Chromosomal Regions Research Articles

Genome‐Wide Diversity in Lowland and Highland Maize Landraces From Southern South America: Population Genetics Insights to Assist Conservation

ABSTRACTMaize (Zea mays ssp. mays L.) landraces are traditional American crops with high genetic variability that conform a source of original alleles for conventional maize breeding. Northern Argentina, one the southernmost regions of traditional maize cultivation in the Americas, harbours around 57 races traditionally grown in two regions with contrasting environmental conditions, namely, the Andean mountains in the Northwest and the tropical grasslands and Atlantic Forest in the Northeast. These races encounter diverse threats to their genetic diversity and persistence in their regions of origin, with climate change standing out as one of the major challenges. In this work, we use genome‐wide SNPs derived from ddRADseq to study the genetic diversity of individuals representing the five groups previously described for this area. This allowed us to distinguish two clearly differentiated gene pools, the highland northwestern maize (HNWA) and the floury northeastern maize (FNEA). Subsequently, we employed essential biodiversity variables at the genetic level, as proposed by the Group on Earth Observations Biodiversity Observation Network (GEO BON), to evaluate the conservation status of these two groups. This assessment encompassed genetic diversity (Pi), inbreeding coefficient (F) and effective population size (Ne). FNEA showed low Ne values and high F values, while HNWA showed low Ne values and low Pi values, indicating that further genetic erosion is imminent for these landraces. Outlier detection methods allowed identification of putative adaptive genomic regions, consistent with previously reported flowering‐time loci and chromosomal regions displaying introgression from the teosinte Zea mays ssp. mexicana. Finally, species distribution models were obtained for two future climate scenarios, showing a notable reduction in the potential planting area of HNWA and a shift in the cultivation areas of FNEA. These results suggest that maize landraces from Northern Argentina may be unable to cope with climate change. Therefore, active conservation policies are advisable.

PIT1/HINFI POLYMORPHISM IN HOLSTEIN CATTLE IN AFYONKARAHISAR PROVINCE

Pit1 gene has been shown to be located on the centromeric region of chromosome 1 in cattle. This gene has responsible for development of pituitary gland and hormone expression in mammals. Pit1 deficiency causes a dwarfism phenotype in mice, dogs and fish. Previous studies has demonstrated to associated with polymorphisms of the Pit1 gene and growth and reproductive performance and milk, meat yield traits. In the cattle, a HinfI polymorphism on Pit1 gene (c.1178G>A ) have been reported that there is an association between milk and reproduction yield parameters. In this study, we aimed existence and distribution of Pit1/HinfI polymorphism in 81 head of Holstein cattle in Afyonkarahisar province. In our study, we found that there were 5 AA, 30 AG and 46 GG genotypes in our survey population. We also detected to frequency of A allele as 0.25 and the G allele as 0.75. We calculated to genetic index values such as PIC (0.3027418) and Heterozygosity (0.3742044) using by RStudio package. Chi-square value was found 0.049 and was exhibited to survey population in Hardy-Weinberg equilibrium. Considering of these findings, we denoted proper of Pit1/HinfI polymorphism using in marker assisted selection studies both of native and culture cattle breeds.

Chemically induced proximity reveals a Piezo-dependent meiotic checkpoint at the oocyte nuclear envelope.

Sexual reproduction relies on robust quality control during meiosis. Assembly of the synaptonemal complex between homologous chromosomes (synapsis) regulates meiotic recombination and is crucial for accurate chromosome segregation in most eukaryotes. Synapsis defects can trigger cell cycle delays and, in some cases, apoptosis. We developed and deployed a chemically induced proximity system to identify key elements of this quality control pathway in Caenorhabditis elegans. Persistence of the polo-like kinase PLK-2 at pairing centers-specialized chromosome regions that interact with the nuclear envelope-induced apoptosis of oocytes in response to phosphorylation and destabilization of the nuclear lamina. Unexpectedly, the Piezo1/PEZO-1 channel localized to the nuclear envelope and was required to transduce this signal to promote apoptosis in maturing oocytes.

Preschool age-specific obesity and later-life kidney health: a Mendelian randomization and colocalization study.

While the association between obesity and kidney diseases has been found in previous studies, the relationship between preschool-age obesity and later-life kidney health remains unclear, posing challenges for effective interventions in this critical life period. Utilizing the hitherto largest genome-wide association studies, we conducted two-sample mendelian randomization (MR) to estimate the association of preschool age-specific obesity on kidney health and diseases, including blood urea nitrogen (BUN), eGFRcrea, eGFRcys, chronic kidney disease (CKD), IgA nephropathy, and diabetic nephropathy. Then, we applied multivariable Mendelian randomization (MVMR) and stepwise MR to elucidate the role of adult obesity and 12 other potential factors in the pathway between preschool age-specific obesity and kidney health. Finally, we employed colocalization analysis to understand the mechanism of preschool age-specific obesity and kidney damage further by detecting shared causal variants. Our two-sample MR results indicated that preschool obesity could be associated with kidney health and disease. In addition, we observed a switch in the direction of associations between age-specific body mass index (BMI) and CKD, manifesting as negative associations before 3 years old and positive associations after 3 years old. Furthermore, MVMR and stepwise MR results suggested potential pathways linking preschool obesity to kidney health, involving factors such as adult BMI, circulating high-density lipoprotein cholesterol levels, and circulating C-reactive protein levels. Finally, we detected that preschool-age BMI and kidney function could share causal variants such as rs76111507, rs62107261, rs77165542 in the region of chromosome 2, and rs571312 in the region of chromosome 18. Our study supports the association between preschool obesity and kidney health, emphasizing the role of adult BMI in this relationship. These findings underscore the importance of interventions starting in early childhood and continuing through adulthood to reduce the long-term risk of obesity-related kidney damage.

Prognostic Relevance of Copy Number Losses in Ovarian Cancer.

Aneuploidy is a prevalent cancer feature that occurs in many solid tumors. For example, high-grade serous ovarian cancer shows a high level of copy number alterations and genomic rearrangements. This makes genomic variants appealing as diagnostic or prognostic biomarkers, as well as for their easy detection. In this study, we focused on copy number (CN) losses shared by ovarian cancer stem cells (CSCs) to identify chromosomal regions that may be important for CSC features and, in turn, for patients' prognosis. Array-CGH and bioinformatic analyses on three CSCs subpopulations were performed. Pathway and gene ontology analyses on genes involved in copy number loss in all CSCs revealed a significant decrease in mRNA surveillance pathway, as well as miRNA-mediated gene silencing. Then, starting from these CN losses, we validated their potential prognostic relevance by analyzing the TCGA cohort. Notably, losses of 4q34.3-q35.2, 8p21.2-p21.1, and 18q12.2-q23 were linked to increased genomic instability. Loss of 18q12.2-q23 was also related to a higher tumor stage and poor prognosis. Finally, specific genes mapping in these regions, such as PPP2R2A and TPGS2A, emerged as potential biomarkers. Our findings highlight the importance of genomic alterations in ovarian cancer and their impact on tumor progression and patients' prognosis, offering advance in understanding of the application of numerical aberrations as prognostic ovarian cancer biomarkers.

A genome-wide association study in Swedish colorectal cancer patients with gastric- and prostate cancer in relatives

BackgroundA complex inheritance has been suggested in families with colorectal-, gastric- and prostate cancer. Therefore, we conducted a genome-wide association study (GWAS) in colorectal cancer patients, who’s relatives had prostate-, and/or gastric cancer.MethodsThe GWAS analysis consisted of 685 cases of colorectal cancer and 4780 healthy controls from Sweden. A sliding window haplotype analysis was conducted using a logistic regression model. Thereafter, we performed sequencing to find candidate variants, finally to be tested in a nested case–control study.ResultsCandidate loci/genes on ten chromosomal regions were suggested with odds ratios between 1.71–3.62 and p-values < 5 × 10–8 in the analysis. The regions suggested were 1q32.2, 3q29, 4q35.1, 4p15.31, 4q26, 8p23.1, 13q33.3, 13q13.3, 16q23.3 and 22q11.21. All regions, except one on 1q32.2, had protein coding genes, many already shown to be involved in cancer, such as ZDHHC19, SYNPO2, PCYT1A, MYO16, TXNRD2, COMT, and CDH13. Sequencing of DNA from 122 colorectal cancer patients with gastric- and/or prostate cancer in their families was performed to search for candidate variants in the haplotype regions. The identified candidate variants were tested in a nested case–control study of similar colorectal cancer cases and controls. There was some support for an increased risk of colorectal-, gastric-, and/or prostate cancer in all the six loci tested.ConclusionsThis study demonstrated a proof of principle strategy to identify risk variants found by GWAS, and identified ten candidate loci that could be associated with colorectal, gastric- and prostate cancer.Graphical

Functional Analysis of CsWOX4 Gene Mutation Leading to Maple Leaf Type in Cucumber (Cucumis sativus L.).

The leaf morphology is an important agronomic trait in crop production. Our study identified a maple leaf type (mlt) cucumber mutant and located the regulatory gene for leaf shape changes through BSA results. Hybrid F1 and F2 populations were generated by F1 self-crossing, and the candidate mlt genes were identified within the 2.8 Mb region of chromosome 2 using map cloning. Through the sequencing and expression analysis of genes within the bulk segregant analysis (BSA) region, we identified the target gene for leaf shape regulation as CsWOX4 (CsaV3_2G026510). The change from base C to T in the original sequence led to frameshift mutations and the premature termination of translation, resulting in shortened encoded proteins and conserved WUSCHEL (WUS) box sequence loss. The specific expression analysis of the CsWOX4/Cswox4 genes in the roots, stems, leaves and other tissue types of wild-type (WT) and mutant plants revealed that CsWOX4 was higher in the root, but Cswox4 (mutant gene) was significantly higher in the leaf. Subcellular localization analysis revealed that CsWOX4 was localized in the nucleus. RNA-seq analysis revealed that the differentially expressed genes were mainly enriched in the mitochondrial cell cycle phase transition, nucleosome and microtubule binding pathways. Simultaneously, the quantitative analysis of the expression trends of 25 typical genes regulating the leaf types revealed the significant upregulation of CsPIN3. In our study, we found that the conserved domain of CsWOX4 was missing in the mutant, and the transcriptome data revealed that the expression of some genes, such as CsPIN3, changed simultaneously, thereby jointly regulating changes in the cucumber leaf type.

False-positive XXY results by interphase FISH in cytogenetically normal XX individuals: two cases highlighting the necessity of additional laboratory follow-up

BackgroundInterphase fluorescence in situ hybridization (FISH) is commonly used for rapid aneuploidy detection in clinical settings. While FISH-based aneuploidy detection provides rapid results desirable for patient management, it usually only utilizes one probe per chromosome, which may lead to rare false-positive findings.Case presentationHere we report two interphase FISH results, which were false-positive for XXY in cytogenetically normal XX individuals. Both false-positive cases were due to hybridization of the Y chromosome centromeric probe DYZ3 to the pericentromeric region of chromosome 15. In both cases, chromosomal microarray revealed no detectable Y chromosome material, suggesting the hybridizations of the DYZ3 probe to chromosome 15 likely represent benign heterochromatic variants of no clinical significance. In one case, the DYZ3 hybridization was also identified in the phenotypically unaffected mother, further suggesting this is likely a rare variant of no clinical significance.ConclusionsThis report marks the first documentation of hybridization of the DYZ3 probe to another chromosome in cytogenetically normal individuals. Our report has important clinical implications, because DYZ3 is widely used by clinical laboratories for Y chromosome detection. Our findings underscore the necessity of confirming abnormal aneuploidy detection FISH results with additional laboratory methods such as chromosomal microarray analysis.

CAMPTODACTYLY ARTHROPATHY COXA-VARA PERICARDITIS (CACP) SYNDROME CAUSED BY TRUNCATING MUTATIONS IN THE PRG-4 GENE, CASE SERIES AND LITERATURE REVIEW

Introduction: Camptodactyly Arthropathy Coxa-vara Pericarditis (CACP) syndrome is an autosomal recessive condition characterized by early-onset camptodactyly, noninflammatory arthropathy, coxa vara deformity, and, rarely, pericardial effusion. The disease gene has been assigned to human chromosome regions 1q25-q31, and truncating mutations have been identified in the proteoglycan-4 (PRG4) gene formerly known as megakaryocyte stimulating factor gene. Methods: A literature review was performed with the findings in patients in terms of CACP syndrome. Also, whole-exome sequencing (WES) was performed for all cases. Segregation analyses of the detected variants were performed according to the possibilities. Results: We present three Turkish patients with CACP syndrome mimicking juvenile idiopathic arthritis (JIA). All patients were exposed to biologic therapy due to recalcitrant JIA. We have detected two pathogenic PRG4 variants. Case 3 had a novel pathogenic PRG4 variant not reported for the CACP syndrome so far. These two variants cause premature truncation of the protein. A deletion was detected in Case 1 in the homozygous state in the PRG4 gene (NM_005807.6: c.3848del, p.Gly1283GlufsTer6, chr1-186281360-G-). A previously described deletion was detected in Case 2 and Case 3 in the homozygous state in the PRG4 gene (NM_005807.6: c.1910_1911delCT, p.Pro637ArgfsTer9, chr1-186276761-CT). Conclusion: In the current study, we report three pathogenic PRG4 variants including a novel mutation. We consider that a detailed anamnesis, including kinship and meticulous physical examination of camptodactyly in the absence of inflammatory response, may reveal CACP syndrome masquerading as JIA. The PRG4 gene analysis presents the early diagnosis for patients and prenatal counseling and preimplantation genetic diagnosis for carrier families.

Evolution of Sex-linked Genes and the Role of Pericentromeric Regions in Sex Chromosomes: Insights from Diploid Willows.

The evolution of sex chromosomes can involve recombination suppression sometimes involving structural changes, such as inversions, allowing subsequent rearrangements, including inversions and gene transpositions. In the two major genus Salix clades, Salix and Vetrix, almost all species are dioecious, and sex-linked regions have evolved on chromosome 7 and 15, with either male or female heterogamety. We used chromosome conformation capture (Hi-C) and PacBio HiFi (high-fidelity) reads to assemble chromosome-level, gap-free X and Y chromosomes from both clades, S. triandra (15XY system), a basal species in the Vetrix clade, and the Salix clade species S. mesnyi (7XY system). Combining these with other available genome assemblies, we found inversions within the sex-linked regions, which are likely to be pericentromeric and probably recombined rarely in the ancestral species, before sex-linkage evolved. The Y-linked regions in all 15XY and 7XY species include partial duplicates containing exon 1 of an ARR17-like gene similar to male-determining factors in other Salicaceae species. We also found duplicates of a Y-specific gene, which we named MSF. The derived Salix clade 7XY chromosome systems appear to have evolved when these two genes transposed from the 15Y to the 7Y. Additionally, the 7Y chromosomes in S. dunnii and S. chaenomeloides probably evolved from the ancestral 7X of the Salix clade, involving a similar transposition, and loss of the ancestral 7Y. We suggest that pericentromeric regions that recombine infrequently may facilitate the evolution of sex linkage.

The complete genome sequence of "Candidatus Liberibacter asiaticus" strain 9PA and the characterization of field strains in the Brazilian citriculture.

CLas is a destructive pathogen responsible for causing the severe citrus disease known as huanglongbing. Our study presents the first fully sequenced Brazilian strain of CLas, designated as 9PA, and includes an analysis of two prophages occurring in this strain. The main objective of our research was to compare the genome features of this Brazilian strain with other fully sequenced genomes and to identify its hypervariable genetic regions. These regions were subsequently used to assess genomic variability within both the chromosomal and prophage regions in Brazilian isolates of CLas. Our findings offer valuable insights into the diversified adaptation of CLas.

Prenatal diagnosis and genetic analysis: rare familial chromosomal duplications larger than 5 Mb without disease phenotypes.

This study aimed to identify large duplications (>5 Mb) that are harmless through long-term clinical follow-ups of fetuses and phenotype analyses of carrier family members. We retrospectively analyzed fetuses undergoing prenatal diagnosis and who had >5 Mb chromosomal duplications. Routine karyotyping and single-nucleotide polymorphism array analysis were performed to identify the source and location information of the duplicated segments. Genotype-phenotype analyses were conducted based on genetic information and phenotypes during postnatal follow-up. Eight eligible cases were included. All fetuses carried maternal or paternal duplications ranging in length from 5.3 to 12.2 Mb. The locations were as follows: 2q32.3q33.1 (Chr2:192322509-199548704), 4q22.1 (Chr4: 88347368-93602855), 4q34.2q35.2 (Chr4:176956406-189189971), 4q34.3q35.2 (Chr4:180613345-189353740), 5p14.3p14.1 (Chr5:19093749-28557664), 10q22.2q23.2 (Chr10:77448435-88786593), 12q21.31q21.32 (Chr12:81983257-87322734), and 13q14.11q14.2 (Chr13: 40825382-47633710). Karyotyping revealed that these duplications occurred within their respective chromosomal regions, except in pedigrees 6 and 7. In the eight pedigrees, the coordinates and lengths of duplicated segments in family members were matched with those in fetuses. Neither the fetuses nor other carriers were clinically symptomatic. Our findings revealed that the eight pedigrees carrying duplications >5 Mb were asymptomatic, providing new data to inform genetic counseling for the observed segments. We focused on unrelated fetuses among eight pedigrees who carried duplications of different chromosomal segments. These duplications had been stably transmitted through 2 or 3 generations of normal individuals. Importantly, phenotypic abnormalities were lacking, which was unexpected given that the maximum segment size was approximately 12.2 Mb. We found that duplications in these regions were benign in the context of prenatal genetic counseling. These results provide a foundation for addressing genotype-phenotype correlations. To our knowledge, this is the first description of normal phenotypes in individuals with duplications in these regions.

Experimental in vivo models for understanding inter-molecular interactions and preventing multifactor disease development

The increased spontaneous fragility in the centromere regions of the chromosomes predisposes to abnormal cellular division due to abnormal interaction with the mitotic spindle, which leads to number chromosomal aberrations. The abnormal structure of the microtubule-associated proteins (MAPs) could also be among the internal factors, predisposing to these pathologies. On the other hand, the increased frequency of the spontaneous chromosomal fragility suggests abnormal structure of the respective chromosomal/chromatin components and thus an increased risk about gene mutations and structural chromosomal aberrations. The spontaneous chromosomal fragility was tested by light microscopy observation of metaphases from peripheral blood lymphocytes of 8 patients with polygene pathologies (neoplasms, neuro-degenerative diseases, and neuro-psychiatric disorders) and of 18 healthy controls. In the tested patients was established significantly higher frequency of the spontaneous chromosomal fragility, including in the centromere chromosomal regions, compared to the controls. Different inter-molecular interactions, which could prevent the pathology appearance, were investigated by appropriate experimental in vivo models. As a whole, in the most cases, the presented data showed significantly lower average titers of anti-ganglioside antibodies and gangliosides in the samples from myocardium and liver than in the samples from brain and pancreas. By taking into consideration that the myocardium and liver are known as the most enriched of GSH anatomic organs, the presented data could be explained with the literature messages of higher amounts of de novo-synthesized free GSH tri-peptide in the same two organs. Moreover, a possibility about the production of antibodies/immunoglobulins by non-lymphoid types of cells, tissues, and organs in appropriate conditions was shown. Because the so-produced antibodies are out of the germinative centers in the specialized lymphoid tissues and organs, the control of their functions by small ions and molecules as gangliosides is very important. In the current study, the attention was particularly directed to the iteractions with the participation of gangliosides, the reduced form of the tri-peptide glutathione (GSH), and the protein HACE1. Besides the tumor-suppressor activity of protein HACE1, also its neuroprotective influence was proven, namely by interactions with specific molecules.

Fidarsi o non fidarsi del test prenatale non invasivo? Riflessioni a partire da un caso di falso negativo

Non-invasive prenatal testing (NIPT) is a screening for foetal chromosomal abnormalities that identifies at-risk pregnancies and is used to propose a possible invasive genetic confirmation testing in case of its positive results. For Down syndrome (trisomy 21), its accuracy is close to 100%, while for other investigated conditions, it presents various limitations. In a neonate who presented with severe hypotonia and syndromic features, the NIPT was negative for all the screened anomalies. However, among the various investigations performed for the diagnosis, there was an altered methylation of the chromosomal region 15q11.2, indicative of Prader-Willi syndrome (PWS), previously excluded by NIPT. The paper therefore questions the significance of the results of this investigation in front of a clinical suspicion and reviews the use of NIPT in clinical practice.

Loss of CFHR5 function reduces the risk for age-related macular degeneration.

Age-related macular degeneration (AMD) is a prevalent cause of vision loss in the elderly with limited therapeutic options. A single chromosomal region around the complement factor H gene ( CFH ) is reported to explain nearly 25% of genetic AMD risk. Here, we used association testing, statistical finemapping and conditional analyses in 12,495 AMD cases and 461,686 controls to deconvolute four major CFH haplotypes that convey protection from AMD. We show that beyond CFH , two of these are explained by Finn-enriched frameshift and missense variants in the CFH modulator CFHR5 . We demonstrate through a FinnGen sample recall study that CFHR5 variant carriers exhibit dose-dependent reductions in serum levels of the CFHR5 gene product FHR-5 and two functionally related proteins at the locus. Genetic reduction in FHR-5 correlates with higher preserved activities of the classical and alternative complement pathways. Our results propose therapeutic downregulation of FHR-5 as promising to prevent or treat AMD.

Structural Variants in COL1A1 and COL1A2 in Osteogenesis Imperfecta.

Osteogenesis Imperfecta (OI) is a heterogeneous skeletal dysplasia characterized by bone fragility, skeletal deformities, and short stature. Most commonly, it is caused by autosomal dominant variants in the type I collagen genes, COL1A1 or COL1A2. Type I collagen is the main protein of the extracellular matrix in the skeleton and changes in its structure or quantity may lead to OI. 85%-90% of OI cases occur due to sequence variants in type I collagen genes, while OI caused by structural abnormalities in type I collagen genes is less common. In most cases, haploinsufficiency of type I collagen is associated with a milder OI phenotype. Large genomic deletions often involve several genes within the same chromosomal region, leading to microdeletion syndromes with OI features. Here, we report eight Swedish patients from five unrelated families with OI due to structural variants in the COL1A1 and COL1A2 genes. One patient with OI type III had a complex rearrangement with a deletion and duplication event in COL1A2, leading to reduced COL1A2 expression. Three other patients from two different families with OI type I had whole gene deletions involving COL1A1. In one family, three affected individuals with OI type I had a small intragenic deletion of exons 11-12 in COL1A2. One patient had a 2.1 Mb de novo deletion encompassing COL1A1 and DLX3 genes and features of OI and tricho-dento-osseous syndrome. Overall, this study highlights the importance of investigating gene dosage abnormalities in patients with OI and further delineates clinical and genetic variability of OI caused by structural variants in type I collagen genes.

Discovery of SZJK-0421: A Novel Potent, Low Toxicity, Selective Second Generation of CRM1 Inhibitor for the Treatment of Both Hematological and Solid Tumors.

Nuclear export factor chromosome region maintenance 1 (CRM1) mediated the transport of various growth-regulatory proteins and was frequently overexpressed in many hematologic and solid tumors. Selinexor (KPT-330) was the only approved CRM1 inhibitor, but the severe gastrointestinal and central nervous system toxicities limited its clinical application. In this manuscript, a series of novel second-generation CRM1 inhibitors were designed, in which SZJK-0421 was a more reversible inhibitor than KPT-330. The treatment of various tumor cells with SZJK-0421 significantly inhibited the function of CRM1. SZJK-0421 displayed good liver microsome stabilities and pharmacokinetic properties. Most importantly, SZJK-0421 reduced the direct damage to the gastrointestinal mucosa, and the brain plasma distribution ratio of SZJK-0421 was very low in Sprague-Dawley (SD) rats (3%), which avoided gastrointestinal reactions such as central nausea and vomiting caused by large permeability of blood-brain barrier. In addition, SZJK-0421 exhibited strong anticancer efficacy in xenograft models of both solid and hematological tumors.

Identification and annotation of centromeric hypomethylated regions with Centromere Dip Region (CDR)-Finder.

Centromeres are chromosomal regions historically understudied with sequencing technologies due to their repetitive nature and short-read mapping limitations. However, recent improvements in long-read sequencing allowed for the investigation of complex regions of the genome at the sequence and epigenetic levels. Here, we present Centromere Dip Region (CDR)-Finder: a tool to identify regions of hypomethylation within the centromeres of high-quality, contiguous genome assemblies. These regions are typically associated with a unique type of chromatin containing the histone H3 variant CENP-A, which marks the location of the kinetochore. CDR-Finder identifies the CDRs in large and short centromeres and generates a BED file indicating the location of the CDRs within the centromere. It also outputs a plot for visualization, validation, and downstream analysis. CDR-Finder is available at https://github.com/EichlerLab/CDR-Finder.

The telomere-to-telomere gap-free genome assembly of Juglans sigillata

Juglans sigillata is an economically valuable nut crop renowned for its nutritional richness, including essential nutrients, antioxidants, and healthy fats, which boost human cardial, brain and gut health. Despite its importance, the lack of a complete genome assembly has been a stumbling block in its biological breeding process. Therefore, we generated deep coverage ultralong Oxford Nanopore Technology (ONT) and PacBio HiFi reads to construct a telomere-to-telomere (T2T) genome assembly. The final assembly spans 537.27 Mb with no gaps, demonstrating a remarkable completeness of 98.1 %. We utilized a combination of transcriptome data and homologous proteins to annotate the genome, identifying 36 018 protein-coding genes. Furthermore, we profiled global cytosine DNA methylations using ONT sequencing data. Global methylome analysis revealed high methylation levels in transposable element (TE)-rich chromosomal regions juxtaposed with comparatively lower methylation in gene-rich areas. By integrating a detailed multi-omics data analysis, we obtained valuable insights into the mechanism underlying endopleura coloration. This investigation led to the identification of eight candidate genes (e.g. ANR) involved in anthocyanin biosynthesis pathways, which are crucial for the development of color in plants. The comprehensive genome assembly and the understanding of the genetic basis of important traits like endopleura coloration will open avenues for more efficient breeding programs and improved crop quality.

Cytogenetic and &lt;i&gt;ISSR&lt;/i&gt;-Markers Polymorphism in the Population of Local Ukrainian Lebedyn Cows

Preservation of the fund of local breeds of agricultural animals, which are breeding material for the creation of new ones and the improvement of existing ones, meets the requirements of the FAO - the protection of biological diversity. The study of the genetic structure of cows of the local Lebedyn breed, which was bred in Ukraine, with the use of cytogenetic and molecular genetic methods, is aimed at establishing information about the structure of the gene pool of these animals and the uniqueness of their genotype. Cytogenetic monitoring showed that the modal number of chromosomes corresponded to the species norm and was 2n=60, no constitutional abnormalities in the form of Robertsonian translocations were detected, the average frequency of genomic disorders (aneuploidy) was 10,2±2,10%, polyploidy was not manifested. structural disorders (chromosomal breaks) accounted for 3,1±1,88% and asynchronous separation of the centromeric regions of chromosomes – 0,8±0,10%. The average share of cytogenetic parameters of cells was determined: lymphocytes with micronucleus – 3,6±0,61‰, binucleus lymphocytes – 4,3±0,97‰ and mitotic index – 3,7±1,20‰. An analysis of the genetic structure of the local, small-numbered Lebedyn cattle breed of Ukraine was carried out using 8 ISSR-systems. All 8 microsatellite primers showed high efficiency. ISSR labeling revealed 88 amplified DNA fragments, of which only 18 were polymorphic. The total share of polymorphic loci was 25,45%. 11 species-specific loci for (ACC)6G, 5 loci for (CTC)6C, 10 for (GAG)6C, 7 for (GA)6CC, 10 for (AG)8CG, 9 for (AG)8CA, 13 for (GA)9C and 14 for (AG)9C. It was established that the studied animals were characterized by karyotype stability, reduced sensitivity to mutagenic factors of various nature, absence of inbreeding depression and reproductive isolation.