe Thomasomyini. Chromosomal data have been an important tool in the taxonomy of the group that presents low variability of diploid number (2n) and highly variable fundamental numbers (FNs). Despite such diversity, the genus has been studied mainly by classical and banding cytogenetic techniques.</p><p><strong>Methods: </strong>This study performed a comparative study between R. emiliae (2n = 44, FN = 52), R. macrurus (2n = 44, FN = 49), R. nitela (2n = 50, FN = 71), and R. mastacalis (2n = 44, FN = 72) using chromosome painting probes of two Oryzomyini species.</p><p><strong>Results: </strong>Our analysis revealed pericentric inversion as the main rearrangement involved in the karyotype evolution of the group, although tandem fusions/fissions were also detected. In addition, we detected eight syntenic associations exclusive of the genus Rhipidomys, and three syntenic associations shared between species of the tribe Thomasomyini and Oryzomyini.</p><p><strong>Conclusion: </strong>Comparative cytogenetic analysis by ZOO-FISH on genus Rhipidomys supports a pattern of chromosomal rearrangement already suggested by comparative G-banding. However, the results suggest that karyotype variability in the genus could also involve the occurrence of an evolutionary new centromere.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141179207","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":"Loss of One X and the Y Chromosome Changes the Configuration of the X Inactivation Center in the Genus Tokudaia.","authors":"Luisa Matiz-Ceron, Miki Okuno, Takehiko Itoh, Ikuya Yoshida, Shusei Mizushima, Atsushi Toyoda, Takamichi Jogahara, Asato Kuroiwa","doi":"10.1159/000539294","DOIUrl":"10.1159/000539294","url":null,"abstract":"<p><strong>Introduction: </strong>X chromosome inactivation (XCI) is an essential mechanism for dosage compensation between females and males in mammals. In females, XCI is controlled by a complex, conserved locus termed the X inactivation center (Xic), in which the lncRNA Xist is the key regulator. However, little is known about the Xic in species with unusual sex chromosomes. The genus Tokudaia includes three rodent species endemic to Japan. Tokudaia osimensis and Tokudaia tokunoshimensis lost the Y chromosome (XO/XO), while Tokudaia muenninki (TMU) acquired a neo-X region by fusion of the X chromosome and an autosome (XX/XY). We compared the gene location and structure in the Xic among Tokudaia species.</p><p><strong>Methods: </strong>Gene structure of nine genes in Xic was predicted, and the gene location and genome sequences of Xic were compared between mouse and Tokudaia species. The expression level of the gene was confirmed by transcripts per million calculation using RNA-seq data.</p><p><strong>Results: </strong>Compared to mouse, the Xic gene order and location were conserved in Tokudaia species. However, remarkable structure changes were observed in lncRNA genes, Xist and Tsix, in the XO/XO species. In Xist, important functional repeats, B-, C-, D-, and E-repeats, were partially or completely lost due to deletions in these species. RNA-seq data showed that female-specific expression patterns of Xist and Tsix were confirmed in TMU, however, not in the XO/XO species. Additionally, three deletions and one inversion were confirmed in the intergenic region between Jpx and Ftx in the XO/XO species.</p><p><strong>Conclusion: </strong>Our findings indicate that even if the Xist and Tsix lncRNAs are expressed, they are incapable of producing a successful and lasting XCI in the XO/XO species. We hypothesized that the significant structure change in the intergenic region of Jpx-Ftx resulted in the inability to perform the XCI, and, as a result, a lack of Xist expression. Our results collectively suggest that structural changes in the Xic occurred in the ancestral lineage of XO/XO species, likely due to the loss of one X chromosome and the Y chromosome as a consequence of the degradation of the XCI system.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140956719","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":"Front & Back Matter","authors":"","doi":"10.1159/000533215","DOIUrl":"https://doi.org/10.1159/000533215","url":null,"abstract":"","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45240466","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":"Front & Back Matter","authors":"","doi":"10.1159/000530487","DOIUrl":"https://doi.org/10.1159/000530487","url":null,"abstract":"","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49441823","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":"Front & Back Matter","authors":"","doi":"10.1159/000529882","DOIUrl":"https://doi.org/10.1159/000529882","url":null,"abstract":"","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48697157","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":"Diversity and Evolution of Highly Repetitive DNA Sequences Constituting Chromosome Site-Specific Heterochromatin in Two Gerbillinae Species.","authors":"Yoshinobu Uno, Kazumi Matsubara, Jun Inoue, Johji Inazawa, Akio Shinohara, Chihiro Koshimoto, Kenji Ichiyanagi, Yoichi Matsuda","doi":"10.1159/000533716","DOIUrl":"10.1159/000533716","url":null,"abstract":"<p><p>Constitutive heterochromatin, consisting of repetitive sequences, diverges very rapidly; therefore, its nucleotide sequences and chromosomal distributions are often largely different, even between closely related species. The chromosome C-banding patterns of two Gerbillinae species, Meriones unguiculatus and Gerbillus perpallidus, vary greatly, even though they belong to the same subfamily. To understand the evolution of C-positive heterochromatin in these species, we isolated highly repetitive sequences, determined their nucleotide sequences, and characterized them using chromosomal and filter hybridization. We obtained a centromeric repeat (MUN-HaeIII) and a chromosome 13-specific repeat (MUN-EcoRI) from M. unguiculatus. We also isolated a centromeric/pericentromeric repeat (GPE-MBD) and an interspersed-type repeat that was predominantly amplified in the X and Y chromosomes (GPE-EcoRI) from G. perpallidus. GPE-MBD was found to contain a 17-bp motif that is essential for binding to the centromere-associated protein CENP-B. This indicates that it may play a role in the formation of a specified structure and/or function of centromeres. The nucleotide sequences of the three sequence families, except GPE-EcoRI, were conserved only in Gerbillinae. GPE-EcoRI was derived from the long interspersed nuclear elements 1 retrotransposon and showed sequence homology throughout Muridae and Cricetidae species, indicating that the repeat sequence occurred at least in the common ancestor of Muridae and Cricetidae. Due to a lack of assembly data of highly repetitive sequences constituting heterochromatin in whole-genome sequences of vertebrate species published to date, the knowledge obtained in this study provides useful information for a deep understanding of the evolution of repetitive sequences in not only rodents but also in mammals.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10242173","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}