Cytogenetic and Genome Research最新文献

Introduction: Sex chromosomes have evolved independently across various lineages, often showing convergent degradation of the sex-limited chromosome. While extensively studied in model organisms with ancient sex chromosomal systems, the evolution of early-stage sex chromosomes remains poorly understood. Eulimnadia texana, a freshwater crustacean with a unique androdioecious breeding system (ZZ, ZW, and viable WW genotypes), provides a rare opportunity to study early sex chromosome evolution. This study examines E. texana's W chromosome for evidence of a small localized non-recombining region, characterized by a transposable element (TE) "hotspot", low gene density, and low GC content.

Methods: Sex-linked markers were mapped onto the W chromosome (Scaffold 1). TEs in the WW genome were identified using RepeatModeler and RepeatMasker. Statistical analyses compared TE distribution between the genome and Scaffold 1, which was then divided into 20 equal-sized "bins" for finer-scale statistical analyses. Gene density and GC content were analyzed across these bins.

Results: While no significant TE accumulation was found across the entire W chromosome compared to the remaining genome, a specific region (6.6-8.8 Mb, fourth bin) showed significantly higher TE accumulation. This region also exhibited low gene density and low GC content, indicative of reduced recombination.

Conclusion: Our findings suggest that E. texana's W chromosome contains a smaller region of crossover suppression, supporting the hypothesis that it is in a proto-sex chromosome in early evolutionary development. This study provides valuable insights into early sex chromosome evolution and establishes E. texana as an ideal model for further investigation of evolutionary processes driving proto-sex chromosome differentiation.

Introduction: Several studies have related shortened leukocyte telomere length (LTL) with age-related diseases and worse prognosis. Telomere length attrition has recently been associated with inflammatory diseases, including psoriasis. However, no study has demonstrated an association between LTL and the risk of disease severity and metabolic comorbidities in Arab patients with psoriasis (Ps).

Methods: 68 Ps and 42 normal controls (NC) were included. LTL and oxidative damage were determined by quantitative (q) PCR. Odds ratios (OR) and 95% confidence intervals (CI) were calculated using logistic regression. Statistical differences between the groups were determined using 2 and t-tests.

Results: Patients with psoriasis had significantly shorter LTL (P= 0.032) and higher oxidative damage (P= 0.015) than those without psoriasis. Patients with moderate-to-severe index (P= 0.03) and metabolic comorbidity showed significantly shorter LTL (P= 0.003) compared to patients with mild index and without metabolic comorbidity, respectively. Patients with short LTL (≤ 0.9) were correlated with higher risk of moderate-to-severe conditions (OR= 6.98, 95% CI= 2.3-20.8, P= 0.001) and metabolic comorbidities (OR= 2.89, 95% CI= 1.02- 8.2, P= 0.04).

Conclusion: LTL shortening may be a consequence of increased oxidative damage, and is related to the risk of severe psoriasis and metabolic comorbidities. Therefore, LTL may be a good candidate biomarker for predicting the risk of poor prognosis in patients with psoriasis.

Introduction: Cytogenetic studies on stingless bees have significantly contributed to our understanding of karyotypic evolution and the composition of euchromatin and heterochromatin regions, including repetitive sequences.

Methods: In this study, we performed classical cytogenetics, chromosomal banding, and mapping of some repetitive sequences in two stingless bee species, Frieseomelitta trichocerata and Plebeia poecilochroa.

Results: The species exhibit the typical diploid chromosome number of each genera, 2n=30 for Frieseomelitta and 2n=34 for Plebeia. Additionally, some individuals of P. poecilochroa presented a small heterochromatic B chromosome, showing a numeric variation of n=17 to 18 in males and 2n=34 to 35 in females. In both species heterochromatin is primarily distributed in the short arm and centromeric regions. Centromeric regions were found to be AT-rich in both species, while subterminal/terminal regions of the short arms of one and six chromosomes presented GC-rich sites in P. poecilochroa and F. trichocerata, respectively. The rDNA clusters mapped on two chromosome pairs in F. trichocerata, and in only one in P. poecilochroa. Microsatellites (GA)n, (GAG)n, and (CAA)n were predominantly mapped in euchromatic regions, while the telomeric motif (TTAGG)n mapped to the ends of most chromosomes, including the B chromosome of P. poecilochroa. The other repetitive probes used, including the rDNA clusters, do not label the B chromosome of P. poecilochroa.

Conclusion: Our cytogenetic data highlight both similarities and differences when compared to other congeneric species, expanding the chromosomal data for both genera.

Background: Fetal chromosome abnormalities, the most common cause of spontaneous abortion, were investigated pre-1980s. In recent years, chromosome testing has been outsourced to testing companies in Japan, and there have been few epidemiological studies of chromosome testing of miscarried fetuses on a nationwide scale.

Methods: We analyzed the chromosome test data of SRL, Inc., one of the largest clinical laboratories that has collected tissue specimens of products of conception derived from miscarried fetuses from hospitals throughout Japan from 2000.

Results: We collected and analyzed 24,175 cases, among which 8,726 (36.1%) were normal chromosomes, 1,298 (5.4%) were sex chromosome abnormalities, 9,735 (40.3%) were autosomal trisomies, 73 (0.3%) were autosomal monosomies, 840 (3.5%) were ploidy, 512 (2.1%) were chromosome structural abnormalities, and 2,991 (12.4%) were mosaics. The frequency of autosomal trisomy increased at the older maternal ages. By chromosome number, trisomies 22, 16, 21, and 15 were associated with advanced maternal age, but trisomies 13, 14, and 18 were not associated with advanced maternal age. The presence or absence of this maternal age effect was correlated with the chromosome segregation being due to maternal meiosis I or meiosis II. For the sex ratios of the fetuses, we focused on trisomies 22, 21, 18, 16, 15, 14, and 13, and found that only trisomy 16 was significantly more frequently seen in female fetuses.

Conclusion: The findings of this study provide insights into the basic understanding of miscarriage and will be useful in counseling and medical education.

Introduction: Gloriosa superba L. is a horticulturally and medicinally important plant native to Africa. However, the few cytogenetic studies of the species are mainly focused on chromosome counting and chromosome morphology-based karyotyping. Fluorescence in situ hybridization (FISH) is a powerful tool for the detection of DNA repetitive elements in a specific region of a chromosome.

Methods: Here, detailed karyotypes of G. superba were constructed by FISH using 5S and 45S rDNAs, and telomeric repeat (TTTAGGG)3 oligonucleotides.

Results and conclusion: Twenty-two chromosomes were observed. Two 5S rDNA hybridization signals were detected in the proximal regions of the short arms of one pair of chromosomes, which were adjacent to the (TTTAGGG)3 terminal signals. Four 45S rDNA signals were detected near the centromere region of the short arm of the four chromosomes, but one of these was very weak and almost undetectable compared to the others. Telomeric repeat hybridization signals were distributed at the terminal region of each chromosome. The chromosomes displayed were intact and the chromosome counts were accurate. Chromosome length ranged from 3.46 to 9.31 μm. These results will facilitate the cytogenetic mapping of other major repeats, thus contributing to an improved understanding of the G. superba genome structure and evolutionary history.

Background: Our study focuses on Yakutian cattle, a Siberian native breed, examining its inbreeding and diversity through genome-wide analysis of runs of homozygosity (ROHs). Yakutian cattle are adapted to Siberia's harsh sub-arctic conditions, enduring temperatures below -70°C. However, the population genetics studies on this breed are scanty, to document the genetic uniqueness in these cattle.

Results: We analyzed 40 Yakutian cattle with strict quality control for ROH detection yielding 683 homozygous segments, averaging 17 per individual with an average length of 9 Mb. ROH regions were found to be involved in important pathways pertaining to cold adaptation. Autozygosity ranged from 1% to 12% of the genome, with a relatively low average inbreeding coefficient (FROH) of 0.057, as compared to other breeds. Also, the different diversity indicators, namely, principal component analysis, heterozygosity, and effective population size analysis, revealed the prevalence of genetic diversity within the breed.

Conclusion: Our findings on ROH are the first of its kind in Yakutian cattle that support their adaptability to colder environments, as evidenced by low inbreeding and high genetic diversity.

Introduction: In chromatin nucleosomes, the presence - instead of canonical histone H3 - of its variant, CENH3 (in plants), is considered the most reliable marker of the location of centromeres. In this study, we investigated the effects of distant hybridization and maternal cytoplasm on centromere size in allopolyploid hybrids between wheat and rye as compared to their parental forms.

Methods: Centromere sizes were measured using 2D images of CENH3 fluorescent signals on interphase nuclei obtained from parental forms and a triticale hybrid (genomic formula AABBBRR), in which the maternal form is wheat and secalotriticum hybrids (genomic formula RRAABBB) in which the maternal form is rye. For measurements, we selected the largest spherical nuclei with large nucleoli in the late G2 phase, in which most of the loading of CENH3 into centromeric chromatin takes place.

Results: When processing the results of the measurement of centromere sizes in the hybrids, the obtained values were compared with those expected for the case of no change in centromere sizes in any of the parental sets of chromosomes. We found no significant differences between expected and measured values.

Conclusion: We believe that, in the case of allopolyploid hybrids between wheat and rye, centromeres of chromosomes from the parental species retain the sizes formed during evolution. This conservatism may be promoted by the high similarity in the structure of the CENH3 molecules between these species.

Background: Extrachromosomal circular DNA (eccDNA) has emerged as a central focus in molecular biology, with various types being found across species through advanced techniques, including high-throughput sequencing. This dynamic molecule exerts a significant influence on aging and immune function and plays pivotal roles in autoimmune diseases, type 2 diabetes mellitus, cancer, and genetic disorders.

Summary: This comprehensive review investigates the classification, characteristics, formation processes, and multifaceted functions of eccDNA, providing an in-depth exploration of its mechanisms in diverse diseases.

Key messages: The goal of this review was to establish a robust theoretical foundation for a more comprehensive understanding of eccDNA, offering valuable insights for the development of clinical diagnostics and innovative therapeutic strategies in the context of related diseases.

Introduction: Duplications reported in 10q21-q22 include borderline to moderate intellectual disability, growth retardation, autism, attention deficit hyperactivity disorder, and minor craniofacial dysmorphism.

Case presentation: We present a patient with a novel 14.7-Mb de novo interstitial duplication at 10q21.1-q22.1 delineated by a high-definition (HD) single nucleotide polymorphism (SNP) array. The boy had minor facial dysmorphism, mild intellectual disability, an autism spectrum disorder-like phenotype, and short stature.

Conclusion: This is the first case in which a novel 10q21.1-q22.1 duplication was detected by the HD SNP array, expanding the spectrum of duplications seen in 10q21-q22. This report provides a detailed clinical examination of a patient with a 10q21.1-q22.1 duplication and suggests that brain development and cognitive function may be affected by an increased dosage sensitivity of the involved JMJD1C and EGR2 genes. This case contributes to the understanding of the genotype-phenotype relationship for genetic counseling and provides further evidence for the identification of a novel microduplication syndrome in 10q21-q22.

Introduction: The Ph1 locus in polyploid wheat enforces strictly bivalent behaviour in meiotic metaphase I, by preventing homoeologues from crossing over. It has always been considered as completely dominant as no homoeologous metaphase I pairing has ever been detected with its single dose present. However, Ph1 also affects pairing and crossing over of homologous chromosomes.

Methods: Homologous crossover frequencies with Ph1 in two, one, and null doses were scored cytologically, as exchanges within a ca. 9.5-9.9 Mbp terminal wheat segment of a wheat-rye translocation T-9 and corresponding segments in chromosome arms 1BS originating from four wheat cultivars.

Results: In all cases, the crossover rates in the tested homologous segment of wheat genome, with a single dose of Ph1 present, were intermediate between those at two and null Ph1 doses. Averaging across all four chromosomes, the crossover rate with a single dose of Ph1 present was 37% higher from that with two doses and 46.4% lower of that with a zero dosage.

Conclusion: The Ph1 locus in wheat affects homologues and appears to operate in a dosage-dependent manner.