BMC GenomicsPub Date : 2025-09-26DOI: 10.1186/s12864-025-11988-x
Yi Zhang, Xinyuan Liu, Yin Wang, Yu Wang
{"title":"BiAEImpute: a robust bidirectional autoencoder framework for High-fidelity dropout imputation in single-cell transcriptomics.","authors":"Yi Zhang, Xinyuan Liu, Yin Wang, Yu Wang","doi":"10.1186/s12864-025-11988-x","DOIUrl":"10.1186/s12864-025-11988-x","url":null,"abstract":"<p><strong>Background: </strong>Single-cell RNA sequencing (scRNA-seq) technology enables an in-depth understanding of cellular transcriptome heterogeneity and dynamics. However, a key challenge in scRNA-seq analysis is the dropout events, wherein certain expressed transcripts remain undetected. Dropouts seriously affect the accuracy and reliability of downstream analysis. Therefore, there is an urgent need to develop an effective imputation method that can accurately impute the missing values to mitigate their adverse effects on scRNA-seq analysis.</p><p><strong>Methods: </strong>We proposed a bidirectional autoencoder-based model (BiAEImpute) for dropout imputation in scRNA-seq dataset. This model employs row-wise autoencoders and column-wise autoencoders to respectively learn cellular and genetic features during the training phase. The synergistic integration of these learned features is then utilized for the imputation of missing values, enhancing the robustness and accuracy of the imputation process.</p><p><strong>Results: </strong>Evaluations conducted on four real scRNA-seq datasets consistently indicate that BiAEImpute exhibits superior performance compared to existing imputation methods. BiAEImpute adeptly restores missing values, facilitates the clustering of cell subpopulations, refines the identification of marker genes, and aids the inference of cell developmental trajectory.</p><p><strong>Conclusion: </strong>BiAEImpute proves to be efficacious and resilient in the imputation of missing data in scRNA-seq, contributing to enhanced accuracy in downstream analyses. The source code of BiAEImpute is available at https://github.com/LiuXinyuan6/BiAEImpute .</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"823"},"PeriodicalIF":3.7,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465494/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BMC GenomicsPub Date : 2025-09-26DOI: 10.1186/s12864-025-12046-2
Shuang Cheng, Liang Hao, Jialu Sun, Haiyan Ren, Haifeng Song
{"title":"Genome-wide analysis of the SnRK gene family in Caragana Korshinskii and their expression profiling under drought and nitrogen deposition.","authors":"Shuang Cheng, Liang Hao, Jialu Sun, Haiyan Ren, Haifeng Song","doi":"10.1186/s12864-025-12046-2","DOIUrl":"10.1186/s12864-025-12046-2","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"838"},"PeriodicalIF":3.7,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465707/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BMC GenomicsPub Date : 2025-09-26DOI: 10.1186/s12864-025-11999-8
Yang Zhang, Yanmin Xu, Yulu Mao, Min Wang, Xiaoli Li, Lanfang Jiang, Jianyu Hao, Dingyi Zhang, Hutai Ji, Xiaofei Ma
{"title":"Genome-wide analysis of the BES1 gene family reveals their involvement in grain development of Triticum aestivum L.","authors":"Yang Zhang, Yanmin Xu, Yulu Mao, Min Wang, Xiaoli Li, Lanfang Jiang, Jianyu Hao, Dingyi Zhang, Hutai Ji, Xiaofei Ma","doi":"10.1186/s12864-025-11999-8","DOIUrl":"10.1186/s12864-025-11999-8","url":null,"abstract":"<p><strong>Background: </strong>The BRI1-EMS SUPPRESSOR1 (BES1) gene family was initially recognized as specifically regulating brassinosteroids to mediate gene expression, which is of vital significance for plant growth and enhancing stress tolerance. Despite extensive studies in multiple plants, there has been a lack of focused and systematic analysis of BES1s in wheat grains.</p><p><strong>Results: </strong>In this study, we performed a comprehensive bioinformatics analysis of the BES1s in wheat, utilizing the latest genomics data from the Chinese Spring. A total of 19 TaBES1 were identified. An analysis of conserved domains, phylogenetic relationships, and gene structure revealed a significant level of conservation among TaBES1s. A gene collinearity analysis indicated that fragment duplication was the primary mechanism responsible for the amplification of TaBES1s. Furthermore, cis-acting elements within the promoters of TaBES1s were found to be implicated in grain development. Subsequently, SNP analysis revealed the genetic variation of TaBES1s across different wheat varieties. Moreover, published RNA-seq data were used, and RNA-seqs of Yaomai36, Pinyu8175, Pinyu8155, and Yaomai30 were performed to identify TaBES1s influencing grain development. Finally, the research found that TaBES1s had no self-activating activity in wheat. However, the interacting proteins of TaBES1-1 and TaBES1-4 are not only involved in starch metabolism but may also be implicated in cell signal transduction.</p><p><strong>Conclusions: </strong>This study further confirmed the potential function of BES1s in the grain development of wheat. These findings that BES1s play a regulatory role in wheat grain development provide a foundation for further understanding the molecular mechanisms underlying crop grain development.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"826"},"PeriodicalIF":3.7,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465741/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BMC GenomicsPub Date : 2025-09-26DOI: 10.1186/s12864-025-12025-7
Yulin Jia, Ninglu Xu, Jinzhi Wu, Chunping Wang, Ming Huang, Youjun Li
{"title":"Genome-wide association study, linkage mapping and transcriptomic analysis revealed candidate genes with the flag leaf traits associated with nitrogen use efficiency in wheat.","authors":"Yulin Jia, Ninglu Xu, Jinzhi Wu, Chunping Wang, Ming Huang, Youjun Li","doi":"10.1186/s12864-025-12025-7","DOIUrl":"10.1186/s12864-025-12025-7","url":null,"abstract":"<p><strong>Background: </strong>Enhancing flag leaf nitrogen use efficiency (NUE) in wheat production can substantially increase crop productivity while minimizing nitrogen application. Quantitative trait loci (QTLs) for NUE-related have been rarely reported in wheat flag leaf traits.</p><p><strong>Results: </strong>In this study, a natural population of 243 varieties and an RIL population of 123 F<sub>7</sub> recombinants were subjected to different nitrogen treatments. A genome-wide association study (GWAS) and linkage analysis were performed for four agronomic traits in terms of flag leaf length, flag leaf width, flag leaf area, and SPAD (chlorophyll content) under low and normal nitrogen conditions. Through GWAS, 1,016 significant SNP loci were identified and clustered into 290 QTLs, including 11 stably mapped QTLs (stable detection in multiple environments). Additionally, an AC population was established to verify the GWAS results and identify reliable QTL intervals. Three stable loci, namely, QFLLR6D.3 QFLWR6A.6, and QSPADR5B.3, were validated in the AC population, located 1.34 Mb, 2.84 Mb, and 5 Mb away from linkage mapping significant QTL, respectively. Through further transcriptome analysis of Chilero leaves at the jointing, anthesis and grain filling stages, four DEGs were identified within QSPADR5B.3. Among them, TraesCS5B02G394300, TraesCS5B02G394200, and TraesCS5B02G39390 encode beta-glucosidases, and TraesCS5B02G396400 encodes a potassium channel.</p><p><strong>Conclusions: </strong>These findings offer potential candidate genes for wheat breeding, and provide a foundation for exploring the molecular targets underlying wheat NUE.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"833"},"PeriodicalIF":3.7,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12466056/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genomic and metabonomic insights into the lignin-degrading potential of a novel halophilic bacterial strain Salinicoccus sp. HZC-1.","authors":"Fengqian Yang, Longzhan Gan, Zhicheng He, Haoran Zhang, Yuxin Yang, Chunbo Dong, Xiao Zou","doi":"10.1186/s12864-025-11981-4","DOIUrl":"10.1186/s12864-025-11981-4","url":null,"abstract":"<p><p>Lignin-derived aromatic compounds have significant potential for multiple industrial applications, and elucidating the processes for bacterial lignin degradation processes can facilitate the utilization of plant biomass. A lignin-degrading bacterial strain, designated HZC-1, was newly isolated from saline-alkali soil and exhibited robust growth in 1-18% (w/v) NaCl and across a pH range of 5.0-11.0. The isolate showed the highest 16S rRNA gene sequence similarity (≤ 97.7%) to known Salinicoccus species. Furthermore, average nucleotide identity (≤ 82.34) and digital DNA-DNA hybridization (≤ 52.9%) analyses supported its classification as a potentially novel species within the genus Salinicoccus. Genomic annotation indicated that strain HZC-1 adapted to saline-alkali environments via multiple mechanisms such as Na<sup>+</sup>/H<sup>+</sup> antiporter and glycine betaine transport systems. By combining genomic and untargeted metabolomic data, it can be inferred that this strain was capable of metabolizing lignin derivatives through non-classical pathways involving enzymes such as β-glucosidase, aromatic cyclohydroxyl dioxygenase and those associated with naphthalene degradation. These findings suggest the potential lignin-degrading capacity of Salinicoccus sp. HZC-1 under saline-alkali conditions, presenting a potentially novel bacterial taxon for waste lignin valorization and bioremediation of aromatic pollutants.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"819"},"PeriodicalIF":3.7,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Combined transcriptomic and metabolomic analysis of the molecular mechanism of seed dormancy release in Notopterygium incisum.","authors":"Wenlong Zhao, Ziqi Wei, Honggang Chen, Jinbao Zhang, Haijing Duan, Ling Jin","doi":"10.1186/s12864-025-12021-x","DOIUrl":"10.1186/s12864-025-12021-x","url":null,"abstract":"<p><strong>Background: </strong>Notopterygium incisum seeds have both morphological and physiological dormancy characteristics and require stratification to break seed dormancy, but the mechanism of seed dormancy release during stratification is still unclear. In this study, different stages of N. incisum seed stratification were employed as experimenta objects, and the dynamic changes during seed dormancy release were studied through embryo morphology, physiological index determination, transcriptome, and metabolome.</p><p><strong>Results: </strong>(1) Stratification treatment reduced the content of stored nutrients in N. incisum seeds, significantly changed enzyme activity, reduced ABA content, and increased GA<sub>3</sub> and IAA contents. (2) A total of 110,539 differentially expressed genes (DEGs) and 1656 metabolites (DAMs) were identified during dormancy release. Transcriptome analysis showed that after the dormancy of N. incisum seeds was released, the expression of genes in the abscisic acid signaling pathway (ABI1, PP2CA, ABI5 and ABF4) and the gibberellin signaling pathway (GAI, GAI1 and RGL1) were significantly down-regulated, and there were significant changes in the differentially expressed genes in the auxin, cytokinin and ethylene signaling pathways. The genes related to starch and sucrose metabolism were up-regulated during dormancy release. The genes related to phenylpropanoid and flavonoid biosynthesis were significantly up-regulated after dormancy release. (3) Combined transcriptomics and metabolomics analysis showed that phenylpropanoid biosynthesis and flavonoid biosynthesis are the key pathways for the dormancy release of N. incisum seeds. (4) Metabolomics analysis showed that the accumulation of metabolites of the phenylpropanoid biosynthesis pathway (p-coumaric acid, coniferyl aldehyde, coniferyl glycoside, 5-caffeoylshikimic acid and sinapinic acid) decreased during and after the dormancy release of N. incisum seeds, while the accumulation of flavonoids such as quercetin, rutin, delphinidin and naringenin chalcone increased significantly after dormancy release.</p><p><strong>Conclusion: </strong>Dormancy release in N. incisum seeds involves differential regulation of hormones, carbohydrates, phenylpropanoids, and flavonoid metabolites. Our results provide important insights into the molecular regulatory network of dormancy release in N. incisum seeds.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"821"},"PeriodicalIF":3.7,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BMC GenomicsPub Date : 2025-09-26DOI: 10.1186/s12864-025-12015-9
Vimbiso Chidoti, Anaïs Loisier, Taona Zinyakasa, Mathieu Bourgarel, Valérie Pinarello, Gift Matope, Ngoni Chiweshe, Dorothée Missé, Ellen Mwandiringana, Hélène De Nys, Florian Liégeois
{"title":"Complete genome sequence analysis of Sarbecovirus (severe acute respiratory syndrome-related coronaviruses) from Zimbabwean insectivorous bats.","authors":"Vimbiso Chidoti, Anaïs Loisier, Taona Zinyakasa, Mathieu Bourgarel, Valérie Pinarello, Gift Matope, Ngoni Chiweshe, Dorothée Missé, Ellen Mwandiringana, Hélène De Nys, Florian Liégeois","doi":"10.1186/s12864-025-12015-9","DOIUrl":"10.1186/s12864-025-12015-9","url":null,"abstract":"<p><p>Bat-borne severe acute respiratory syndrome-related coronaviruses (bat SARSr-CoVs), belonging to the Sarbecovirus subgenus of the Betacoronavirus genus pose a potential risk for zoonotic spillover. This study reports the complete genome sequences of bat sarbecoviruses from Nycteris macrotis and Rhinolophus simulator insectivorous bat species in Zimbabwe. Using genome walking and nested PCR approaches, six full viral genomes were amplified, sequenced and assembled: one from Nycteris macrotis (MAG1042) and five from Rhinolophus simulator bats species (MAG388, MAG562, MAG575, MAG850, and MAG859). Comparative genomic analysis revealed a high degree of sequence conservation (99.6-99.9%) among the Rhinolophus simulator-characterised sequences, while the Nycteris macrotis characterised sequence exhibited 96.7% identity with the Rhinolophus simulator consensus (MAG Cons) genomes, suggesting genus-specific evolution. Furthermore, the spike region exhibited notable divergence, with only 88% sequence identity between the two genera. A complete absence of ORF8, and truncation of ORF7b genes were observed, while the RNA dependent RNA polymerase genes were highly conserved across all strains. Phylogenetic analysis demonstrated distinct continental clustering, with the Zimbabwean genomic sequences forming a well-supported clade within the African lineage (Lineage 4). These newly characterized Zimbabwean sarbecoviruses sequences represent the most recent evolutionary branches within the Lineage 4-African clade, indicating ongoing viral diversification in local bat populations. These findings expand understanding of SARSr-CoV diversity in African bats and underscore the importance of geographical isolation in viral evolution.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"828"},"PeriodicalIF":3.7,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465345/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Orogeny shapes the diversification of an ancient and relict spider family (Hypochilidae), with the stepwise uplift of the Qinghai-Tibetan plateau driving the radiation of Asian lineages.","authors":"Jiang-Ni Li, Li-Li Shao, Shu-Qiang Li, Hui-Feng Zhao","doi":"10.1186/s12864-025-11974-3","DOIUrl":"10.1186/s12864-025-11974-3","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"831"},"PeriodicalIF":3.7,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BMC GenomicsPub Date : 2025-09-26DOI: 10.1186/s12864-025-11982-3
Tyron Chang, Dustin C Hancks
{"title":"A subclass of small RNAs is encoded by exons of protein-coding genes.","authors":"Tyron Chang, Dustin C Hancks","doi":"10.1186/s12864-025-11982-3","DOIUrl":"10.1186/s12864-025-11982-3","url":null,"abstract":"<p><strong>Background: </strong>Small RNAs regulate gene expression in species across the tree of life. miRNAs, which impact a variety of cellular and physiological processes ranging from development and stress adaptation to host defense, are one of the best characterized classes of small RNA. Many miRNAs are produced from longer non-coding transcripts generated from host genes via a series of RNA cleavage reactions. The location of a small RNA within a host gene can shape the processing of the mature small RNA. For example, a type of miRNAs derived from host gene intronic sequence, referred to as miRtrons, are Drosha-independent and reliant on splicing for biogenesis. Relatedly, processing of a small RNA from an exon of a protein-coding mRNA, in principle, may destabilize it and compromise translation of the host gene. Prior to extensive transcriptome analysis, informatics analyses identified six human miRNAs embedded in exons of protein-coding genes and experimental studies have characterized additional anecdotal examples. Still, whether protein-coding mRNAs encoding small RNAs represent an appreciable class of host genes given the now recognized complexity of the transcriptome is unclear.</p><p><strong>Results: </strong>Our analysis finds 201 small RNAs (118 human and 83 mouse) encoded by expressed exons of protein-coding genes (5'-UTR, CDS, 3'-UTR). Forty-six of these cases (29 human and 17 mouse) are also present in MirGeneDB which includes the most up-to-date miRNA classifications. Many of these small RNAs are poorly characterized with 96% of the protein-coding host gene relationships identified here not previously known. Furthermore, the identification of nearly fifty human and mouse small RNAs embedded within coding exons of canonical ORFs suggests that overlapping hybrid genes might be more common than previously appreciated in higher organisms. Expression analysis for a subset of these small RNAs indicates that many display differential expression across human tissues with the pattern correlating significantly with the expression of the candidate protein-coding host gene.</p><p><strong>Significance: </strong>Overall, our analysis suggests that the number of protein-coding transcripts serving as host genes is greater than previously recognized. Our small RNA host gene classifications may serve as a resource to shed new light on small RNA biology, specific host genes, and gene regulation.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"827"},"PeriodicalIF":3.7,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BMC GenomicsPub Date : 2025-09-26DOI: 10.1186/s12864-025-12014-w
Samitha S N Liyanage, Brian G Bosworth, Kaylan A Martin, Kyle R Wood, Alexandra E Nowicki, Jason W Abernathy, Nithin Muliya Sankappa, Benjamin H Beck, Timothy J Bruce, Matthew K Litvak, Rex A Dunham, Luke A Roy, Xu Wang, Ian A E Butts
{"title":"Age-related reproductive performance and transcriptome profiling of testis in male blue catfish, Ictalurus furcatus.","authors":"Samitha S N Liyanage, Brian G Bosworth, Kaylan A Martin, Kyle R Wood, Alexandra E Nowicki, Jason W Abernathy, Nithin Muliya Sankappa, Benjamin H Beck, Timothy J Bruce, Matthew K Litvak, Rex A Dunham, Luke A Roy, Xu Wang, Ian A E Butts","doi":"10.1186/s12864-025-12014-w","DOIUrl":"10.1186/s12864-025-12014-w","url":null,"abstract":"<p><p>Catfish farming is the largest aquaculture industry in the U.S., where hybrid catfish produced by channel catfish, Ictalurus punctatus ♀ × blue catfish, I. furcatus ♂, represent > 50% of the harvest. Previous studies indicated a high degree of variation in reproductive performance among individuals. Therefore, it is crucial to establish a connection between paternal age and reproductive success. This study investigated the reproduction of 103 blue catfish males aged 2 to 10 years. Morphometric data were collected, and blood was drawn to quantify testosterone (T), 11-ketotestosterone (11-KT), osmolality, and ions. Histological images of the testis assessed stages of spermatogenesis, and sperm were activated for kinematic analysis. The testis transcriptome was profiled across distinct ages, 2, 4, 7, and 9. For fish aged 2 to 10 years, those over 7 years had the largest size, with a rapid increase until age 7 and a slight increase afterwards. Absolute sperm production was affected by age, with the highest levels observed at age 6, followed by a decreasing trend. T and 11-KT did not increase after age 6, while sperm kinematics were not impacted by age. Transcriptomics identified 5220 differentially expressed genes (DEGs) in all comparisons. The most DEGs were identified at age 7 with 2261 down-regulated and 1824 up-regulated genes. Functional enrichment revealed significant changes in axoneme, motile cilium, and sperm flagellum at age 7. In contrast, immune processes were increased in the testis at age 9 with viral and bacterial defense responses. Results suggest that farmers should maintain consistent supplies of age 6 and 7 males to increase hatchery efficiency.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"817"},"PeriodicalIF":3.7,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}