Genes最新文献

{"title":"Genome-Wide Identification of the <i>LEA</i> Gene Family in <i>Myricaria laxiflora</i> and Its Responses to Abiotic Stress.","authors":"Di Wu, Tonghua Zhang, Linbao Li, Haibo Zhang, Yang Su, Jinhua Wu, Junchen Wang, Chunlong Li, Guiyun Huang","doi":"10.3390/genes16070763","DOIUrl":"10.3390/genes16070763","url":null,"abstract":"<p><strong>Background: </strong>The <i>late embryogenesis abundant</i> (<i>LEA</i>) gene family plays a critical role in abiotic stress tolerance during plant growth and development. Myricaria laxiflora, as a key pioneer species in the extreme hydrological fluctuation zone of the Yangtze River, has evolved unique adaptation mechanisms potentially linked to gene family evolution. However, the molecular mechanisms underlying how the <i>LEA</i> gene family responds to alternating flooding-drought cycles remain unclear.</p><p><strong>Methods and results: </strong>In this study, we identified 31 <i>LEA</i> genes through whole-genome and transcriptome analyses using bioinformatics approaches, and classified them into nine subfamilies based on protein sequence similarity. These genes were distributed across 12 chromosomes. Our analysis revealed that <i>LEA</i> promoters contain cis-acting elements associated with anaerobic induction, abscisic acid (ABA) response, and combined low-temperature/light stress, suggesting their role in a multi-tiered environmental signal integration network. Spatio-temporal expression profiling further indicated that root-specific <i>LEA</i> genes maintain cellular integrity via membrane lipid binding, while leaf-predominant members cooperate with the antioxidant system to mitigate photoinhibition damage.</p><p><strong>Conclusions: </strong>This study elucidates the dynamic regulatory mechanisms of the <i>LEA</i> gene family during flooding-drought adaptation in <i>M. laxiflora</i>, providing molecular targets for ecological restoration in the Yangtze River Basin.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12294544/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic Analysis of Diabetic Erectile Dysfunction Rats After Red Blood Cell Exosome Treatment.","authors":"Yantong Lv, Biaohu Quan, Xinyue Liu, Qichao Cui, Xi-Jun Yin","doi":"10.3390/genes16070768","DOIUrl":"10.3390/genes16070768","url":null,"abstract":"<p><strong>Background: </strong>As the prevalence of diabetes continues to rise each year, increasing attention is focused on its complications, including erectile dysfunction (ED). However, effective therapeutic agents for diabetes mellitus erectile dysfunction (DMED) are often inadequate. Exosomes, which are extracellular vesicles containing proteins and microRNAs, demonstrated remarkable capabilities in modulating pathophysiological processes related to tissue repair, anti-inflammatory responses, and immune regulation.</p><p><strong>Methods: </strong>Transcriptomic analysis was conducted to investigate gene alterations and associated pathways in the penile smooth muscle of DMED rats, both before and after exosome treatment. And the genes (<i>Rxra</i>, <i>PPAR-γ</i>, and <i>CPt1a</i>) related to the PPAR pathway were verified through qRT-PCR.</p><p><strong>Results: </strong>Results show that 13,947 genes were expressed in both the DMED group and the Exo group. Analysis of gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed significant enrichment in the Exo group for molecular pathways including PPAR and cAMP signaling. These genes are primarily involved in immune regulation and collagen deposition biological processes within the smooth muscle of the penis in DMED rats.</p><p><strong>Conclusions: </strong>Transcriptome analysis revealed important genes and pathways that regulate various biological processes. These findings offer a novel approach for decreasing collagen deposition in this tissue.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12295123/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic Regulation of Immune Response in Dogs.","authors":"Pablo Barragán-Sánchez, María Teresa Balastegui, Pablo Jesús Marín-García, Lola Llobat","doi":"10.3390/genes16070764","DOIUrl":"10.3390/genes16070764","url":null,"abstract":"<p><p>The mammalian immune system, including key components such as toll-like receptors (TLRs), lymphocytes, and cytokines, plays a vital role in defending against diseases. In dogs, genetic polymorphisms and epigenetic regulation of immune-related genes contribute to breed-specific differences in susceptibility or resistance to infectious, autoimmune, and inflammatory diseases. Cytokines, essential for immune cell differentiation and activation, exhibit variable expression among breeds due to genetic factors like single-nucleotide polymorphisms (SNPs) and miRNA regulation. This variability influences immune responses not only to infections but also to chronic inflammatory conditions and cancer, providing insights for improved diagnosis, treatment, and breeding. Selective breeding has further shaped diverse immune phenotypes across breeds, especially through genetic variations in the major histocompatibility complex (MHC) region, which affect vulnerability to immune-mediated and immunodeficiency disorders. Recent studies emphasize the role of specific miRNAs in modulating immune responses during parasitic and viral infections, opening new avenues for precision veterinary medicine and immunotherapy. This review highlights the genetic and epigenetic regulation of immune genes in dogs and explores their potential applications in advancing veterinary diagnostics, therapeutics, and breeding strategies to enhance canine health.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12295078/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative Evaluation of AAV8 and AAV9 Gene Therapy in Fabry Knockout (<i>Gla</i>^-/y) and Symptomatic (G3S^Tg/+<i>Gla</i>^-/y) Murine Models.","authors":"Fu-Pang Chang, Ya-Ting Lee, Pao-Hsung Liu, Pei-Sin Chen, Yun-Ru Chen, Dau-Ming Niu","doi":"10.3390/genes16070766","DOIUrl":"10.3390/genes16070766","url":null,"abstract":"<p><strong>Background: </strong>Fabry disease (FD) is an X-linked lysosomal storage disorder caused by mutations in the GLA gene, resulting in α-galactosidase A (α-Gal A) deficiency and progressive accumulation of globotriaosylceramide (Gb3). Current therapies, such as enzyme replacement and chaperone therapy, have limitations, including incomplete biodistribution and mutation-specific efficacy. Gene therapy using adeno-associated virus (AAV) vectors presents a promising alternative.</p><p><strong>Methods: </strong>In this study, we assessed the dose-dependent effects of AAV8 and AAV9 vectors encoding human GLA in Gla knockout (<i>Gla</i>^-/y) mice by measuring α-Gal A activity and monitoring safety. To evaluate therapeutic efficacy, symptomatic Fabry mice (G3S^Tg/<i>+</i><i>Gla</i>^-/y) were used.</p><p><strong>Results: </strong>AAV9-GLA produced significantly higher and more sustained enzyme activity than AAV8-GLA across plasma, liver, heart, and kidney. In symptomatic mice, AAV9-GLA achieved superior reductions in serum Gb3 and lyso-Gb3 levels, greater Gb3 clearance in heart and kidney tissues, and improved proteinuria. Anti-GLA IgG titers remained below threshold for the first four weeks and increased modestly by week eight, indicating a limited humoral immune response. No significant clinical signs or weight loss were observed in <i>Gla</i>^-/y mice over the 3.5-month study period, supporting the favorable safety profile of AAV-mediated gene therapy.</p><p><strong>Conclusions: </strong>These findings demonstrate that AAV9 provides enhanced biodistribution and therapeutic efficacy compared to AAV8, supporting its potential for the treatment of Fabry disease.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12294720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LncRNAOmics: A Comprehensive Review of Long Non-Coding RNAs in Plants.","authors":"Chinmay Saha, Saibal Saha, Nitai P Bhattacharyya","doi":"10.3390/genes16070765","DOIUrl":"10.3390/genes16070765","url":null,"abstract":"<p><p>The large portion of the eukaryotic genomes was considered non-functional and called the \"dark matter\" of the genome, now appearing as regulatory hubs coding for RNAs without the potential for making proteins, known as non-coding RNA. Long non-coding RNA (lncRNA) is defined as functional RNA molecules having lengths larger than 200 nucleotides without the potential for coding for proteins. Thousands of lncRNAs are identified in different plants and animals. LncRNAs are characterized by a low abundance, fewer exons than mRNA, tissue-specific expression, and low sequence conservation compared to protein-coding genes (PCGs). LncRNAs, like PCGs, are regulated by promoters and enhancers with characteristic chromatin signatures, DNA methylation, multiple exons, introns, and alternate splicing. LncRNAs interact with DNA, mRNA, microRNA, and proteins, including chromatin/histone modifiers, transcription factors/repressors, epigenetic regulators, spliceosomal, and RNA-binding proteins. Recent observations indicate that lncRNAs code for small peptides, also called micropeptides (<100 amino acids), and are involved in the development and growth of plants, suggesting the bi-functional activities of lncRNAs. LncRNAs have emerged as the major regulators of diverse functions, principally by altering the transcription of target genes. LncRNAs are involved in plant growth, development, immune responses, and various physiological processes. Abiotic, biotic, nutrient, and other environmental stresses alter the expressions of numerous lncRNAs. Understanding the mechanisms of actions of lncRNAs opens up the possibility of improving agronomic traits by manipulating lncRNAs. However, further studies are required in order to find the interactions among the deregulated lncRNAs and validate the findings from high-throughput studies to harness their potential in crop improvement.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12294436/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polymorphisms in <i>CACNA1A</i>, <i>CACNA1C</i>, and <i>CACNA1H</i> Genes in Korean Pediatric Patients with Developmental Delay and Intellectual Disability: A Focus on Epilepsy Comorbidity.","authors":"Ji Yoon Han","doi":"10.3390/genes16070767","DOIUrl":"10.3390/genes16070767","url":null,"abstract":"<p><p><b>Background:</b> Developmental delay and intellectual disability (DD/ID) are frequently accompanied by epilepsy, and growing evidence implicates variants in voltage-gated calcium channel genes in their pathogenesis. This study aimed to investigate the association of polymorphisms in <i>CACNA1A</i>, <i>CACNA1C</i>, and <i>CACNA1H</i> with DD/ID and epilepsy comorbidity in Korean children. <b>Methods:</b> We retrospectively analyzed 141 pediatric patients diagnosed with DD/ID who underwent whole-exome sequencing (WES) and were not found to have pathogenic monogenic variants. Nine single-nucleotide polymorphisms (SNPs) across <i>CACNA1A</i>, <i>CACNA1C</i>, and <i>CACNA1H</i> were selected based on functional annotation scores and prior literature. Genotype data were extracted from WES variant files, and allele and genotype frequencies were compared with control data from the gnomAD East Asian population and the Korean Reference Genome Database (KRGDB). Subgroup analyses were performed according to epilepsy comorbidity. <b>Results:</b> The <i>CACNA1A</i> rs16023 variant showed a significantly higher B allele frequency in DD/ID patients than in both control datasets and was also associated with epilepsy comorbidity. Genotype distribution analysis revealed that the BB genotype of rs16023 was more frequent in patients with epilepsy. <b>Conclusions:</b> The <i>CACNA1A</i> rs16023 variant may contribute to genetic susceptibility to DD/ID and epilepsy in Korean children, potentially through regulatory mechanisms. These findings support the relevance of calcium channel genes in neurodevelopmental disorders and highlight the importance of integrating functional annotation in variant prioritization.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12294729/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Artificial Intelligence-Assisted Diagnosis of Skeletal Dysplasias in Pediatric Patients: A Comparative Benchmark Study of Large Language Models and a Clinical Expert Group.","authors":"Nikola Ilić, Nina Marić, Dimitrije Cvetković, Marko Bogosavljević, Gordana Bukara-Radujković, Jovana Krstić, Zoran Paunović, Ninoslav Begović, Sanja Panić Zarić, Slađana Todorović, Katarina Mitrović, Aleksandar Vlahović, Adrijan Sarajlija","doi":"10.3390/genes16070762","DOIUrl":"10.3390/genes16070762","url":null,"abstract":"<p><strong>Background/objectives: </strong>Skeletal dysplasias are a heterogeneous group of rare genetic disorders with diverse and overlapping clinical presentations, posing diagnostic challenges even for experienced clinicians. With the increasing availability of artificial intelligence (AI) in healthcare, large language models (LLMs) offer a novel opportunity to assist in rare disease diagnostics. This study aimed to compare the diagnostic accuracy of two advanced LLMs, ChatGPT (version GPT-4) and DeepSeek, with that of a clinical expert panel in a cohort of pediatric patients with genetically confirmed skeletal dysplasias.</p><p><strong>Methods: </strong>We designed a prospective vignette-based diagnostic benchmarking study including 45 children with confirmed skeletal dysplasias from two tertiary centers. Both LLMs were prompted to provide primary and differential diagnoses based on standardized clinical case vignettes. Their outputs were compared with those of two human experts (a pediatric endocrinologist and a pediatric orthopedic surgeon), using molecular diagnosis as the gold standard.</p><p><strong>Results: </strong>ChatGPT and DeepSeek achieved a comparable diagnostic top-3 accuracy (62.2% and 64.4%, respectively), with a high intermodel agreement (Cohen's κ = 0.95). The expert panel outperformed both models (82.2%). While LLMs performed well on more common disorders, they struggled with ultra-rare and multisystemic conditions. In one complex case missed by experts, the DeepSeek model successfully proposed the correct diagnosis.</p><p><strong>Conclusions: </strong>LLMs offer a complementary diagnostic value in skeletal dysplasias, especially in under-resourced medical settings. Their integration as a supportive tool in multidisciplinary diagnostic workflows may enhance early recognition and reduce diagnostic delays in rare disease care.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12294814/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic Analysis of <i>MMP-2</i> and <i>MMP-3</i> Polymorphisms Reveals the Association of <i>MMP-3</i> rs522616 with Susceptibility to Persistent Apical Periodontitis.","authors":"Tulio L Olano-Dextre, José F Mateo-Castillo, Celso K Nishiyama, Carlos F Santos, Gustavo P Garlet, Renato M Silva, Ariadne Letra, Lucimara Teixeira das Neves","doi":"10.3390/genes16070758","DOIUrl":"10.3390/genes16070758","url":null,"abstract":"<p><p><b>Objective</b>: The aim of the present study was to investigate the association of polymorphic variants in matrix metalloproteinase-2 (<i>MMP-2</i>) and matrix metalloproteinase-3 (<i>MMP-3</i>) genes and the occurrence of persistent apical periodontitis (PAP). <b>Methods</b>: DNA samples from 180 individuals were recruited and divided into two groups: Case group, 79 subjects with a history of PAP; control group, 101 healthy subjects. Five single nucleotide polymorphisms (SNPs) were selected for genotyping: rs243865, rs2285053, and rs2287074 in the <i>MMP-2</i> gene, and rs679620 and rs522616 in the <i>MMP-3</i> gene. The chi-square test or Exact Fisher (<i>p</i> < 0.05) and Odds Ratio (CI = 95%) were used to compare the frequencies of genotypes and alleles between the two groups. <b>Results</b>: A positive association was found for the <i>MMP-3</i> rs522616 AG genotype (<i>p</i> = 0.025), the AG + GG genotypes (<i>p</i> = 0.015), and the G allele (<i>p</i> = 0.016) with PAP. <b>Conclusions</b>: The <i>MMP-3</i> variant rs522616 was associated with PAP. Similar studies are needed analyzing other genes involved in extracellular matrix dynamics under inflammatory conditions to clarify the role of the genetic factors of PAP.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12294307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AdBSK1-Mediated Hormone Signaling Regulates Flowering Transition in <i>Actinidia deliciosa</i> '<i>Guichang</i>'.","authors":"Lina Guo, Xiaoyu Cui, Jiayin Li, Chao Zhang, Yumei Fang","doi":"10.3390/genes16070760","DOIUrl":"10.3390/genes16070760","url":null,"abstract":"<p><strong>Background: </strong>The <i>Actinidia deliciosa cultivar</i> '<i>Guichang</i>' is a remarkable kiwifruit variety. The phenotypic traits of this variety are influenced by the climatic conditions in Guizhou. The flowering time, which is shaped by multiple environmental factors, has a substantial impact on both the fruit yield and quality.</p><p><strong>Objectives and methods: </strong>This study was designed to explore the molecular mechanisms underlying the transition from bud to flowering in '<i>Guichang</i>' through transcriptomic and proteomic analyses.</p><p><strong>Results: </strong>The transcriptomic results revealed that 6201 genes were up-regulated, while 5849 genes were down-regulated during this transition. Key genes related to hormone signaling, such as <i>AdPIF4</i>, <i>AdBSK</i>, <i>AdBRI1</i>, and <i>AdCYCD3</i>, were recognized as crucial regulators. The proteomic analysis detected a total of 10,488 proteins. Among them, AdBSK1 was regulated, while AdPIF4, AdBRI1, and AdCYCD3 showed stable expressions. A moderate positive correlation (with a Pearson correlation coefficient of 0.445) was found between the expression levels of transcriptomics and proteomics. When AdBSK1 was over-expressed in Arabidopsis, it promoted earlier flowering. This was achieved by down-regulating <i>FLC</i> and up-regulating <i>FT</i> and <i>SOC1</i>.</p><p><strong>Conclusions: </strong>This study clarifies the molecular mechanisms involved in the bud-to-flowering transition in '<i>Guichang</i>'. It emphasizes the intricate interactions among hormonal pathways, key genes, and proteins, which are consistent with the broader understanding of plant flowering regulation in recent research. These findings are significant for deepening our understanding of, and potentially controlling, the flowering mechanisms.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12294449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Eight New <i>Sedum</i> Plastomes: Comprehensive Analyses and Phylogenetic Implications.","authors":"Liying Xu, Shiyun Han, Yingying Xiao, Mengsa Zhang, Xianzhao Kan","doi":"10.3390/genes16070761","DOIUrl":"10.3390/genes16070761","url":null,"abstract":"<p><p><b>Background:</b><i>Sedum</i>, with the largest number of species in the family <i>Crassulaceae</i>, is a taxonomically complex genus and an important group of horticultural plants within this family. Despite extensive historical research using diverse datasets, the branching patterns within this genus and the family remain debatable. <b>Methods:</b> In this study, we conducted sequencing and comparative analyses of plastomes from eight <i>Sedum</i> species, focusing on the diversities in nucleotide, microsatellite repeats, putative RNA editing, and gene content at IR junctions. The phylogenetic inferences were further conducted at the order level-<i>Saxifragales</i>. <b>Results:</b> Our IR junction analyses of the eight investigated <i>Sedum</i> species detected a unique 110 bp IR extension into <i>rps19</i>, a feature highly conserved across <i>Crassulaceae</i> species, indicating a remarkably family-specific pattern. Additionally, we obtained 79 PCGs from 148 <i>Saxifragales</i> species and constructed a phylogenetic tree using a larger set of plastomes than in previous studies. Our results confirm the polyphyly of <i>Sedum</i> and reveal that <i>S. emarginatum</i> is more closely related to <i>S. makinoi</i> than to <i>S. alfredii</i>, which is sister to <i>S. plumbizincicola</i>. Furthermore, we also performed analyses of codon usage, putative RNA editing sites, and microsatellite repeats. <b>Conclusions:</b> These findings and the generated sequence data will enrich plastid resources and improve understanding of the evolution of <i>Sedum</i>, <i>Crassulaceae</i>, and <i>Saxifragales</i>.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12294699/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}