Biochemical Genetics最新文献

{"title":"Splicing Alterations Associated with Multiple Homozygous TNXB Variants in a Patient with Suspected Classical-Like Ehlers-Danlos Syndrome.","authors":"Bunta Imanaka, Yuiko Hasegawa, Kazumi Kawato, Yuma Kimoto, Itsuki Oda, Nobuhiko Okamoto, Kazumasa Saigoh, Mina Nakama","doi":"10.1007/s10528-026-11416-z","DOIUrl":"https://doi.org/10.1007/s10528-026-11416-z","url":null,"abstract":"<p><p>Ehlers-Danlos syndrome (EDS) comprises a heterogeneous group of heritable connective tissue disorders characterized by joint hypermobility, skin hyperextensibility, and tissue fragility. Classical-like EDS (clEDS) is typically associated with pathogenic biallelic variants in TNXB. The patient showed generalized joint hypermobility involving the knees, fingers, elbows, and feet, along with soft, pliable skin. She had a history of three dislocations of the right elbow and one dislocation of the left elbow. She also reported orthostatic dizziness and chronic constipation, suggesting possible autonomic nervous system involvement. Cardiovascular assessment detected mild mitral valve regurgitation. Based on these findings, hypermobility syndrome or EDS was suspected, and gene panel testing was conducted for classical and pseudo-classical EDS. The patient was found to be homozygous for multiple TNXB (NM_001365276.2) variants, including c.11,925 + 6 C > G, c.12,156 C > G (p. Arg4052=), c.12,210 + 5G > A, c.12,210 + 39dup, and c.12,210 + 43T > G, and also carried a mosaic variant c.8012 C > T (p. Ala2671Val). To investigate the potential effects of these variants on splicing, RT-PCR using peripheral blood RNA and in vitro minigene splicing assays were performed. Analysis of the patient-derived cDNA and cDNA derived from mutant minigenes revealed alternative splicing leading to intron 40 retention alongside the normal transcript. Intron 40 retention was more pronounced with multiple variants and was most prominently associated with c.12,210 + 5G > A in the minigene assays. These results suggest that c.12,210 + 5G > A can influence TNXB splicing, generating in-frame transcripts. The aberrant transcripts are predicted to affect the fibrinogen C-terminal domain. Although the clinical significance of these variants remains uncertain, these findings highlight the importance of integrating population frequency data, clinical assessment, and functional analyses when interpreting uncertain TNXB variants in patients with suspected clEDS.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2026-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148248735","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":"Lactate as a Signaling Molecule in the Tumor Microenvironment: Implications for Cancer Progression","authors":"Shireen S. Kamil,&nbsp;Alaa Shahid Jassim Al-Bdery,&nbsp;Ali H. Al-Marzoqi,&nbsp;Hussein T. Abdulabbas,&nbsp;Ameer Jaber Shakir","doi":"10.1007/s10528-026-11402-5","DOIUrl":"10.1007/s10528-026-11402-5","url":null,"abstract":"<div><p>Aerobic glycolysis is a process commonly utilized by tumor cells to produce excessive lactate, acidification of the extracellular milieu and promoting tumor progression. Lactate plays its roles as a metabolic intermediate and as a signaling molecule in the tumor microenvironment (TME). In this literature review, we first describe how cancer cells alter their metabolism, focusing on the Warburg effect, LDHA-mediated lactate catalysis, and MCT1/4’s role in its removal. Next, we explain GPR81-mediated signal transduction and inhibition of HIF-1α and NF-κB degradation, which connects metabolism to oncogenic signaling pathways. We discuss lactate-driven histone lactylation as an epigenetic process that enhances gene expression for growth, angiogenesis, and immune evasion. We also examine lactate effects on Immune cells by inhibition of CD8 + T and NK cells, macrophage polarization toward the M2 phenotype, and inhibition of dendritic cell (DC) maturation. Lactate shuttling between cancer-associated fibroblasts and tumor cells promotes metabolic symbiosis and therapy resistance. Lastly, this review examines treatment options targeting LDH and MCTs, either on their own or in combination with immunotherapy. We also discuss challenges including compensatory pathway activation and off-target effects. Understanding the mechanisms of lactate ‘s effects on the TME facilitates the development of more effective metabolic and immunometabolic cancer treatments. From a clinical perspective, targeting lactate metabolism through LDHA inhibitors and MCT blockers, alone or combined with immune checkpoint inhibitors, represents a promising strategy to recondition the immunosuppressive TME and improve therapeutic outcomes. However, metabolic plasticity, pathway redundancy, and insufficient tumor selectivity remain significant translational challenges that warrant further investigation.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":"64 5","pages":"6319 - 6351"},"PeriodicalIF":1.9,"publicationDate":"2026-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148196844","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":"Protective Role of Erzhi Pills in H₂O₂-Induced Oxidative Stress, Inflammation, and Angiogenesis in ARPE-19 Cells.","authors":"Yinyin Ding, Yue Dong, Wei Wei","doi":"10.1007/s10528-025-11214-z","DOIUrl":"10.1007/s10528-025-11214-z","url":null,"abstract":"<p><p>This research was purposed to explore the role and mechanism of Erzhi pills (EZP) in age-related macular degeneration (AMD). TCSMP, PubChem, SwissTargetPrediction, and TargetNet databases were utilized to identify the active ingredients and targets of EZP, while disease targets were obtained from the DISEASES and DisGeNET databases. All identified targets were standardized using the UniProt platform. Overlapping targets between the drug and disease were determined using the Jvenn tool, and these targets were subsequently imported into the STRING database for network analysis. Enrichment analyses were conducted using the gProfiler web tool. The hub gene network was constructed utilizing Cytoscape software. Molecular docking studies were performed to assess the interactions between key components and their respective targets. A total of 16 active ingredients and 310 targets of EZP were identified, with 46 targets overlapping with disease-related targets, which implicated pathways involving inflammatory response, angiogenesis, and HIF-1α signaling. The top five hub genes identified were KDR, STAT3, mTOR, ESR1, and HIF1A. In vitro experiments, the CCK-8 assay, DCFH-DA staining, ELISA, tube formation assay, RT-qPCR, and Western blot analysis were conducted to evaluate the cellular biological behaviors and protein expression levels. The results showed that EZP could reduce H₂O₂-induced ROS accumulation, proinflammatory cytokine release, and promote angiogenesis. EZP inactivated HIF-1α pathway. EZP might target HIF-1α pathway to suppress oxidative stress, inflammation, and angiogenesis in H₂O₂-exposed ARPE-19 cells.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"4538-4555"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13186814/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144797809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the Integrated Gut-Brain Metabolic Model for ADHD.","authors":"Ezgi Tas, Kutlu O Ulgen","doi":"10.1007/s10528-025-11234-9","DOIUrl":"10.1007/s10528-025-11234-9","url":null,"abstract":"<p><p>Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental condition marked by hyperactivity, impulsivity, and inattentiveness that are disproportionate to the patient's developmental stage. Individuals with ADHD often experience gastrointestinal (GI) issues, indicating a potential link with the gut microbiome. This study aims to explore how various parameters influence the production and consumption of metabolites in the brain by developing an integrated gut-brain metabolic model, examining the impact of gut microbiota-derived metabolites on the human brain. Genome-scale metabolic models (GEMs), which consider gene-protein-reaction relationships, are utilized to simulate metabolic processes in gut microorganisms. A comprehensive genome-scale metabolic model of the human brain, comprising 812 metabolites, 994 reactions, 671 genes, and 71 metabolic pathways, serves as the healthy brain reference. To mimic an ADHD brain, the gene NOS1 is removed from the healthy model. An integrated gut-brain model is created using a three-compartment approach (gut, blood, and brain). This modeling technique, which accounts for microbial genome-environment interactions and their metabolite interactions with other human organs, helps identify the GI mechanisms underlying ADHD toward enhancing the quality of life for affected individuals. Moreover, understanding the relationship between ADHD, age, gender, and diet can help in developing more effective, personalized approaches to managing ADHD.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"4091-4129"},"PeriodicalIF":1.6,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938240","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":"Cuproptosis-Related Gene FDX1 Induces Malignant Progression and Immune Suppression in Triple-Negative Breast Cancer.","authors":"Haohang Sun, Qi Chen, Xiwei Zhang, Mengze Chen, Ji Dai, Meidi Yan","doi":"10.1007/s10528-025-11242-9","DOIUrl":"10.1007/s10528-025-11242-9","url":null,"abstract":"<p><p>Triple-negative breast cancer (TNBC), a particularly aggressive cancer, significantly menaces women's health. Recently, a novel form of cell death known as cuproptosis has been identified, with the key gene FDX1 emerging as a potential oncogenic factor. We analyzed the heterogeneity of breast cancer (BC) epithelial cells using available single-cell RNA sequencing (scRNA-seq) datasets. We developed knockdown cell lines in vitro and verified the knockdown efficiency with qPCR. The malignant phenotypes of the cells were assessed through cell counting kit-8, colony formation, Transwell, and scratch healing assays. We also co-cultured the cells with CD8⁺ T cells and evaluated their activation using Transwell, CFSE, lactate dehydrogenase release assay, and enzyme-linked immunosorbent assay. IHC analysis was conducted to reveal the impact of FDX1 on tumor growth in mice. Based on scRNA-seq data, we discovered that in TNBC, epithelial cells were more abundant, and T-cell infiltration was less frequent compared to other subtypes of BC. FDX1 + epithelial cells, which are associated with cuproptosis, were highly enriched in TNBC. The expression of FDX1, a key gene in cuproptosis, upregulated in these cells. This upregulation is essential for sustaining the growth, invasion, and migration of TNBC cells. Co-culture experiments revealed that FDX1 expression could modulate the activation and cytotoxicity of T cells. Tumor growth in mice was largely curbed by the knockdown of FDX1 expression. In TNBC, FDX1 expression aids in the survival and proliferation of cancer cells while dampening the immune response of CD8⁺ T cells.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"4173-4195"},"PeriodicalIF":1.6,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144999356","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":"Exploring Differentially Expressed Genes and Understanding the Underlying Mechanisms in Glioblastoma.","authors":"Didem Seven, Arif Ekici, Steffen Uebe, Bilge Bilgiç, Altay Sencer, Aydın Aydoseli, Andre Reis, Nur Buyru","doi":"10.1007/s10528-025-11241-w","DOIUrl":"10.1007/s10528-025-11241-w","url":null,"abstract":"<p><p>Glioblastoma is the most aggressive and malignant tumor of the central nervous system. Current treatment options, including surgical excision, radiotherapy, and chemotherapy, have Limited efficacy, with a median survival rate of approximately 15 months. To develop novel therapeutics, it is crucial to understand the underlying molecular mechanisms driving glioblastoma. However, obtaining healthy tissue counterparts for comparison is often challenging due to the critical nature of the tissues and the tumor's location. This study aimed to compare the transcriptomic profiles of glioblastoma tissues with those of adjacent healthy tissues, to elucidate key pathways and identify upstream regulators involved in glioblastoma pathogenesis. Twenty-six pairs of glioblastoma tissues and their adjacent healthy tissues were obtained during surgery. The tumor and healthy origins were confirmed through histopathological examination. Twelve pairs were analyzed via transcriptome analysis by using the Ion GeneStudio S5 system. Ingenuity pathway analysis was performed to identify the associated pathways and upstream regulators. Selected 51 upstream regulators were analyzed using qRT-PCR. Three pairs were excluded from the RNA-sequencing (RNA-seq) analysis due to similarities between normal and tumor tissues. The dysregulated pathways were primarily associated with neuronal connections and neurotransmitter pathways. The expression patterns of upstream regulators were consistent with RNA-seq results. Molecular changes linked to the initiation of tumors can begin at an early stage, potentially preceding the appearance of clinical symptoms. The dysregulated pathways were particularly associated with specific brain tissue types. The expression of upstream regulators was consistent across both methods; however, their functional roles need further investigation.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"4232-4252"},"PeriodicalIF":1.6,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032543","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":"HTSNPedia: A Molecular Perspective and Risk Estimator Database for Hypertension-Associated Genes.","authors":"Jeyanthi Sankar, Agnal Arumugam, A Antony Prakash, Ling Shing Wong, Karthikeyan Muthusamy","doi":"10.1007/s10528-025-11232-x","DOIUrl":"10.1007/s10528-025-11232-x","url":null,"abstract":"<p><p>Hypertension is a major public health concern, affecting more than one billion adults worldwide. The etiology of hypertension is associated with various genetic and epigenetic interactions. The candidate genes from various signaling pathways, such as RAAS, KKS and endothelin system, play a significant role in the progression of hypertension. The research aimed to develop a comprehensive knowledge base pertaining to hypertension, which would facilitate the integration of information related to SNPs associated with hypertension, pertinent biological pathways, risk assessment factors, molecular mechanisms, pharmacogenomic aspects of hypertension, a blood pressure calculator, and the existing literature on hypertension. This database has been implemented using HTML and Java programming languages. The deployment of the HTSNPedia database is expected to enhance the efficiency of identifying novel pharmacological drug candidates for the treatment of hypertension. A comprehensive understanding of the interrelationships among signaling pathways, molecular mechanisms, and risk-associated SNPs related to hypertension may significantly contribute to advancements in human health, particularly for individuals affected by this condition. The HTSNPedia is an openly accessible database, available at the following URL: https://www.generisk.in/HTSNPedia/main.html.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"4585-4597"},"PeriodicalIF":1.6,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938243","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":"Influence of Genotypes and Contrasting Production Environments on Curcuminoids and its Stability in Turmeric (Curcuma longa L.).","authors":"Raghuveer Silaru, Aarthi Sounderarajan, Yuvaraj Kotha Madduri, Prasath Duraisamy","doi":"10.1007/s10528-025-11239-4","DOIUrl":"10.1007/s10528-025-11239-4","url":null,"abstract":"<p><p>Understanding the genotype × environment interaction (GEI) on the performance and stability of curcuminoids among turmeric genotypes across production environments is essential for selecting suitable genotypes for different production environments. In the present investigation, 21 turmeric genotypes of various geographical locations in India were assessed for curcuminoids (CUR-curcumin, DMC-demethoxycurcumin, and BDMC-bis demethoxycurcumin) under three environmental conditions viz, green house, vertical structures and open field. The analysis of variance indicated significant GEI effects on curcuminoids, underscoring the importance of GEI on genotype performance. In vertical structures, IISR Pragati and Waigon Turmeric were found to be superior for all three curcuminoids. In greenhouse conditions, CIM Pitambar, CO 3, and Acc. 1545 were superior for BDMC, while CIM Pitambar, IISR Prathiba, and IISR Pragati excelled for DMC, and Acc. 1545 for CUR. Under field conditions, Waigon Turmeric recorded higher BDMC and DMC, while Roma, Acc. 1545, and IISR Prathiba had the highest CUR. Our findings revealed that the curcuminoids relative ratio among the genotypes, which grouped into four patterns, was primarily influenced by genotype rather than environment. The promising genotypes for curcuminoids across the production environments were Waigon Turmeric, Rajendra Sonali, Roma, IISR Prathiba, Acc. 1545, NDH 8, IISR Pragati, and CIM Pitambar. Additionally, IISR Pragati for BDMC, Acc. 69/22/5/I3 for DMC, and Rajendra Sonali for CUR exhibited both superior performance and greater stability compared to other genotypes. In the present study, Field conditions, followed by greenhouse conditions, were found to be the best for all three curcuminoid across three production environments. These findings are crucial for extraction industries and farmers to choose the best genotypes and suitable production environments for targeted production of higher curcuminoids in turmeric.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"4147-4172"},"PeriodicalIF":1.6,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937836","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":"Upregulation of Hsa_circ_0077007 Expression is Used for Prognosis and Targeted Therapy of Colorectal Cancer.","authors":"Xiaoyan Zhang, Junjie Lu","doi":"10.1007/s10528-025-11244-7","DOIUrl":"10.1007/s10528-025-11244-7","url":null,"abstract":"<p><p>To evaluate the expression of hsa_circ_0077007 in the serum of colorectal cancer (CRC) patients and offer a foundational theory for the prognosis of CRC. The present study focuses on investigating the biological function and therapeutic target of hsa_circ_0077007 in colorectal cancer CRC. Retrieve the GEO database and use the GEO2R tool to analyze the GSE dataset (GSE223001 and GSE159669) to obtain aberrantly expressed circRNAs. Serum hsa_circ_0077007 expression was measured by qRT-PCR in 107 CRC patients. Kaplan-Meier curve was used to analyze the repercussions of hsa_circ_0077007 expression on overall survival and prognosis. After the knockout of hsa_circ_0077007, the biological cellular functions of CRC were characterized. Finally, the downstream molecular expression mechanism of hsa_circ_0077007 was further explored. Hsa_circ_0077007 was among the abnormal circRNAs in GSE223001 and GSE159669. Compared to normal controls, CRC patients exhibited elevated levels of hsa_circ_0077007 expression in their serum. Additionally, the expression levels of hsa_circ_0077007 were significantly increased across four distinct CRC cellular lines, especially SW620 and LoVo cellular lines. Furthermore, high levels of hsa_circ_0077007 expression were associated with a reduced overall survival rate. In vitro, loss-of-function assays for hsa_circ_0077007 resulted in a marked reduction in cell proliferation, invasion, and migration, accompanied by a boost in cell apoptosis. Hsa_circ_0077007 can sponge miR-383-5p, and then inhibit the expression of miR-383-5p. High expression of hsa_circ_0077007 is indicative of shorter survival rates among CRC patients. The hsa_circ_0077007 has been demonstrated to enhance cellular proliferation, invasion, and migration, while concurrently inhibiting apoptosis.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"4217-4231"},"PeriodicalIF":1.6,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022538","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":"Unraveling the Chloroplast Genome of Stellaria media: Comprehensive Analysis, Taxonomic Implications, and Evolutionary Perspectives.","authors":"Suhas K Kadam, Asif S Tamboli, Jin-Suk Youn, Jae Hong Pak, Yeon-Sik Choo","doi":"10.1007/s10528-025-11229-6","DOIUrl":"10.1007/s10528-025-11229-6","url":null,"abstract":"<p><p>The chloroplast (Cp) genome offers valuable perceptions into plant evolution, systematics, and phylogenetics. Here we are reporting complete chloroplast genome of Stellaria media (L.) Vill. collected from Dokdo Island, South Korea. The genome, assembled at 6340 × coverage, is 147,329 bp with a typical quadripartite structure, covering two inverted repeat (IR) regions of 25,600 bp and one single copy of large (79,366 bp) and small region (16,763 bp) each. Genome annotation identified 129 genes, including 84 protein-coding genes, 8 rRNA and 37 tRNA genes. In the IR region, ycf3 and clpP1 each contain two introns, while 17 genes, including rpl2, trnL-CAA, ycf2, and ndhB are present in duplicate, whereas rps19 is present as a single copy, reflecting structural conservation and evolutionary mechanisms such as intron retention and gene duplication. Comparative genomic analysis revealed substantial variations both among Stellaria species and in the formerly classified Stellaria dichotoma var. lanceolata. Codon usage showed a biasness toward codons ending with A/U, with leucine being most frequently encoded amino acid. Phylogenetic reconstruction based on complete chloroplast genomes positioned S. media within the Alsineae tribe and highlighted monophyletic relationships in the genus. Sliding window analysis identified hypervariable regions, including ycf1, ndhF-rpl32, and trnK-rps16 as potential molecular markers. This study provides crucial perceptions into chloroplast genome evolution, comparative genomics, and phylogeny within Caryophyllaceae, contributing essential data for taxonomic and conservation research. Additionally, multiple lines of evidence, including comparative chloroplast genomics, analyses of long and short repeat sequences, codon usage patterns, and phylogenetic relationships, support the taxonomic revision of inclusion of the genus Myosoton within Stellaria, and the exclusion of Stellaria dichotoma var. lanceolata from the genus Stellaria.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"4556-4584"},"PeriodicalIF":1.6,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870780","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}