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Quantum computing-assisted validation of a conserved macrophage suppression module shared by ASFV and PEDV. 量子计算辅助验证ASFV和PEDV共享的保守巨噬细胞抑制模块。
IF 2 4区 生物学
Genes & genomics Pub Date : 2026-09-01 Epub Date: 2026-07-28 DOI: 10.1007/s13258-026-01796-2
Jongwon Byun, Hakjin Kim, Changhee Chandler Pyo, Kwang-Eun Choi, Seon-Kyu Kim, Sun-Uk Kim, Taeho Kwon
{"title":"Quantum computing-assisted validation of a conserved macrophage suppression module shared by ASFV and PEDV.","authors":"Jongwon Byun, Hakjin Kim, Changhee Chandler Pyo, Kwang-Eun Choi, Seon-Kyu Kim, Sun-Uk Kim, Taeho Kwon","doi":"10.1007/s13258-026-01796-2","DOIUrl":"10.1007/s13258-026-01796-2","url":null,"abstract":"<p><strong>Background: </strong>African swine fever virus (ASFV) and porcine epidemic diarrhea virus (PEDV) differ in viral biology and cellular tropism, yet both pathogens suppress macrophage-mediated immune responses in pigs.</p><p><strong>Objective: </strong>To identify a conserved macrophage suppression module shared by ASFV and PEDV and evaluate quantum computing as an independent framework for biological network validation.</p><p><strong>Methods: </strong>Integrated analysis of publicly available GEO datasets (GSE231435 for ASFV and GSE306895) identified 471 shared downregulated genes. A network- and multi-omics-informed 20-gene core was selected and encoded as a 20-qubit modularity-based Quadratic Unconstrained Binary Optimization (QUBO) problem. Community detection was benchmarked using the Quantum Approximate Optimization Algorithm (QAOA) on both the IBM Quantum Aer simulator and the 156-qubit IBM Fez (Heron r2) quantum processor and compared with brute-force enumeration and simulated annealing.</p><p><strong>Results: </strong>A conserved macrophage suppression module shared by ASFV and PEDV was identified. For the STRING protein-protein interaction network, QAOA at circuit depth p = 3 reproduced the brute-force optimum with an approximation ratio of 1.000. In contrast, performance progressively declined in the denser co-expression network with increasing circuit depth, consistent with noise accumulation under current Noisy Intermediate-Scale Quantum (NISQ) conditions. Multi-run consensus analysis identified stable hub genes, including MMP9 and SLA-DOA, as well as genes exhibiting variable community assignments.</p><p><strong>Conclusion: </strong>These findings reveal a conserved macrophage suppression module shared between ASFV and PEDV and demonstrate that quantum computing can serve as an independent validation framework for biologically meaningful host-response networks. Network topology emerged as a key determinant of QAOA performance on real NISQ hardware.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1183-1191"},"PeriodicalIF":2.0,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148601946","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}
引用次数: 0
Characterization of a draft chromosome-scale genome assembly for the mutton snapper, Lutjanus analis. 羊鲷染色体尺度基因组组装草图的表征,Lutjanus分析。
IF 2 4区 生物学
Genes & genomics Pub Date : 2026-09-01 Epub Date: 2026-07-22 DOI: 10.1007/s13258-026-01790-8
Lora G Holman, Tami Hildahl, Eric Saillant
{"title":"Characterization of a draft chromosome-scale genome assembly for the mutton snapper, Lutjanus analis.","authors":"Lora G Holman, Tami Hildahl, Eric Saillant","doi":"10.1007/s13258-026-01790-8","DOIUrl":"10.1007/s13258-026-01790-8","url":null,"abstract":"<p><strong>Background: </strong>The mutton snapper (Lutjanus analis) is a reef fish commonly found in tropical waters of the Western Atlantic Ocean. Genomic studies of this species are needed to support conservation efforts and breeding programs.</p><p><strong>Objective: </strong>Here, we report the development of a chromosome-scale reference assembly for the mutton snapper and conduct an initial comparative genomic analysis with other lutjanids.</p><p><strong>Methods: </strong>The genome of one mutton snapper specimen was sequenced using PAC-Bio HiFi long reads and Illumina short reads. Contigs and scaffolds were assembled in the Flye pipeline and anchored using Hi-C proximity guided assembly. Gene prediction and functional annotations were obtained in AUGUSTUS and eggNOG-mapper, respectively. The mutton snapper genome was compared to those of other lutjanids to infer gene family evolution and chromosome synteny conservation.</p><p><strong>Results: </strong>Assembly and polishing yielded 946 contigs and 926 scaffolds (N50 of 3.16 Mb, complete BUSCO score 98.1%) that were anchored using Hi-C scaffolding in 24 draft chromosomes. The anchored assembly featured a N50 of 42.47 Mb and contained 97.6% of the unanchored assembly length. The 24 mutton snapper chromosomes showed a one-to-one syntenic relationship with their counterparts in medaka, and other Lutjanids. AUGUSTUS predicted 29,023 genes, 24,335 of which (83.85%) could be functionally annotated. Gene family evolution analysis revealed 1,014 significantly expanded or contracted hierarchical ortholog groups in mutton snapper. Expansions and contractions were linked to several biological functions including growth, oocyte maturation, and response to exogenous stressors.</p><p><strong>Conclusion: </strong>The draft genome will be a valuable tool for forthcoming applied genomic studies of mutton snapper.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1203-1212"},"PeriodicalIF":2.0,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148548721","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}
引用次数: 0
ONT-only genome assembly of a Korean male individual using a semen sample. 使用精液样本的韩国男性个体的ONT-only基因组组装。
IF 2 4区 生物学
Genes & genomics Pub Date : 2026-09-01 Epub Date: 2026-07-08 DOI: 10.1007/s13258-026-01792-6
Jian Lee, Ji-Hwan Park, Soobok Joe, Jun Kim
{"title":"ONT-only genome assembly of a Korean male individual using a semen sample.","authors":"Jian Lee, Ji-Hwan Park, Soobok Joe, Jun Kim","doi":"10.1007/s13258-026-01792-6","DOIUrl":"10.1007/s13258-026-01792-6","url":null,"abstract":"<p><strong>Background: </strong>Long-read sequencing has enabled the generation of high-quality human genome assemblies, but many previous assemblies were based on blood-derived DNA and often relied on limited data types from a single sequencing strategy.</p><p><strong>Objective: </strong>This study aimed to generate high-quality phased genome assemblies of a Korean individual using multiple independent long-read datasets produced from a single sequencing platform and to evaluate their utility for chromosome-scale assembly and variant detection.</p><p><strong>Methods: </strong>Genomic DNA was extracted from a semen sample of a Korean male. Long-read, ultra-long-read, and chromatin conformation capture sequencing data were generated using Oxford Nanopore Technologies. These datasets were integrated to construct phased genome assemblies, followed by correction of noticeable phasing errors and assessment of assembly continuity, chromosomal representation, telomeric repeat recovery, and variant detection performance.</p><p><strong>Results: </strong>The final phased assemblies spanned approximately 2.9 Gb and represented 23 pairs of chromosomes with an NG50 of 150 Mb. Telomeric repeats were detected at 36 and 37 of the 48 chromosomal ends in the two assemblies, indicating high end-to-end completeness. In addition, we successfully identified structural variants, including small variants. These results demonstrate that combining multiple Oxford Nanopore data types can produce highly continuous and informative phased human genome assemblies.</p><p><strong>Conclusions: </strong>We generated high-quality phased genome assemblies of a Korean individual using Oxford Nanopore long-read sequencing data derived from semen DNA. This publicly available genome resource will support broader applications of long-read sequencing in human genomics and variant analysis.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1193-1202"},"PeriodicalIF":2.0,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148404392","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}
引用次数: 0
GWAS-based identification of a candidate gene and development of a predictive KASP marker for seed protein and oil contents in soybean. 基于gwas的大豆种子蛋白质和油脂含量KASP预测标记候选基因的鉴定与开发。
IF 2 4区 生物学
Genes & genomics Pub Date : 2026-09-01 Epub Date: 2026-07-20 DOI: 10.1007/s13258-026-01795-3
Jeong Woo Lee, Jung Min Kim, Dae June Kim, Bo-Keun Ha, Soon-Jae Kwon
{"title":"GWAS-based identification of a candidate gene and development of a predictive KASP marker for seed protein and oil contents in soybean.","authors":"Jeong Woo Lee, Jung Min Kim, Dae June Kim, Bo-Keun Ha, Soon-Jae Kwon","doi":"10.1007/s13258-026-01795-3","DOIUrl":"10.1007/s13258-026-01795-3","url":null,"abstract":"<p><strong>Background: </strong>Soybean [Glycine max (L.) Merrill] is one of the most widely cultivated crops worldwide. Its seeds contain about 40% protein and 20% oil, serving as essential nutrient sources for humans. Given the nutritional importance of seed protein and oil, identifying genes that regulate their levels is crucial for improving soybean seed quality.</p><p><strong>Objective: </strong>This study aimed to identify genetic factors associated with seed protein and oil content using a genome-wide association study (GWAS).</p><p><strong>Methods: </strong>Seed protein and oil contents were quantified in 192 soybean mutant accessions in a mutant diversity pool (MDP), and GWAS was conducted using 17,631 SNPs filtered from genotyping-by-sequencing. Expression of a candidate gene was examined across seed developmental stages (R5 to R7), and a significant SNP was converted into a Kompetitive Allele-Specific PCR (KASP) marker for validation.</p><p><strong>Results: </strong>GWAS detected significant SNPs associated with seed protein and oil content. Chr20_7635098 was identified as a nonsynonymous SNP located in the exon of Glyma.20g042400. This gene showed differential expression across seed developmental stages between mutant accessions with contrasting protein and oil contents. The KASP marker for Chr20_7635098 was validated using the MDP and six domestic soybean cultivars showing predictive accuracies of ≥ 80.50% for protein content and ≥ 61.18% for oil content.</p><p><strong>Conclusion: </strong>Overall, this study identified a candidate gene linked to both seed protein and oil content, providing valuable insights for molecular breeding strategies aimed at efficiently improving these nutritional traits.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1233-1246"},"PeriodicalIF":2.0,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148520183","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}
引用次数: 0
Transcriptome mining and comparative genomics reveal 36 putative novel marafivirus species and conserved evolution of the marafibox regulatory element. 转录组挖掘和比较基因组学揭示了36个假定的新型马拉菲病毒物种和马拉菲盒调控元件的保守进化。
IF 2 4区 生物学
Genes & genomics Pub Date : 2026-09-01 Epub Date: 2026-07-07 DOI: 10.1007/s13258-026-01789-1
Dongjin Choi, Seungwoo Baek, Myeung Seok Choi, Yoonsoo Hahn
{"title":"Transcriptome mining and comparative genomics reveal 36 putative novel marafivirus species and conserved evolution of the marafibox regulatory element.","authors":"Dongjin Choi, Seungwoo Baek, Myeung Seok Choi, Yoonsoo Hahn","doi":"10.1007/s13258-026-01789-1","DOIUrl":"10.1007/s13258-026-01789-1","url":null,"abstract":"<p><strong>Background: </strong>Marafiviruses are plant-infecting RNA viruses associated with several economically important crops, but their genomic diversity remains incompletely characterized.</p><p><strong>Objective: </strong>This study aimed to identify previously unrecognized marafivirus genomes and investigate their genomic features and evolutionary relationships.</p><p><strong>Methods: </strong>Publicly available plant transcriptome datasets were systematically mined to detect marafivirus-like sequences. Recovered genomes were analyzed using comparative sequence analysis, phylogenetic reconstruction, and genome organization characterization.</p><p><strong>Results: </strong>A total of 62 marafivirus-like genomes were recovered from 33 independent sources representing diverse plant hosts. Polyprotein-based comparative and phylogenetic analyses grouped these genomes into 36 lineages likely representing novel species. All newly identified viruses clustered within the Marafivirus clade. Genome organization analysis revealed conserved polyprotein architecture and widespread presence of the marafibox promoter element. Conservation of additional open reading frames among closely related isolates aided identification of potentially functional genes.</p><p><strong>Conclusion: </strong>These findings substantially expand the known diversity of marafiviruses and demonstrate the effectiveness of transcriptome mining for discovering previously unrecognized plant viruses.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1213-1222"},"PeriodicalIF":2.0,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148396484","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}
引用次数: 0
Baicalein alleviates high glucose-induced mesangial cell fibrosis and inflammation in diabetic nephropathy: roles of AMPK activation and TGF-β1 inhibition. 黄芩素缓解高糖诱导的糖尿病肾病肾系膜细胞纤维化和炎症:AMPK活化和TGF-β1抑制的作用
IF 2 4区 生物学
Genes & genomics Pub Date : 2026-08-01 Epub Date: 2026-07-01 DOI: 10.1007/s13258-026-01774-8
Hongtao Tan, Yingshan Li, Yicong Li, Junxian Chen, Weiwei Yuan
{"title":"Baicalein alleviates high glucose-induced mesangial cell fibrosis and inflammation in diabetic nephropathy: roles of AMPK activation and TGF-β1 inhibition.","authors":"Hongtao Tan, Yingshan Li, Yicong Li, Junxian Chen, Weiwei Yuan","doi":"10.1007/s13258-026-01774-8","DOIUrl":"10.1007/s13258-026-01774-8","url":null,"abstract":"<p><strong>Background: </strong>Diabetic nephropathy (DN), a major diabetic microvascular complication, is the primary cause of end-stage renal disease worldwide. It is characterized by mesangial cell fibrosis and chronic inflammation, which current treatments cannot completely reverse. Baicalein, a major flavonoid from Scutellaria baicalensis Georgi, has anti-inflammatory and antifibrotic activities, but its role and mechanism in high glucose (HG)-induced mesangial cell injury (a key DN feature) remain unclear.</p><p><strong>Objective: </strong>This study investigated baicalein's effects on rat glomerular mesangial cells (HBZY-1) and validated key findings in human primary glomerular mesangial cells.</p><p><strong>Methods: </strong>CCK-8 assay identified 10-20 μM as baicalein's non-cytotoxic range (cell viability ≥ 90%).</p><p><strong>Results: </strong>Further experiments demonstrated that baicalein dose-dependently inhibited HG-induced increases in fibrotic markers (α-SMA, FN, COL1A1) at both mRNA (qRT-PCR) and protein levels (Western blot, immunofluorescence), and reduced proinflammatory cytokines (IL-6, TNF-α, MCP-1) at transcriptional (qRT-PCR) and secretory levels (ELISA). Western blot analysis demonstrated that baicalein dose-dependently activated the AMPK pathway by increasing p-AMPK/AMPK at Thr172 and inhibited the TGF-β/Smad pathway by reducing TGF-β1 and p-Smad2/3/Smad2/3. Using the AMPK inhibitor Compound C, we confirmed baicalein's anti-fibrotic, anti-inflammatory, and TGF-β/Smad-inhibitory effects were closely associated with AMPK activity. Molecular docking showed baicalein stably bound the AMPK β-subunit's C-terminal domain (PDB ID: 4EAK), suggesting a potential interaction that may contribute to AMPK activation.</p><p><strong>Conclusion: </strong>Baicalein protects against HG-induced mesangial cell injury via an AMPK-associated mechanism linked to the suppression of fibrosis and inflammation, highlighting it as a promising DN therapeutic candidate for further preclinical and clinical study.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1145-1161"},"PeriodicalIF":2.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148360335","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}
引用次数: 0
MiR-125a C > T, MiR-152 C > T, MiR-938 G > A, and MiR-491 G > A single nucleotide polymorphisms and their influence on genetic susceptibility to type 2 diabetes. MiR-125a C > T、MiR-152 C > T、MiR-938 G > A和MiR-491 G > A单核苷酸多态性及其对2型糖尿病遗传易感性的影响
IF 2 4区 生物学
Genes & genomics Pub Date : 2026-08-01 Epub Date: 2026-06-10 DOI: 10.1007/s13258-026-01781-9
Sang A Choi, Seung-Ho Hong
{"title":"MiR-125a C > T, MiR-152 C > T, MiR-938 G > A, and MiR-491 G > A single nucleotide polymorphisms and their influence on genetic susceptibility to type 2 diabetes.","authors":"Sang A Choi, Seung-Ho Hong","doi":"10.1007/s13258-026-01781-9","DOIUrl":"10.1007/s13258-026-01781-9","url":null,"abstract":"<p><strong>Background: </strong>Diabetes mellitus (DM) is a chronic metabolic disorder that carries the risk of severe complications, such as cardiovascular disease, renal impairment, and an increased susceptibility to Alzheimer's disease. Considering these significant health implications, it is crucial to deepen our understanding of this condition. MicroRNAs (miRNAs), small non-coding RNAs that regulate gene expression, play a critical role in various biological processes and, when dysregulated, can contribute to the development of diseases such as diabetes mellitus.</p><p><strong>Objective: </strong>This study aimed to investigate the association between type 2 diabetes mellitus (T2DM) and specific miRNA polymorphisms (miR-125a C > T, miR-152 C > T, miR-938 G > A, and miR-491 G > A) in a Korean population.</p><p><strong>Methods: </strong>We examined the distribution of miRNA polymorphisms through genotyping in 238 T2DM patients and 343 healthy controls using polymerase chain reaction-restriction fragment length polymorphism technique.</p><p><strong>Results: </strong>Our findings indicate that the miR-938 GA genotype and its dominant model were significantly associated with an elevated risk of T2DM. Moreover, specific combinations of genetic variations were linked to either an increased or decreased risk of developing T2DM.</p><p><strong>Conclusions: </strong>These results suggest that miRNA polymorphisms may influence an individual's genetic susceptibility to T2DM and offer potential therapeutic targets and diagnostic tools.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1067-1075"},"PeriodicalIF":2.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148210797","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}
引用次数: 0
Correction to: Cochlear synaptic vulnerability scales with pathological noise intensity in a noise-induced hearing loss model. 校正:噪音性听力损失模型中带有病理性噪音强度的耳蜗突触易感性量表。
IF 2 4区 生物学
Genes & genomics Pub Date : 2026-08-01 DOI: 10.1007/s13258-026-01770-y
Byeonghyeon Lee, Tae-Jun Kwon, Hyun Tae Kim, Un-Kyung Kim
{"title":"Correction to: Cochlear synaptic vulnerability scales with pathological noise intensity in a noise-induced hearing loss model.","authors":"Byeonghyeon Lee, Tae-Jun Kwon, Hyun Tae Kim, Un-Kyung Kim","doi":"10.1007/s13258-026-01770-y","DOIUrl":"10.1007/s13258-026-01770-y","url":null,"abstract":"","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1163-1171"},"PeriodicalIF":2.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13476301/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148257872","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}
引用次数: 0
Chloroplast genome characterization of Adenophora taquetii and comparative analysis with related Adenophora species. 龙舌兰叶绿体基因组特征及其与近缘种的比较分析。
IF 2 4区 生物学
Genes & genomics Pub Date : 2026-08-01 Epub Date: 2026-06-15 DOI: 10.1007/s13258-026-01783-7
Song-I Han, Sheikh Mansoor, Jiwon Kim, Nur Azizah Arryanie Binti Morshidi, Jae-Hoon Kim, Kyung-Hwan Boo
{"title":"Chloroplast genome characterization of Adenophora taquetii and comparative analysis with related Adenophora species.","authors":"Song-I Han, Sheikh Mansoor, Jiwon Kim, Nur Azizah Arryanie Binti Morshidi, Jae-Hoon Kim, Kyung-Hwan Boo","doi":"10.1007/s13258-026-01783-7","DOIUrl":"10.1007/s13258-026-01783-7","url":null,"abstract":"<p><strong>Background: </strong>Adenophora taquetii is an endemic species of Jeju Island, Republic of Korea, and has medicinal and ornamental value. However, genomic resources for this species, particularly the chloroplast genome data, remain limited.</p><p><strong>Objective: </strong>We sequenced, assembled, and characterized the complete chloroplast genome of A. taquetii and compared it with those of other Adenophora species.</p><p><strong>Methods: </strong>Whole-genome sequencing data were generated using an Illumina HiSeq platform. Raw reads were preprocessed using Trimmomatic, mapped with BWA-MEM, and used for chloroplast genome assembly with NOVOPlasty, Fast-Plast, and GetOrganelle. Genome annotation was performed using GeSeq, comparative analysis was conducted using mVISTA in LAGAN mode, simple sequence repeats (SSRs) were identified using MISA, single-nucleotide polymorphism (SNP) matrices were generated using SAMtools, and phylogenetic analysis was performed using maximum likelihood and Bayesian inference based on aligned complete chloroplast genome sequences.</p><p><strong>Results: </strong>The chloroplast genome of A. taquetii was 161,772 bp long and exhibited the typical quadripartite structure of angiosperm chloroplast genomes, comprising a large single-copy (LSC) region (113,770 bp), a small single-copy (SSC) region (27,738 bp), and two inverted repeat (IR) regions (10,132 bp each). Comparative analysis revealed substantial variation in chloroplast genome size among related species, ranging from 157,851 bp in A. stricta to 218,673 bp in A. verticillata. In total, 143 genes were annotated in A. taquetii, including 96 protein-coding, 38 tRNA, and 9 rRNA genes. In addition, 25 SSRs and 1,161 SNPs were identified, and phylogenetic analysis supported a close relationship between A. taquetii and A. stricta.</p><p><strong>Conclusion: </strong>The complete chloroplast genome of A. taquetii provides a useful genomic resource for comparative chloroplast genomics, species identification, and phylogenetic studies within the genus Adenophora.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1077-1086"},"PeriodicalIF":2.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148251269","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}
引用次数: 0
DKK1 activated the NF-κB pathway by binding with CKAP4 to induce PASMC oxidative stress and promote pulmonary arterial hypertension. DKK1通过与CKAP4结合激活NF-κB通路,诱导PASMC氧化应激,促进肺动脉高压。
IF 2 4区 生物学
Genes & genomics Pub Date : 2026-08-01 Epub Date: 2026-06-22 DOI: 10.1007/s13258-026-01773-9
Shaojin Wang, Xiuyan Wang, Lili Miao, Yating Zhang, Peng Zhang
{"title":"DKK1 activated the NF-κB pathway by binding with CKAP4 to induce PASMC oxidative stress and promote pulmonary arterial hypertension.","authors":"Shaojin Wang, Xiuyan Wang, Lili Miao, Yating Zhang, Peng Zhang","doi":"10.1007/s13258-026-01773-9","DOIUrl":"10.1007/s13258-026-01773-9","url":null,"abstract":"<p><strong>Background: </strong>Pulmonary arterial hypertension (PAH) is a hemodynamic disorder that can progress to right heart failure and result in death.</p><p><strong>Objective: </strong>This study investigated the molecular mechanisms underlying the onset and progression of PAH to identify potential therapeutic targets.</p><p><strong>Methods: </strong>Peripheral blood samples from PAH patients were analyzed to assess serum levels of DKK1 and CKAP4, as well as NF-κB pathway activation. Supernatants from hypoxia-treated pulmonary artery endothelial cells (PAECs), plasmid-transfected cells, and SC75741-treated cells were used to modulate pulmonary artery smooth muscle cells (PASMCs). RT-qPCR, Western blot, and ELISA were employed to quantify DKK1 and CKAP4 expression and evaluate NF-κB pathway activation in PASMCs. EdU staining and CCK-8 viability assay were performed to assess cell proliferation, while DCFH-DA staining and ELISA were used to measure ROS, SOD, and MDA levels.</p><p><strong>Results: </strong>DKK1 and CKAP4 expression were positively correlated, and both were upregulated with increasing pulmonary artery systolic pressure (PASP) in PAH patients. The supernatant from hypoxia-exposed PAECs induced NF-κB pathway activation, cell proliferation, and oxidative stress in PASMCs, effects that were inhibited by siDKK1, siCKAP4, and SC75741.</p><p><strong>Conclusions: </strong>Hypoxia stimulated PAECs to secrete DKK1, which in turn upregulated CKAP4 expression and activated the NF-κB pathway in PASMCs, promoting cell proliferation and oxidative stress.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1117-1130"},"PeriodicalIF":2.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148294661","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}
引用次数: 0
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