Functional & Integrative Genomics最新文献

{"title":"AZD7648 (DNA-PKcs inhibitor): a two-edged sword for editing genomes","authors":"Muhammad Waseem Sajjad,&nbsp;Ifrah Imran,&nbsp;Fatima Muzamil,&nbsp;Rubab Zahra Naqvi,&nbsp;Imran Amin","doi":"10.1007/s10142-025-01560-x","DOIUrl":"10.1007/s10142-025-01560-x","url":null,"abstract":"<div><p>Clustered regularly interspaced short palindromic repeats (CRISPR-Cas9) has been the most practical technique in genome editing for the last decade. Its molecular mechanism includes steps that occur in a sequence, starting from a break in a double strand to repair. After a double-strand break in the DNA strand, the repairing of DNA done via Homology-Directed Repair (HDR) is considered important in different organisms as it is ideal for precise genome editing and the reduction of unintended mutations. Still, it is mostly dominated by the Non-Homologous End Joining (NHEJ) pathway. A recent study by Cullot et al. published in <i>Nature Biotechnology</i> showed interesting features of AZD7648 (a DNA-PKcs inhibitor) that increase the probability of HDR event while DNA repairing (Cullot et al. 2024).</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-025-01560-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143521675","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":"Immunomodulatory effects of traditional chinese medicine on cancer: insights from network pharmacology and single-cell RNA sequencing data on the treatment of lung adenocarcinoma with shenling baizhu powder","authors":"Xianqiang Zhou,&nbsp;Jiameng Gao,&nbsp;Yixin Zhang,&nbsp;Cuiling Feng","doi":"10.1007/s10142-025-01550-z","DOIUrl":"10.1007/s10142-025-01550-z","url":null,"abstract":"<div><p>Shenling Baizhu Powder (SLBZP), commonly used as a complementary and alternative therapy for lung adenocarcinoma (LUAD), is believed to enhance patients’ immune function. However, its underlying mechanisms remain unclear. By integrating network pharmacology and single-cell RNA sequencing (scRNA-seq) data, the study investigates the immune therapeutic effects of SLBZP in LUAD. Immune infiltration landscape analysis revealed significant differences in immune cell infiltration levels between normal and LUAD groups. ScRNA-seq analysis showed that LUAD progression was associated with an increased abundance of macrophage infiltration, and the characteristics of 13 macrophage clusters were closely related to target genes. Using machine learning, we identified 4 macrophage-related gene sets associated with LUAD: ALOX5, IL2RA, MMP9, and PPARG. Immune infiltration analysis demonstrated a strong correlation between these target genes and immune responses. Molecular docking results indicated that SLBZP could modulate these target genes through various bioactive compounds, indirectly affecting macrophages to enhance the immune system’s functional state. This study provides new insights into the role of tonifying TCM formulas in tumor immune modulation and offers theoretical support for future clinical research.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143513351","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":"Retraction Note: Carnosic acid nanocluster-based framework combined with PD-1 inhibitors impeded tumorigenesis and enhanced immunotherapy in hepatocellular carcinoma","authors":"Wenhua Wu,&nbsp;Yaping Li,&nbsp;Xiaokang Wu,&nbsp;Junrong Liang,&nbsp;Weiming You,&nbsp;Xinyuan He,&nbsp;Qinhui Feng,&nbsp;Ting Li,&nbsp;Xiaoli Jia","doi":"10.1007/s10142-025-01558-5","DOIUrl":"10.1007/s10142-025-01558-5","url":null,"abstract":"","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143521616","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":"Deep transcriptome and metabolome analysis to dissect untapped spatial dynamics of specialized metabolism in Saussurea costus (Falc.) Lipsch","authors":"Aasim Majeed,&nbsp;Romit Seth,&nbsp;Balraj Sharma,&nbsp;Amna Devi,&nbsp;Shikha Sharma,&nbsp;Mamta Masand,&nbsp;Mohammed Saba Rahim,&nbsp;Naveen Verma,&nbsp;Dinesh Kumar,&nbsp;Ram Kumar Sharma","doi":"10.1007/s10142-025-01549-6","DOIUrl":"10.1007/s10142-025-01549-6","url":null,"abstract":"<div><p><i>Saussurea costus</i> (Falc.) is an endangered medicinal plant possessing diverse phytochemical compounds with clinical significance and used to treat numerous human ailments. Despite the source of enriched phytochemicals, molecular insights into spatialized metabolism are poorly understood in <i>S. costus</i>. This study investigated the dynamics of organ-specific secondary metabolite biosynthesis using deep transcriptome sequencing and high-throughput UHPLC-QTOF based untargeted metabolomic profiling. A <i>de novo</i> assembly from quality reads fetched 59,725 transcripts with structural (53.02%) and functional (66.13%) annotations of non-redundant transcripts. Of the 7,683 predicted gene families, 3,211 were categorized as ‘single gene families’. Interestingly, out of the 4,664 core gene families within the Asterids, 4,560 families were captured in <i>S. costus</i>. Organ-specific differential gene expression analysis revealed significant variations between leaves vs. stems (23,102 transcripts), leaves vs. roots (30,590 transcripts), and roots vs. stems (21,759 transcripts). Like-wise, putative metabolites (PMs) were recorded with significant differences in leaves vs. roots (250 PMs), leaves vs. stem (350 PMs), and roots vs. stem (107 PMs). The integrative transcriptomic and metabolomic analysis identified organ-specific differences in the accumulation of important metabolites, including secologanin, menthofuran, taraxerol, lupeol, acetyleugenol, scopoletin, costunolide, and dehydrocostus lactone. Furthermore, a global gene co-expression network (GCN) identified putative regulators controlling the expression of key target genes of secondary metabolite pathways including terpenoid, phenylpropanoid, and flavonoid. The comprehensive functionally relevant genomic resource created here provides beneficial insights for upscaling targeted metabolite biosynthesis through genetic engineering, and for expediting association mapping efforts to elucidate the casual genetic elements controlling specific bioactive metabolites.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143513353","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":"Single-cell profiling and clinical characteristics analysis of lung squamous carcinoma","authors":"Jie Liu,&nbsp;Tian Zhao,&nbsp;Zhengliang Sun,&nbsp;Jinyi Wang,&nbsp;Zhengjun Chai,&nbsp;Guohan Chen","doi":"10.1007/s10142-025-01556-7","DOIUrl":"10.1007/s10142-025-01556-7","url":null,"abstract":"<div><p>Lung squamous carcinoma (LUSC) is a highly heterogeneous disease. However, the tumor microenvironment (TME) landscape and clinical characteristics for LUSC have not yet been elucidated. To map the TME and clinical characteristics of LUSC, we performed single-cell RNA sequencing for 504 LUSC samples on basis of TCGA and Gene Expression Omnibus. We introduced the computational algorithms “ESTIMATE” and “CIBERSORT” to analyze immune cell infiltration and immune-checkpoint-related gene signatures in various LUSC clusters. Weighted gene co-expression network analysis was used to explore the connections between molecular characteristics and clinical traits in LUSC. A prognostic model was constructed by performing multivariate COX. Two gene clusters exhibiting disparate immune and clinical characteristics were identified. Our findings indicate that patients in cluster 2, who have a more favorable prognosis, exhibit immune characteristics such as elevated levels of immunosuppression-associated M2 macrophages, resting memory CD4 T cells, resting dendritic cells (DC), and TNFRSF4, alongside reduced infiltration of activated DC and lower expression of TNFRSF18.Whereafter, the Risk Score model was built on basis of 3-DEGs signature consisted of cystatin C (CST3), transglutaminase type 2 (TGM2), JUN, which were proved by q-PCR and immunofluorescence. Besides, high-Risk Score may be responsible for poor prognosis in LUSC patients. Our study identified that tumor-infiltrating immune cell subtypes and the Risk Score model might shed light on the heterogeneity in LUSC patients. The TME, three DEGs and Risk Score can effectively serve as biomarkers to elucidate the immune landscape and predict prognosis in LUSC patients. They may provide insights to the investigations on therapeutic strategies for LUSC.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143496662","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":"Innovative perspectives on glioblastoma: the emerging role of long non-coding RNAs","authors":"Ahmed S. Doghish,&nbsp;Abdelhamid Mahmoud,&nbsp;Mai A. Abd-Elmawla,&nbsp;Mohamed Bakr Zaki,&nbsp;Nora M. Aborehab,&nbsp;Abdulrahman Hatawsh,&nbsp;Abdullah F. Radwan,&nbsp;Ghadir A. Sayed,&nbsp;Rewan Moussa,&nbsp;Mustafa Ahmed Abdel-Reheim,&nbsp;Osama A. Mohammed,&nbsp;Hanan Elimam","doi":"10.1007/s10142-025-01557-6","DOIUrl":"10.1007/s10142-025-01557-6","url":null,"abstract":"<div><p>Glioblastoma (GBM) is a highly aggressive and treatment-resistant brain tumor. Recent advancements have highlighted the crucial role of long noncoding RNAs (lncRNAs) in GBM’s molecular biology. Unlike protein-coding RNAs, lncRNAs regulate gene expression through transcription, post-transcriptional modifications, and chromatin remodeling. Some lncRNAs, like HOTAIR, CCAT2, CRNDE, and MALAT1, promote GBM development by affecting tumor suppressors and various signaling pathways like PI3K/Akt, mTOR, EGFR, NF-κB, and Wnt/β-catenin. Conversely, certain lncRNAs such as TUG1, MEG3, and GAS8-AS1 act as tumor suppressors and are associated with better prognosis. The study presented in the manuscript aims to explore the involvement of lncRNAs in GBM, focusing on their roles in tumor progression, proliferation, invasion, and potential implications for early detection and immunotherapy. The research seeks to elucidate the mechanisms by which specific lncRNAs influence GBM characteristics and highlight their potential as therapeutic targets or biomarkers in managing this aggressive form of brain cancer.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481069","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":"HOXA13 promotes immune evasion in bladder cancer by suppressing antigen processing and presentation, and phagosome pathways","authors":"Fee-Wai Chin,&nbsp;Soon-Choy Chan,&nbsp;De-Ming Chau,&nbsp;Teng-Aik Ong,&nbsp;Azad Hassan Abdul Razack,&nbsp;Khatijah Yusoff,&nbsp;Abhi Veerakumarasivam","doi":"10.1007/s10142-025-01553-w","DOIUrl":"10.1007/s10142-025-01553-w","url":null,"abstract":"<div><p>Homebox A13 <i>(HOXA13)</i> and homeobox B13 <i>(HOXB13)</i> expression dysregulation have been previously reported in bladder cancer. However, their roles in bladder carcinogenesis remain unclear. This study characterizes the distinct transcriptomic profile and pathway enrichment of <i>HOXA13</i> and <i>HOXB13</i> knockdown in bladder cancer cells. Separate in vitro knockdown models for <i>HOXA13</i> and <i>HOXB13</i> were established using small interfering RNAs (siRNAs), and knockdown efficiency was validated through reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Transcriptomic profiling was conducted using RNA sequencing, followed by differential gene expression analysis, and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment analysis. <i>HOXA13</i> knockdown significantly enriched pathways that are associated with immune evasion (i.e. antigen processing and presentation pathway, and phagosome pathway) through the upregulation of major histocompatibility complex (MHC) class I and II genes. These findings highlight the pivotal role of <i>HOXA13</i> in promoting immune evasion in bladder cancer. Meanwhile, <i>HOXB13</i> knockdown significantly enriched estrogen signaling pathway and PI3K-Akt signaling pathway, which are critical for cell proliferation and survival. While the role of <i>HOXB13</i> in bladder cancer progression requires further delineation, the primary focus of this study is on <i>HOXA13</i> due to its involvement in immune evasion mechanisms. This study provides novel insights into the potential therapeutic strategies for targeting <i>HOXA13</i> in bladder cancer, and highlights the distinct roles of <i>HOXA13</i> and <i>HOXB13</i> in bladder carcinogenesis.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481174","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":"Natural compounds as regulators of miRNAs: exploring a new avenue for treating colorectal cancer","authors":"Ahmed S. Doghish,&nbsp;Sherif S. Abdel Mageed,&nbsp;Osama A. Mohammed,&nbsp;Mustafa Ahmed Abdel-Reheim,&nbsp;Mohamed Bakr Zaki,&nbsp;Ashraf Hassan Mohamed,&nbsp;Nehal I. Rizk,&nbsp;Ahmed I. Abulsoud,&nbsp;Nourhan M. Abdelmaksoud,&nbsp;Walaa A. El-Dakroury,&nbsp;Shaza H. Aly","doi":"10.1007/s10142-025-01547-8","DOIUrl":"10.1007/s10142-025-01547-8","url":null,"abstract":"<div><p>Colorectal cancer (CRC) ranks as the second leading cause of cancer-related death globally, impacting both genders equally. The increasing global mortality rates from CRC are strongly linked to contemporary dietary habits, characterized by excessive meat consumption, alcohol intake, and insufficient physical activity. Thus, there is an unprecedented need to develop less hazardous and new therapies for CRC. CRC affects a substantial global population. The main treatments for CRC include chemotherapy and surgical intervention. Nonetheless, the advancement of innovative, safer, and more effective pharmaceuticals for CRC therapy is of paramount importance due to the widespread adverse effects and the dynamic nature of drug resistance. A growing amount of research suggests that natural chemicals may effectively battle CRC and, in certain cases, serve as alternatives to chemotherapeutics. Evidence suggests that miRNAs control important cancer features, including the maintenance of proliferative signals. These features also involve evasion of growth inhibition, resistance to cell death, and immortalization of replication. Additionally, miRNAs play a role in angiogenesis, invasion, and metastasis. Numerous compounds, including those exhibiting cytotoxic and apoptogenic properties against different malignancies, such as CRC, are sourced from diverse marine and medicinal plants. These chemicals stimulate several signaling pathways originating from different phytochemical families. This article evaluates the existing understanding of the anti-CRC capabilities of several phytochemical substances. Furthermore, their impact on several signaling pathways associated with cancer is examined. This article also highlights the potential of medicinal plants as a source of promising anti-CRC chemicals through modulating miRNA expression and the role of nanoparticle-based miRNA therapeutics in enhancing CRC treatment by improving tumor targeting and minimizing off-target effects.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143455661","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":"A curated tissue-specific proteome, phosphoproteome, and kinome map of Drosophila melanogaster with an integrated outlook in circadian physiology","authors":"Sandip Das,&nbsp;Arpita Kannihalli,&nbsp;Srishti Banerjee,&nbsp;Nikita Chakraborty,&nbsp;Sandipan Ray","doi":"10.1007/s10142-025-01554-9","DOIUrl":"10.1007/s10142-025-01554-9","url":null,"abstract":"<div><p>The fruit fly <i>Drosophila melanogaster</i> is a simple multicellular model system widely used in biomedical research. Here, we aimed to curate a comprehensive tissue and organ-specific proteome, phosphoproteome, and kinome atlas of <i>D. melanogaster.</i> Using information from published literature and databases, we have systematically curated the protein expression profiles, phosphorylation patterns, and the associated kinases and phosphatases in 11 tissue types across the different developmental stages and mature <i>D. melanogaster</i> and its derived cell lines. Gene annotation and pathway enrichment analysis were performed using the DAVID. Protein-protein interaction analysis was carried out using STRING, BioGrid, OmniPath, and InWeb-IM. <i>Drosophila</i> kinase and phosphatase gene orthologs in humans and mice were identified through the FlyBase database, utilizing the DRSC integrative ortholog prediction tool. We mapped a total of 18,377 proteins, 9021 phosphoproteins, 433 kinases, and 141 phosphatases in <i>D. melanogaster</i>. Subsequent categorization of the proteins into different tissue types indicated the enrichment of some tissue-specific pathways and expression clusters. We identified 295 and 289 <i>Drosophila</i> kinase orthologs in humans and mice through an ortholog screening. In the rhythmicity analysis, we observed 24-hour periodicity in 5289 transcripts, 678 proteins, 437 phosphoproteins, 166 kinases, and 89 phosphatases. The findings of our study are integrated as a convenient resource for understanding the proteome-level organizations in <i>Drosophila</i>, their oscillating expression, and their tissue-specific roles in maintaining cellular and physiological functions. We anticipate that this study will help to enhance the systems-level analysis of <i>D. melanogaster</i> as a model organism.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143446604","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":"Evolution of phenylalanine ammonia-lyase protein family from algae to angiosperm","authors":"Chao Zhang,&nbsp;Huan Guo,&nbsp;Zhongling Li,&nbsp;Shuning Yue","doi":"10.1007/s10142-025-01548-7","DOIUrl":"10.1007/s10142-025-01548-7","url":null,"abstract":"<div><p>Phenylpropanes, the precursors of various phenolic compounds in plants, are widely distributed. Phenylalanine ammonia-lyase (PAL) is the main enzyme that catalyzes the early step of the phenylpropanoid pathway to generate trans-cinnamic acid, which is the common precursor for the lignin and flavonoid biosynthetic pathways. Therefore, in this study, we focused on PAL evolution. A total of 584 PAL-like protein sequences were obtained, and only two PAL-like genes were found in algae, primary. Three main groups are separated by their different evolutionary stages. Group I mainly cluster ancient plants, and groups II and III are formed by angiosperms, which separate monocots (group II) and eudicots (group III). According to the sequence alignment, five main differences in amino acids may correlate with this separation, which involve the change of amino acid phosphorylation. The prediction analysis of GO and KEGG annotation information of each PAL protein showed that the proteins were clustered in cytoplasm and correlated with phenylalanine ammonia-lyase activity. Our results suggested that the PAL enzyme family expanded alongside the development of vascular tissues and underwent duplication events that facilitated gene cluster expansion and phenotypic diversity. Analysis of a reassembled and publicly available gene database confirmed that only two PAL genes were present in algae, whereas land plants possess a significantly greater number of PAL-like genes. This expansion is closely of PAL genes in land plants is closely associated with gene duplication events occurring at various evolutionary stages after algae plants. Futhermore, investigation into miRNAs revealed limited specificity across the plant evolution spectrum, with their primary role being the regulation and modulation of gene function. Additionally, analysis of PAL proteins across the plant kingdom ultimately elucidates that the evolution of their functions is intricately linked to the widespread distribution of cis-acting elements. This evolutionary trajectory reflected the natural selection processes that plants had undergone over time to enhance their eadaptability to diverse environments. These findings provide a valuable reference for future research into the functional evolution of PAL genes and their role in .plant adaptation and phenotypic diversity. </p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143438634","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}