BMC Genomics最新文献

{"title":"Extraction, structural characterization and SNP identification of related genes of collagen from local pigs in Guizhou.","authors":"Yu Dan Zhang, Xiao Yang, Wei Xia, Ying Qu Liu, Yi Yu Zhang, Wei Chen","doi":"10.1186/s12864-026-12826-4","DOIUrl":"https://doi.org/10.1186/s12864-026-12826-4","url":null,"abstract":"<p><strong>Background: </strong>Collagen, as one of the important components of living organisms, plays a crucial role in supporting and maintaining tissue structure and biological functions. The local pig breed in Guizhou is renowned for its elastic skin, tender meat, and excellent taste. The collagen content in pig skin accounts for approximately 87.7% of the protein content. However, as a by-product after slaughter, the utilization rate of pig skin is not high. Additionally, the content and structural characteristics of collagen have a certain impact on the quality of meat.</p><p><strong>Method: </strong>In this study, the skin and longissimus dorsi muscle of local pig breeds in Guizhou (Qiannan pig, Baixi pig, Qianbei pig, Zongdi pig, Kele pig, Congjiang pig) were used as raw materials to optimize the extraction method of collagen, and to explore the differences in the content, type and structure of collagen in the skin and longissimus dorsi muscle tissues of different pig breeds. Based on whole-gene resequencing technology, the screening and identification of differential genes and variant sites in three pig breeds, namely the two pig breeds with the greatest differences in collagen content (Baixi pig and Kele pig) and the pig breed with differences in collagen structure in skin tissue (Zongdi pig), were completed.</p><p><strong>Results and conclusions: </strong>This study determined that the optimal conditions for extracting collagen from local pig tissues in Guizhou are: pH 2.0, enzyme dosage 2%, feed-to-liquid ratio 1:20 (w/v), temperature 37℃, enzymatic hydrolysis time 8 h. Based on the experimental results, it is speculated that the difference in collagen content in the tissues of white-washed pigs and Kela pigs may be related to the COL1A1 and COL4A4 genes and their SNP loci. The structural differences in collagen in the skin of Zongdi pigs may be related to the COL4A3 and COL4A4 genes and their SNP loci, which is helpful to reveal the molecular mechanism of the skin characteristics of local pig breeds in Guizhou, open up new ways for the breeding of characteristic pig breeds in Guizhou.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147855866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"BSepDB: a database of bacterial selenoprotein genes and proteins.","authors":"Zhengyue Hong, Hengtao Li, Yan Zhang","doi":"10.1186/s12864-026-12927-0","DOIUrl":"https://doi.org/10.1186/s12864-026-12927-0","url":null,"abstract":"<p><strong>Background: </strong>Selenoproteins represent a structurally and functionally distinct class of proteins that contribute to cellular antioxidant defense and a wide range of other essential biological processes in specific organisms. They contain the 21st amino acid selenocysteine (Sec) in their active sites, which is encoded by an in-frame UGA stop codon through a translational reprogramming mechanism. Due to the dual functionality of the UGA codon, selenoprotein genes are frequently misidentified and misannotated in genomic databases, especially in bacteria where selenoproteins exhibit greater complexity and diversity compared to their eukaryotic counterparts. Thus, a comprehensive resource is urgently required to enable accurate identification of selenoprotein genes across diverse bacterial genomes.</p><p><strong>Results: </strong>We have developed BSepDB, a specialized database dedicated to systematic curation of bacterial selenoprotein genes and proteins, providing an exhaustive resource for the research community. The current version (BSepDB v. 1.0) encompasses over 57,000 selenoprotein entries derived from 16,621 bacterial species, representing the largest and most taxonomically diverse repository of bacterial selenoproteins to date. To facilitate intuitive data exploration, BSepDB offers multiple user-friendly interfaces, such as interactive browsing and search tools, an integrated BLAST search function, and options for bulk data download. Additionally, the curated entries in BSepDB are cross-referenced with established genomic databases (e.g., GenBank and RefSeq) to improve the accuracy of selenoprotein annotations in large-scale genomic projects.</p><p><strong>Conclusions: </strong>BSepDB serves as a valuable resource for researchers investigating selenium utilization and the functional diversity of selenoproteins in bacteria. The database is freely available at https://bsepdb.metalbioinfolab.net.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147855814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic investigation of agonistic behaviors of boxer shrimps (Stenopus species): insights into the potential neural signaling roles of dopamine and acetylcholine.","authors":"Terance Ho Him Wong, Lai Him Chow, Ziwei Wu, Tom Kwok Lun Hui, Ling Ming Tsang","doi":"10.1186/s12864-026-12899-1","DOIUrl":"https://doi.org/10.1186/s12864-026-12899-1","url":null,"abstract":"<p><strong>Background: </strong>Agonistic behaviors are crucial and common among animals due to their importance in securing an individual's fitness, and neural signaling molecules are known to mediate these behaviors. Stenopus, a genus of shrimp-like decapod crustaceans characterized by a pair of enlarged pereiopods, exhibits prominent agonistic behaviors when encountering conspecifics of the same sex owing to its monogamous social structure. These shrimps represent another potentially excellent model organism for investigating the neural signaling basis of agonistic behaviors in crustaceans aside from traditional models. Yet, their underpinning molecular aspects have never been studied. Using S. hispidus and S. cyanoscelis as representatives, the present study is the first that systematically examines the genetics of agonistic behaviors in Stenopus. Three organs, including (1) antennae + antennules, (2) central nervous system, and (3) eyestalk ganglia, were RNA-sequenced to identify the differentially expressed genes (DEGs) and pathways potentially conserved in winners and losers of Stenopus after fighting interactions.</p><p><strong>Results: </strong>Our results suggested that Stenopus agonistic interactions might be systemic activities involving the simultaneous modulation and interplay of multiple signaling cascades, organismal systems, and metabolic pathways. In particular, winners and losers typically exhibited enriched gene ontologies involved in neural signaling, and sensory and behavioral processes. Regarding enriched pathways, while those related to glycan biosynthesis and metabolism were enriched in winners, cholesterol metabolism and one-carbon pool by folate were enriched in losers. These different sets of pathways suggested that while fighting interactions in Stenopus were injurious to both combatants, the damage in losers appeared to be more traumatic. Furthermore, four neural signaling systems, including dopamine, acetylcholine, octopamine, and glutamate, were identified as potentially major mediators of agonistic behaviors and fighting interactions in both Stenopus species, with the first two appearing to be relatively more important. A comparison of the neural signaling systems involved in mediating aggression among pan-crustaceans suggested that Stenopus appeared to stand out by its seemingly major reliance on dopamine and acetylcholine, as opposed to the primarily serotonin-based regulation of aggression observed in most examined pan-crustaceans.</p><p><strong>Conclusions: </strong>The different metabolic responses between winners and losers in Stenopus highlight the profound, asymmetric physiological costs of social conflict at the molecular level. Furthermore, their unique reliance on dopamine and acetylcholine reveals diverse evolutionary trajectories in the neuroendocrine regulation of aggression, providing new insights into the current paradigms of invertebrate social behavior.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147855819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide insights into genetic diversity and selection signatures during the formation of Yanyun sheep.","authors":"Pengkun Yang, Zhixu Pang, Changsong Xu, Quanhong Yao, Zhongfa Wang, Yangyang Pan, Kaijie Yang, Liying Qiao, Wenzhong Liu","doi":"10.1186/s12864-026-12901-w","DOIUrl":"https://doi.org/10.1186/s12864-026-12901-w","url":null,"abstract":"<p><strong>Background: </strong>Yanyun (YY) sheep are a composite breed developed by targeted crossbreeding of Dorper, Hu, and East Friesian sheep to improve growth, reproduction, and environmental adaptability, yet the genomic basis underlying their formation and selective improvement remains unclear.</p><p><strong>Results: </strong>Whole-genome analyses showed that YY sheep retain moderate genetic diversity with low genomic inbreeding (FROH), indicating limited autozygosity. Population structure analyses supported that YY sheep form a genetically distinct yet admixed group consistent with their breeding history. Genome-wide selection scans identified multiple candidate regions associated with growth, metabolism, reproduction, immune function, and environmental adaptability, including loci showing consistent differentiation and haplotype-based selection signals across multiple population comparisons.</p><p><strong>Conclusions: </strong>These results provide a genome-wide view of the genetic diversity, population structure, and selection landscape of YY sheep, and identify candidate genomic regions for future investigation of economically important and adaptive traits in composite sheep breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147833189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated transcriptomic and proteomic analyses reveal muscle fiber-type transformation in meat rabbits.","authors":"Cheng Jia, Wu Qianwen, Ji Zhengwei, Yao Zhongqiang, Wang Ling, Lu Hongzhao, Zeng Wenxian","doi":"10.1186/s12864-026-12906-5","DOIUrl":"https://doi.org/10.1186/s12864-026-12906-5","url":null,"abstract":"<p><strong>Background: </strong>Skeletal muscle fiber composition plays a critical role in determining muscle growth and meat quality in livestock species. However, the molecular mechanisms underlying muscle fiber-type transformation in meat rabbits remain poorly understood.</p><p><strong>Results: </strong>Here, we integrated transcriptomic and label-free proteomic analyses to investigate skeletal muscle development in Ira rabbits at three developmental stages (D0, D35, and D70). Immunofluorescence staining revealed a gradual increase in slow-twitch muscle fibers in the gastrocnemius during postnatal growth. Enzyme activity assays showed decreased lactate dehydrogenase (LDH) activity and increased succinate dehydrogenase (SDH) activity, indicating a metabolic shift toward oxidative metabolism. Transcriptomic analysis identified thousands of differentially expressed genes across developmental stages, whereas proteomic profiling revealed numerous differentially expressed proteins associated with metabolic pathways. We identified ten candidate genes (NOS1, CASQ2, ANKRD1, ANKRD2, CXCL10, GPC3, NEDD4, MYORG, MYLK2, EZH2) and nine key proteins (TRAF3IP3, APBB2, PGK1, TMCO5A, PKM, PVALB, PDLIM7, PHKG1, PHKA1) that may be associated with muscle fiber-type transformation during postnatal skeletal muscle development. Functional enrichment analysis indicated that these molecules were associated with multiple metabolic pathways including glycolysis/gluconeogenesis and butanoate metabolism.</p><p><strong>Conclusions: </strong>These findings provide a multi-omics perspective on skeletal muscle development in rabbits and contribute to a better understanding of the molecular basis of muscle fiber-type transformation during postnatal growth.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147833165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temperature-dependent dynamics of DNA methylation and plasmid copy number in Yersinia pestis.","authors":"Konanov D N, Balykova A N, Vvedensky A V, Lukina-Gronskaya A V, Liubimova O N, Kovrizhnikov A V, Speranskaya A S, Krivonos D V, Eroshenko G A, Ilina E N, Govorun V M, Kutyrev V V","doi":"10.1186/s12864-026-12915-4","DOIUrl":"https://doi.org/10.1186/s12864-026-12915-4","url":null,"abstract":"<p><p>A number of mechanisms that control Yersinia pestis behavior during its complex life cycle in both mammalian hosts and arthropod vectors are known to be thermally regulated. In bacteria, the response to temperature shifts often involves epigenetic factors, particularly changes in DNA methylation. In this study, we aimed to fully characterize the methylome of eleven Y. pestis strains from different subspecies. We described its temperature-dependent features by comparing cultures grown at 22 °C (typical flea environment) and 37 °C (mammalian host temperature). Only two methylation motifs were detected: GATC with 6 mA modifications and CCWGG with 4mC modifications. GATC sites were almost fully methylated across the genome, except regions encoding the Type II secretion system and O‑antigen biosynthesis cluster, and four loci in the pMT1 plasmid. CCWGG sites were reproducibly less methylated at 37 °C than at 22 °C. This cytosine under‑methylation was more pronounced in strains from the ancient 0.PE4 lineage than in the highly pathogenic 0.ANT5 and 2.MED1 strains. Six genes showed reproducible differential methylation in CCWGG sites, including the virulence factor gene yopD and the plasmid gene parA, which is involved in plasmid replication and segregation. Subsequently, we observed a significant increase in the copy number of all Y. pestis plasmids in samples grown at 37 °C compared to those at 22 °C.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147833211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic loci and key candidate genes associated with fatty acid composition in the breast muscle of Sansui ducks identified through GWAS.","authors":"Yulong Feng, Mengru Xu, Meijuan Li, Yuxi Lu, Guotao Dai, Chengcheng Tian, Yu Zhao, Hehe Liu, Anqi Huang","doi":"10.1186/s12864-026-12905-6","DOIUrl":"https://doi.org/10.1186/s12864-026-12905-6","url":null,"abstract":"<p><strong>Background: </strong>The composition of fatty acids, particularly the content of unsaturated fatty acids (UFA), is closely related to meat quality and flavor in ducks.</p><p><strong>Result: </strong>In this study, 38 fatty acids were detected in the breast muscle of Sansui ducks, yielding 50 distinct fatty acid composition traits. The results showed that the predominant fatty acids were C18:1n-9, C16:0, C18:2n-6, C18:0, and C20:4n-6. Moreover, the breast muscle of Sansui duck was rich in UFA, accounting for 64.01% of the total fatty acids. Genome-wide association analysis (GWAS) identified 158 single nucleotide polymorphisms (SNPs) significantly associated with fatty acid composition traits, which were annotated to 70 protein-coding genes, including LDLRAD3, ACVR1, FGF6, and CASQ2. Additionally, linkage disequilibrium (LD) analysis revealed a candidate region (10,533,318 - 10,546,189 bp) on chromosome 14, where NSG2 was identified as a key candidate gene influencing C17:1 content. Functional enrichment analysis suggested that pathways such as Adherens junctions and MAPK signaling may play significant roles in fatty acid biosynthesis.</p><p><strong>Conclusion: </strong>These findings reveal the genetic structure of fatty acids composition in the breast muscle of Sansui duck, providing strong evidence for understanding the genetic regulatory mechanisms of fatty acid composition.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147833209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"BandHiC: a memory-efficient and user-friendly Python package for organizing and analyzing Hi-C matrices down to sub-kilobase resolution.","authors":"Weibing Wang, Junping Li, Yusen Ye, Lin Gao","doi":"10.1186/s12864-026-12680-4","DOIUrl":"https://doi.org/10.1186/s12864-026-12680-4","url":null,"abstract":"<p><strong>Background: </strong>Recent advances in high-resolution Hi-C and Micro-C technologies have enabled finer-scale characterization of 3D genome architecture. However, these improvements also introduce substantial computational challenges, as the memory requirements of Hi-C/Micro-C contact matrices scale quadratically with resolution, leading to prohibitive resource consumption.</p><p><strong>Results: </strong>To address this, we developed BandHiC, a memory-efficient and user-friendly Python package for organizing and analyzing Hi-C matrices down to sub-kilobase resolution. BandHiC adopts a banded storage strategy that preserves only a configurable diagonal bandwidth of the dense contact matrix, reducing memory usage by up to 99% while maintaining fast random access and intuitive indexing operations. In addition, it provides flexible masking mechanisms to handle missing values, outliers, and unmappable regions, and supports efficient vectorized operations optimized with NumPy, thereby enabling scalable analysis of ultra-high-resolution Hi-C datasets.</p><p><strong>Conclusions: </strong>BandHiC provides a memory-efficient and scalable framework that enables sub-kilobase-resolution Hi-C matrix analysis on standard hardware. Its seamless integration with the NumPy ecosystem and user-friendly design make it a practical and accessible foundation for future advances in 3D genomics. The source code of the BandHiC Python package is publicly available on GitHub (https://github.com/xdwwb/BandHiC-Master), and comprehensive documentation is provided at its website (https://xdwwb.github.io/BandHiC-Master/). Installation can be performed conveniently through Python's pip package manager.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147833195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Population structure and genome-wide adaptive differentiation of wild Chinese mitten crab (Eriocheir sinensis) across river basins in China.","authors":"Yulin Bai, Wenqian Wang, Huiming Ding, Yidong Liang, Junlei Ma, Ting Zhang, Anqi Wang, Changsui Hu, Jianxiang Gao, Dongpo Xu","doi":"10.1186/s12864-026-12784-x","DOIUrl":"https://doi.org/10.1186/s12864-026-12784-x","url":null,"abstract":"<p><p>Chinese mitten crab (Eriocheir Sinensis) is a commercially important species in Chinese aquaculture, yet the genetic structure of wild populations remains poorly understood. A total of 240 wild E. sinensis samples were collected from Liaohe (LH), Yalujiang (YLJ), Huanghe (HH), Yangtze (including Anqing section (YZA), Taixing section (YZT)), Oujiang (OJ), Minjiang (MJ), and Beilunhe (BLH) River basins to investigate the genetic structure of native populations. Through genotyping-by-sequencing (GBS) and stringent quality filtering, a total of 3,120,408 high-quality single- nucleotide polymorphism (SNP) loci were identified. Principal component analysis (PCA) showed that the BLH and MJ populations formed distinct clusters, whereas OJ, YZA, YZT, HH, LH, and YLJ populations were loosely clustered. Phylogenetic tree and population genetic structure analyses revealed that the BLH River population in southern China was the only significantly differentiated group within the native range of the Chinese mitten crab, while northern populations (HH, LH, and YLJ) exhibited stronger admixture, indicating higher levels of gene flow. Additionally, gene flow occurred more frequently among geographically proximate populations, while weaker gene flow persisted between geographically distant groups. Further selective sweep analyses comparing representative southern and northern populations (BLH and LH) identified key genes under strong geographic selection, primarily involved in transcriptional regulation, metabolism and transport, stress response and damage repair, and signal transduction. Overall, this study provides comprehensive insights into the genetic resources of wild E. sinensis across Chinese river basins, laying a foundation for conservation and germplasm resource development.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147833213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global transcriptional and metabolic reprogramming underlies Fusarium wilt resistance in figleaf gourd (Cucurbita ficifolia).","authors":"Gengyun Li, Xuejiao Li, Zhengan Yang, Hang Wu, Li Chen, Junqiang Xu, Tianrui Gong, Yun Zheng, Jun He, Bin Xu, Shuilian He","doi":"10.1186/s12864-026-12894-6","DOIUrl":"https://doi.org/10.1186/s12864-026-12894-6","url":null,"abstract":"<p><p>Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum (FOC), poses a major threat to economically important crops worldwide. Figleaf gourd (Cucurbita ficifolia) has been widely adopted as a rootstock for FOC-susceptible cucumber (Cucumis sativus) due to its strong resistance, although the underlying molecular mechanisms remain elusive. In this study, we leveraged the contrasting FOC resistance between C. ficifolia and C. sativus to perform a comparative analysis aimed at elucidating the molecular basis of Fusarium wilt resistance in C. ficifolia. Compared to C. sativus, resistant C. ficifolia exhibited milder wilting, enhanced antioxidant enzyme activities, and reduced oxidative damage. Transcriptome profiling revealed 1,599 species-specific expressed genes and 3,379 orthologous genes with interspecies expression divergence. Several key defense-related pathways, such as MAPK signaling and plant-pathogen interaction, contained critical node genes that exhibited species-specific regulation, potentially contributing to the enhanced resistance of C. ficifolia. This global divergence in gene expression was associated with distinct metabolic shifts, leading to the specific activation of defense-related metabolic pathways in C. ficifolia and the subsequent accumulation of protective compounds such as brassinosteroids, phenylpropanoids, and flavonoids. These findings indicate that C. ficifolia's superior FOC resistance is not attributable to a single factor but emerges from a sophisticated orchestration of gene expression and metabolic output. This study provides novel molecular insights into Fusarium wilt resistance and offers candidate genes and metabolic targets for breeding disease-resistant cucurbit crops.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147833234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}