Camellia drupifera is an economically important woody oil plant rich in edible seed oil. High-quality and well-developed floral buds are key determinants of its yield. However, studies on the regulatory mechanisms underlying its floral bud development remain relatively limited. In this study, proteomics and metabolomics profiles, along with physiological traits, tested during the final three developmental stages of floral buds. The results showed that the contents of indole-3-acetic acid (IAA), abscisic acid (ABA), and 1-aminocyclopropane-1-carboxylic acid (ACC, a precursor of ethylene) decreased significantly in the second (GZII) and third (GZIII) stages. Gibberellin 3 (GA3) maintained a relatively stable content in GZII with a slight decrease, but decreased significantly in GZIII. These changes in hormone contents may promote the growth of stamens and pistils. During the transition among the three floral bud developmental stages, the relative water content, superoxide dismutase (SOD) activity, soluble sugar content, and soluble protein content decreased significantly, accompanied by an increase in hydrogen peroxide (H2O2) content. Integration of differentially accumulated metabolites (DAMs) and differentially expressed proteins (DEPs) analysis showed that the upregulated proteins in the energy metabolism pathway, including pyruvate kinase (PK), citrate synthase (CS), succinate dehydrogenase (SDH), aldolase (ALDO), and hexokinase (HK), promoted the production of adenosine triphosphate (ATP)—a critical energy source for the entire floral development process, including plant hormone synthesis. The decreased IAA content might be attributed to the downregulation of enzymes involved in tryptophan metabolism, such as aldehyde dehydrogenase (ALDH), 3-dehydroquinate dehydratase/shikimate dehydrogenase (aroDE), and chorismate mutase/prephenate dehydratase (aroH). The contents of ABA and GA3 were affected by the downregulation of 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (ispH). Furthermore, the contents of anthocyanins (antioxidant metabolites) decreased significantly in GZII and GZIII, which was caused by the downregulation of key enzymes in the anthocyanin synthesis pathway, including 4-coumarate-CoA ligase (4CL), flavonoid 3’-hydroxylase (F3’H), flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), and anthocyanidin synthase (ANS). This study provides a foundation for further investigating the regulatory metabolites and enzymes involved in C. drupifera floral bud development, and lays a theoretical basis for solving the problem of flower abscission in C. drupifera.
We aimed to investigate whether secretory carrier membrane protein 3 (SCAMP3) knockdown could attenuate hypoxic pulmonary hypertension (HPH) potentially involving WW domain-containing E3 ubiquitin protein ligase 1 (WWP1). Fifty mice were randomly assigned to a blank group, an HPH group, a small interference (si)-negative control (NC) group, a si-SCAMP3 group and a si-SCAMP3 + si-WWP1 group (n = 10 per group). Pulmonary function, right ventricular systolic pressure (RVSP) and the Fulton index [RV/(LV + S)] were measured. Hematoxylin-eosin staining was performed to evaluate pulmonary vascular morphology and the pulmonary vascular remodeling indexes were calculated. Compared with the normoxia group, the hypoxia group exhibited significantly increased SCAMP3 relative expression, OD450 value and SCAMP3 protein expression in HPASMCs, while the apoptosis rate and WWP1 protein expression were significantly decreased (P < 0.05). Compared with the hypoxia group, the hypoxia + si-SCAMP3 group showed significantly reduced SCAMP3 relative expression, OD450 value and SCAMP3 protein expression, but significantly increased apoptosis rate and WWP1 protein expression (P < 0.05). Compared with the hypoxia + si-SCAMP3 group, the hypoxia + si-SCAMP3 + si-WWP1 group exhibited partial restoration of SCAMP3 expression increased OD450 value and SCAMP3 protein expression, and decreased apoptosis rate and WWP1 protein expression (P < 0.05). These findings suggest that SCAMP3 knockdown may inhibit hypoxia-induced proliferation and promote apoptosis potentially involving WWP1, thereby alleviating pulmonary vascular remodeling in HPH mice.
The systematics and sustainable fisheries management of Neolissochilus sumatranus (Weber and de Beaufort 1916) remain challenging due to taxonomic controversies and limited molecular data. Hence, this study utilized next-generation sequencing to generate a mitogenome of N. sumatranus, morphologically identified from northern Sumatra, Indonesia. The assembled mitogenome of this species is 16,584 bp long and consists of 37 genes and a control region (CR). The comparative analysis with nine other Neolissochilus species revealed a highly conserved genetic organization, with relative synonymous codon usage showing high frequencies for arginine, leucine, and serine. Most protein-coding genes (PCGs) in N. sumatranus used ATG as the initiation codon, a pattern widely observed in vertebrate mitogenomes. Conversely, incomplete stop codons (TA- and T–) are proposed to be completed post-transcriptionally through polyadenylation during mRNA maturation. The nonsynonymous-to-synonymous substitution ratios were below ‘1’ for 12 PCGs, except Cytb in Neolissochilus species, indicating that the majority of these genes are subject to purifying selection. The secondary structures of all 22 transfer RNAs in N. sumatranus retained the canonical cloverleaf configuration, displaying no reduction of the dihydrouridine arm typically observed in tRNA-Ser1, thereby reflecting structural variation within cyprinids. The comparative assessment of the CR among Neolissochilus species demonstrated four conserved sequence blocks (CSB-D, CSB-1, CSB-2, and CSB-3) exhibiting species-specific variation, while the tandem repeats were detected in only six of the eight analyzed species. These non-coding regions also exhibited differences in length and nucleotide composition among the examined Neolissochilus species, highlighting their utility for comparative genetic studies. However, their applicability as population-level markers remains to be evaluated using multiple specimens per species to capture intraspecific variation. The mitogenome-based phylogenetic inference corroborates the monophyly of Torinae and suggests a close evolutionary relationship among N. sumatranus, N. hendersoni, and N. soroides, which may be associated with their shared biogeographic history in the Sundaland region. The cladistic relationships between the genera Neolissochilus and Tor remain poorly resolved, with Neolissochilus benasi and Tor remadevii potentially constituting distinct lineages outside the core Neolissochilus and Tor clades, respectively. The phylogenetic positions of Tor douronensis and T. tambra are inconsistent despite their taxonomic synonymy, emphasizing the need for morpho-genetic studies across mainland and island Southeast Asian populations. Overall, the novel mitogenome of N. sumatranus clarifies its phylogenetic position within Torinae and provides a foundation for future systematics study.
Lumbar disc degeneration (LDD) is a major cause of chronic low back pain, and current treatments only provide symptomatic relief. This study aimed to investigate the role of miR-4632-5p and its target MAP3K11 in the pathogenesis of LDD. Bioinformatics analysis was used to predict target genes of miR-4632-5p. LDD tissues (n=22) and normal intervertebral disc (IVD) tissues (n=19) were collected to detect the expression of miR-4632-5p and MAP3K11 by RT-qPCR. A dual-luciferase reporter assay validated their direct interaction. In vitro, TNF-α-induced human nucleus pulposus cells (HNPCs) degeneration models were used to evaluate the effects of miR-4632-5p/MAP3K11 on cell viability, apoptosis, oxidative stress, and inflammatory cytokine secretion via CCK-8, flow cytometry, and ELISA. miR-4632-5p was significantly downregulated in LDD tissues, whereas MAP3K11 was upregulated (P<0.0001), and their expression showed a strong negative correlation (r=-0.82, P<0.0001). miR-4632-5p targeted the 3′UTR of MAP3K11, reducing dual luciferase activity by 35.9
Heart failure is a leading cause of hospitalization worldwide, and evaluating the severity of heart failure often relies on the ejection fraction. Matrix metalloproteinases (MMPs) are crucial for tissue remodeling, and their dysregulation is linked to various pathologies, including cardiovascular diseases. Prior studies have demonstrated that MMP-9 gene deletion can promote angiogenesis, attenuate inflammation, and prevent vascular leakiness. Although MMP-9 is known to contribute to heart failure, it remains unclear whether the lack of the MMP-9 gene impacts heart failure with reduced ejection fraction (HFrEF) by preserving EF. We investigated whether removing the MMP-9 gene can help maintain ejection fraction during the transition from diastolic to systolic heart failure. To test the hypothesis, surgical creation of an arteriovenous fistula (AVF) was made between the abdominal aorta and inferior vena cava 0.5 cm below the left kidney of the mice using a 25-gauge needle to create a chronic volume overload, a “single-hit” model of HFrEF. The mice were grouped into four separate categories: (i) Wild type (WT) sham, (ii) WT-AVF, (iii) MMP9-KO-sham, and (iv) MMP9-KO-AVF. The “in-gel” zymography technique quantified proteolytic activity on substrate gels. Protein expression levels of heart tissues were assessed by the Western blots. The multi-organ injury was assessed using tissue-specific creatine kinase isoforms, and cardiac function-related datasets were collected using an ultrasound procedure and myobath. The results showed that MMP-9 gene ablation preserves ejection fraction during HFrEF by enhancing the processes of (a) cell synthesis, adhesion, and contraction signaling, (b) mitigating multi-organ injury, (c) mitigating mitophagy, and (d) mitigating endocardial endothelial myocyte uncoupling. Above panel is signaling of cell synthesis, expansion and contraction modes. Lower panel role of mitochondrial mitophagy in HFrEF
The complete mitochondrial genome of Turrum coeruleopinnatum was sequenced and characterized to expand mitogenomic resources for Carangidae and to evaluate its phylogenetic placement and candidate selection signals. The circular mitogenome was 16,553 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. Its overall A + T content was 54.04
Barbatia virescens is an important economic bivalve along the Chinese coast, but its natural resources have been severely impacted by habitat degradation and overfishing. In this study, we applied RAD-seq to five wild populations and generated 79.48 Gb of raw data, from which 237,101 high-quality SNPs were identified. All populations exhibited relatively high genetic diversity (mean: Ho = 0.158, He = 0.248, π = 0.263, and FIS = 0.290) with low genetic differentiation (FST < 0.05). Results from PCA, structure analysis and Neighbor-Joining (NJ) tree supported weak population structure. Relative migration analyses suggested generally high connectivity among populations, although the XP population exhibited comparatively reduced connectivity under stricter network thresholds. The findings provide a basis for sustainable management and the preservation of genetic resources in B. virescens.
Circular RNAs (circRNAs) have emerged as important regulators of tumor progression; however, their roles in papillary thyroid carcinoma (PTC) remain incompletely understood. In this study, we investigated the expression, biological function, and molecular mechanism of circGABRB2_006 in PTC. CircGABRB2_006 was significantly upregulated in PTC tissues and cell lines and was associated with aggressive clinicopathological characteristics, including increased tumor number, larger tumor size, advanced TNM stage, and lymph node metastasis. Functional assays demonstrated that circGABRB2_006 promoted PTC cell proliferation, migration, invasion, epithelial–mesenchymal transition (EMT), tumor growth, and pulmonary metastasis, whereas its silencing exerted the opposite effects. Mechanistically, circGABRB2_006 predominantly localized in the cytoplasm and acted as a molecular sponge for miR-296-5p, thereby relieving miR-296-5p-mediated repression of fibroblast growth factor receptor 1 (FGFR1). Rescue experiments further confirmed that the oncogenic effects of circGABRB2_006 were largely dependent on the miR-296-5p/FGFR1 axis. Collectively, these findings demonstrate that circGABRB2_006 drives malignant progression of PTC through the miR-296-5p/FGFR1 signaling axis, highlighting its potential as a biomarker and therapeutic target in PTC.
Integrating high-throughput sequencing with phylogenetic analysis now spans everything from single genes to long-read pangenomes and metagenomes, yet practitioners still face fragmented, tool-centric guidance. This review revisits algorithms, tools, and workflows for sequence and phylogenetic analysis in the NGS-based omics era, with a focus on comparative performance and scenario-driven decision-making. We first organise classical approaches to tree reconstruction – distance methods, maximum parsimony, maximum likelihood, and Bayesian inference – around core criteria of consistency, efficiency, robustness, and computational cost. We then examine multiple sequence alignment strategies, contrasting progressive, consistency-based, and structure-aware algorithms (such as MAFFT variants and T-Coffee family tools) with segment-based and incremental approaches (for example DIALIGN, anchored domains, and local updates) and alignment-free representations based on k-mers, absent words, and related statistics. For inference, we compare heuristic engines optimised for ultra-large alignments (FastTree, VeryFastTree, online tree optimisation) with full ML frameworks (IQ-TREE, RAxML-NG) and Bayesian platforms for time-scaled phylogenies and phylodynamics (MrBayes, BEAST family). We explicitly discuss trade-offs in accuracy, memory, scalability, and uncertainty support, and show how GPU-enabled implementations change the feasible design space. Beyond these core components, we address current trends that strongly influence method choice: long-read assemblies and pangenomes; data quality issues, contamination, recombination, and horizontal gene transfer; phylogenetic placement and alignment-free screening in metagenomics; and real-time pathogen surveillance using Nextstrain-style workflows. A dedicated section covers workflow management and containerisation (Snakemake, Nextflow, Docker/Singularity) together with benchmarking datasets and FAIR reporting, positioning reproducible pipelines as a first-class requirement rather than an afterthought. To make the review directly actionable, we provide a methodological checklist, a decision framework figure mapping input data to recommended strategies, and a large comparative table summarising algorithmic principles, best use cases, strengths, limitations, scalability, uncertainty support, and reproducibility notes for widely used tools. Applications in infectious disease genomics, oncology, and microbiome research illustrate how these choices translate into biological and clinical insight in practice.
Shilajit, a natural product with a documented history of use in traditional medicine for millennia, poses considerable challenges in elucidating its biological origin and pharmacological properties. In this study, a multidisciplinary approach integrating DNA metabarcoding and biochemical profiling was employed to investigate processed shilajit samples from the Pamir-Alai Mountains. Environmental DNA analysis identified 50 plant taxa across taxonomic levels ranging from order to species, indicating substantial botanical contributions to shilajit’s composition. Among the identified taxa, Apiaceae and Asteraceae were the most represented families, while Vincetoxicum rossicum, Populus alba, and Quercus suber were the dominant species detected through metabarcoding analysis. Complementary biochemical analyses demonstrated notable antioxidant capacity and the presence of diverse bioactive compounds. Furthermore, oxidative stress-related biomarkers (NO, MDA, and GSH) were evaluated in the brain tissue of healthy rats following shilajit administration. No statistically significant differences were observed between the control and shilajit treated groups, suggesting that shilajit maintains physiological oxidative balance in healthy brain tissue. These findings provide important baseline biochemical data and support future investigations of shilajit's biological effects in validated oxidative stress and neurological disease models.
Nuclear factor erythroid 2-related factor 2 (NRF2) is a central transcriptional regulator of the antioxidant response and a key inhibitor of ferroptosis, and its overexpression is frequently observed in various cancers. However, the mechanisms underlying its dysregulation in nasopharyngeal carcinoma (NPC) remain poorly understood. In this study, we combined bioinformatic analysis with functional experiments to investigate the post‑transcriptional regulation of NRF2 in NPC. Using weighted gene co-expression network analysis (WGCNA) based on the GSE68799 dataset and differential expression analysis of NPC transcriptomic data, we identified NRF2 as a candidate gene associated with NPC progression. Functional studies confirmed that NRF2 inhibits ferroptosis in NPC cells. Mechanistically, we demonstrated that the m6A reader protein insulin‑like growth factor 2 mRNA‑binding protein 2 (IGF2BP2) binds to and stabilizes NRF2 mRNA in an m6A‑dependent manner. Depletion of IGF2BP2 downregulated NRF2 expression and accelerated NRF2 mRNA decay. Notably, inhibition of methyltransferase activity by S-Adenosyl-L-homocysteine (SAH) reduced m6A modification on NRF2 mRNA and impaired its interaction with IGF2BP2. Furthermore, IGF2BP2 knockdown impaired the NRF2/HO-1/GPX4 axis, leading to a significant reduction in GPX4 enzymatic activity and promoted ferroptosis, effects that were rescued by the NRF2 activator dimethyl fumarate (DMF). Collectively, these results reveal that IGF2BP2 stabilizes NRF2 mRNA via m6A modification to suppress ferroptosis, thereby promoting NPC cell survival.
Deciphering the evolutionary history of genes is foundational for biomedical research, enabling the identification of compensatory mutations in disease-associated genes and the selection of evolutionarily relevant model organisms. However, challenges of multi-isoform handling, the presence of incomplete genomes/proteomes initial datasets, and problems of evolutionary history representation are still present. To address these issues, we introduce a novel framework based on the Clusters of Orthologous Groups (COG) method, primarily designed for improving phylogenetic tree clustering in studying evolutionary history of eukaryotes, P-COGs (Pavlov’s COGs). It encourages the use of a single sequence dataset for both constructing phylogenetic trees and inferring COGs. We demonstrate the tool’s utility through an evolutionary study of the voltage-dependent chloride channel genes family (CLCN). Moreover, P-COGs allowed us to observe multiple clusters of orthologous genes in CLCN that were not identified by other COG-based tools. Additionally, we resolved the evolutionary history of hundreds of cancer-associated genes with P-COGs to support accurate evolution-based variant effect prediction. The resulting COG graphs are accessible via our interactive web application ( https://epicenter.1spbgmu.ru/shiny/pavlovscogs/ ). P-COGs is openly available at https://github.com/bugds/Pavlovs_COGs .
Periodontitis (PD) is a complex inflammatory condition driven by the interplay of microbial, genetic, epigenetic, and environmental factors. While bacterial biofilms are regarded as the primary cause, growing evidence underscores the significant role of genetic predisposition in determining susceptibility to the disease, its progression, and treatment outcomes. This review explores the genetic polymorphisms of PD, focusing on genes related to inflammatory mediators, immune responses, antimicrobial peptides, matrix metalloproteinases, and vitamin D receptor pathways. Key epigenetic mechanisms including DNA methylation, histone modifications, non-coding RNAs, and emerging RNA methylation pathways are explored in their roles in modulating inflammation, tissue destruction, bone metabolism, and interactions between the host and microbes. Advances in transcriptomic technologies, particularly RNA sequencing, have enhanced our ability to identify molecular biomarkers and cell-specific gene expression profiles associated with disease severity and responses to treatment. The potential for leveraging genetic and epigenetic profiling presents an exciting avenue for personalized periodontal care, including the use of epigenetic therapies targeting pathways involved in inflammation and tissue regeneration. Nonetheless, the current body of evidence has limitations. These include significant variability across studies, inconsistent disease classification systems, small sample sizes, and a predominance of preclinical or exploratory research. Many biomarkers and therapeutic targets proposed to date require further validation before they can be routinely applied in clinical practice. While integrating genetic, epigenetic, transcriptomic, and clinical data holds promise for advancing precision periodontology, rigorous large-scale, and multicenter studies are essential to confirm clinical applicability, validate biomarkers, and facilitate their incorporation into evidence-based treatment protocols.
The mitogenomics of Pao baileyi (Sontirat 1985), a tropical pufferfish with ornamental and research value, remain unreported. To understand its molecular characteristics and enrich mitogenome data for Tetraodontidae fish, in this study, we focused on the mitogenome of wild P. baileyi. The complete mitogenome sequence was obtained through high-throughput sequencing, and systematic analysis of the structural characteristics of the genome, base composition, and codon usage bias was conducted. A phylogenetic tree was constructed using Monacanthidae species as outgroups to explore the position of P. baileyi within Tetraodontidae. Results showed that the P. baileyi mitogenome is a closed-loop double-stranded DNA molecule with gene composition and arrangement conforming to Tetraodontidae mitogenome characteristics. It contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and 1 control region. The base composition has an AT bias, codon usage exhibits specific preferences, and all tRNA genes have a cloverleaf secondary structure. Phylogenetic analysis revealed that P. baileyi is closely related to other Pao species and forms a distinct evolutionary branch with other genera and species in Tetraodontidae, providing a basis for species classification. This is the first report of the complete mitogenome characteristics of P. baileyi, providing basic data for phylogenetic relationships, germplasm resource conservation, and ornamental breeding research on Tetraodontidae fish.
Septic cardiomyopathy (SCM) is heart failure caused by sepsis and often causes an excessive inflammatory response. As a natural sesquiterpene alcohol, the anti-inflammatory properties of β-Eudesmol have been confirmed in various inflammatory diseases, but its effect on SCM remains unclear. Therefore, this study aimed to investigate the effect of β-Eudesmol on SCM and elucidate its potential mechanisms. An SCM rat model was established by cecal ligation and puncture (CLP) for experimental investigation. The levels of cytokines as well as the indicators of cardiac function injury, BNP and cTnl, were detected by ELSA. Myocardial tissue injury was detected by HE staining and TUNEL staining. The expression of key genes and proteins was detected by RT-qPCR and western blotting. The results show that treatment with β-Eudesmol alleviated myocardial apoptosis and inflammatory injury in SCM rats. Specifically, it significantly reduced serum levels of BNP and cTnI, and decreased the levels of IL-6, IL-1β, TNF-α, and LPS, while also inhibiting inflammatory cell infiltration and apoptosis within the myocardial tissue. Furthermore, we found that β-Eudesmol treatment also reduced serum IL-17 levels in rats and inhibited the expression of IL-17A, CXCL1, CXCL2, and CCL20 mRNA and p-GSK3B/GSK3B. Mechanistic studies revealed that β-Eudesmol enhanced GSK3B activity by inhibiting GSK3B phosphorylation, thereby suppressing the expression of IL-17 and its mediated chemokines, and ultimately alleviating inflammatory injury to the SCM. Overall, β-Eudesmol alleviates SCM myocarditis inflammation by inhibiting IL-17-mediated chemokine expression through enhancing GSK3B activity.
Triple-negative breast cancer (TNBC) is a particularly aggressive subtype of breast cancer, known for its high malignancy, elevated risk of recurrence and metastasis, and limited therapeutic options, resulting in the poorest prognosis among breast cancer types. This study explores the anticancer effects of VALD-3, a Schiff base ligand derivative, on breast cancer cells. While VALD-3 exhibited cytotoxic effects on both triple-negative breast cancer (TNBC) and estrogen receptor-positive (ER+) MCF-7 cells, it more potently inhibited TNBC cell viability. More importantly, VALD-3 induced characteristic pyroptotic features selectively in TNBC cells, including cell swelling, balloon-like protrusions, and the release of inflammatory cytokines due to pore formation in the plasma membrane, ultimately inhibiting tumor growth. Mechanistically, VALD-3 increased reactive oxygen species (ROS) levels and JNK phosphorylation, leading to the recruitment of Bax to the mitochondria and the formation of a Bax-Bcl-2 heterodimer, which facilitated cytochrome c release into the cytoplasm. This cascade activated caspase-3 and triggered gasdermin E(GSDME)- dependent pyroptosis in TNBC cells. Thus, VALD-3 treatment initiated the ROS/JNK/Bax-mitochondrial apoptosis pathway, leading to caspase-3 activation and GSDME cleavage, thereby executing pyroptosis. These findings suggest that GSDME-dependent pyroptosis is a novel mechanism by which VALD-3 eradicates cancer cells and offer new insights into potential clinical applications for anticancer therapies.
To explore the correlation between serum and glucocorticoid inducible kinase-1 (SGK1) expression levels and the multiple myeloma (MM) progression in patients after autologous stem cell transplantation (ASCT). A total of 100 MM patients who received ASCT in the Hematology Department of our hospital during January 2020 to December 2022 were selected as the research subjects. The mRNA level of SGK1 was detected by RT-PCR. Taking the median relative expression level of SGK1 mRNA (2.15) as the critical value, these subjects were divided into SGK1 high expression group (SGK1 mRNA ≥ 2.15, n = 43) and SGK1 low expression group (SGK1 mRNA < 2.15, n = 57). The expression level of SGK1 was detected by IHC. The correlation was analyzed by Spearman correlation coefficient. The survival curve drawn through Kaplan-Meier method was further verified using Log-rank test. Cox proportional hazard regression model was used for multivariate analysis to screen independent risk factors. The receiver’s working characteristic (ROC) curve was drawn to evaluate the predictive value. The H-Score was significantly higher in the SGK1 high expression group (8.52 ± 2.13) than the low expression group (3.27 ± 1.68) (t = 11.240, P < 0.001). After induction therapy, SGK1 high expression group had much lower proportion of achieving complete remission (CR), and markedly higher serum levels of β2-MG and LDH than SGK1 low expression group (P < 0.05). The expression of SGK1 in patients with partial remission (PR) was significantly higher than those with CR and very good partial remission (VGPR) (P < 0.01). Median TTP, median PFS and median OS were significantly lower in SGK1 high expression group than the SGK1 low expression group (Log-rank P < 0.01). Three months after transplantation, the positive rate of Minimal residual disease (MRD) was 48.84
Recurrent pregnancy loss (RPL) is characterized by two or more consecutive pregnancy losses, often associated with genetic, immunological, endocrine, and anatomical abnormalities. Among these, chromosomal abnormalities, including aneuploidies and submicroscopic copy number variations (CNVs), play a critical role in adverse pregnancy outcomes. A total of 125 fetal specimens were collected, of which 118 were included after applying predefined exclusion criteria. DNA isolated from products of conception and fetal tissues was subjected to quantitative fluorescent PCR (QF-PCR) for rapid aneuploidy screening. A subset of 30 samples with selected QF-PCR outcomes underwent array comparative genomic hybridization (aCGH). Identified CNVs were interpreted according to ACMG/ClinGen guidelines, followed by bioinformatics analyses using FunRich, WebGestalt, KEGG, and STRING to explore functional annotations and pathway enrichment. Among 118 samples, QF-PCR identified aneuploidy in 36 cases (30.5
The economic importance of the sea urchin Glyptocidaris crenularis drives the need to elucidate the genetic mechanisms controlling its sex differentiation and development, a key step for enabling targeted genetic improvement. This study presents a chromosome-scale genome assembly for G. crenularis characterized by 22 chromosome-length scaffolds and a total length of 787.45 Mb. The phylogenetic tree revealed that G. crenularis diverged early among sea urchins. Synteny analysis among species suggested that superscaffold 10 might be the sex chromosome. Subsequent transcriptomic profiling further revealed 273 genes (298 transcripts) on chromosome 10 whose expression differed significantly between testis and ovary tissues. The genomic resources established in this study provide a foundation for investigating the population genetics, evolution, and functional mechanisms of this species, while the identified sex chromosomes and candidate genes pave the way for elucidating the molecular basis of sex determination in sea urchins.
