Pub Date : 2025-09-30DOI: 10.1016/j.ygeno.2025.111126
Hongwei Jin , Bin Feng , Wenxiao Gong, Xiaoliang Chen, Dongli Wang, Yan Li, Weijun Huang, Wenting Peng
•
With the proposal of the concept of “metagenomics” and the development of sequencing technology, 16S rRNA gene profiling has been widely applied in the survey of microbial diversity. This study explored the gut microbiota of children with hand, foot and mouth disease (HFMD). This study investigated the gut microbiota of 24 children with asymptomatic and symptomatic hand, foot, and mouth disease (HFMD) and 19 healthy controls using 16S rRNA sequencing. The gut microbiota, both in asymptomatic and symptomatic HFMD patients, was distinct from the controls, with the composition of gut microbiota in the HFMD cases represented a significant difference. The dysbiosis of gut microbiota of the HFMD cases included a reduction of butyrate-producing bacteria and an up-regulation of inflammation-inducing bacteria. These may have impaired the intestinal biological mucosal barrier and host immune functions, promoting the invasion of the enterovirus.
{"title":"Evaluation of gut microbial diversity and correlation in asymptomatic and symptomatic patients with hand, foot and mouth disease","authors":"Hongwei Jin , Bin Feng , Wenxiao Gong, Xiaoliang Chen, Dongli Wang, Yan Li, Weijun Huang, Wenting Peng","doi":"10.1016/j.ygeno.2025.111126","DOIUrl":"10.1016/j.ygeno.2025.111126","url":null,"abstract":"<div><div><ul><li><span>•</span><span><div>With the proposal of the concept of “metagenomics” and the development of sequencing technology, 16S rRNA gene profiling has been widely applied in the survey of microbial diversity. This study explored the gut microbiota of children with hand, foot and mouth disease (HFMD). This study investigated the gut microbiota of 24 children with asymptomatic and symptomatic hand, foot, and mouth disease (HFMD) and 19 healthy controls using 16S rRNA sequencing. The gut microbiota, both in asymptomatic and symptomatic HFMD patients, was distinct from the controls, with the composition of gut microbiota in the HFMD cases represented a significant difference. The dysbiosis of gut microbiota of the HFMD cases included a reduction of butyrate-producing bacteria and an up-regulation of inflammation-inducing bacteria. These may have impaired the intestinal biological mucosal barrier and host immune functions, promoting the invasion of the enterovirus.</div></span></li></ul></div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111126"},"PeriodicalIF":3.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212420","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}
Pub Date : 2025-09-30DOI: 10.1016/j.ygeno.2025.111120
Songyi Ye , Chenyu Wu , Shuaijing Huang , Haowen Fan , Zhiqing Zhang , Jinling Chen , Wenliang Ge
Cryptorchidism, affecting 1 %–9 % of male neonates, represents one of the most prevalent congenital genitourinary anomalies. Studies highlighted Leydig cell derived insulin-like 3 (Insl3) as pivotal in the initial phase of testicular descent. However, the pathogenic mechanisms underlying decreased Insl3 remain poorly elucidated. Here, we showed that triggering receptor expressed on myeloid cells-2 (Trem2) acted as a central mediator in macrophage-Leydig cell communication, influencing testicular descent via Insl3 regulation. In boys with cryptorchidism, Trem2 in testes was markedly downregulated. 63.16 % of Trem2−/− mice exhibited cryptorchidism and abnormal sperm motility and morphology, concomitant with decreased Leydig cells and Insl3. In vitro studies using human testicular cultures also revealed that Trem2 expression positively correlated with Insl3 expression. Mechanistically, ketoconazole elevated TNF-α due to suppression of the Trem2-Dap12-Syk-PI3K axis, ultimately disrupting total Leydig cell number and Insl3 expression. Collectively, these findings unveil Trem2 as a paracrine sentinel for Insl3-dependent testicular descent, thereby mitigating cryptorchidism.
{"title":"Trem2-dependent Insl3 regulation via Dap12-Syk-PI3K pathway: A new pathogenic mechanism in cryptorchidism","authors":"Songyi Ye , Chenyu Wu , Shuaijing Huang , Haowen Fan , Zhiqing Zhang , Jinling Chen , Wenliang Ge","doi":"10.1016/j.ygeno.2025.111120","DOIUrl":"10.1016/j.ygeno.2025.111120","url":null,"abstract":"<div><div>Cryptorchidism, affecting 1 %–9 % of male neonates, represents one of the most prevalent congenital genitourinary anomalies. Studies highlighted Leydig cell derived insulin-like 3 (Insl3) as pivotal in the initial phase of testicular descent. However, the pathogenic mechanisms underlying decreased Insl3 remain poorly elucidated. Here, we showed that triggering receptor expressed on myeloid cells-2 (Trem2) acted as a central mediator in macrophage-Leydig cell communication, influencing testicular descent <em>via</em> Insl3 regulation. In boys with cryptorchidism, Trem2 in testes was markedly downregulated. 63.16 % of <em>Trem2</em><sup>−/−</sup> mice exhibited cryptorchidism and abnormal sperm motility and morphology, concomitant with decreased Leydig cells and Insl3. <em>In vitro</em> studies using human testicular cultures also revealed that Trem2 expression positively correlated with Insl3 expression. Mechanistically, ketoconazole elevated TNF-α due to suppression of the Trem2-Dap12-Syk-PI3K axis, ultimately disrupting total Leydig cell number and Insl3 expression. Collectively, these findings unveil Trem2 as a paracrine sentinel for Insl3-dependent testicular descent, thereby mitigating cryptorchidism.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111120"},"PeriodicalIF":3.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212025","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}
Pub Date : 2025-09-30DOI: 10.1016/j.ygeno.2025.111119
Huihan Ai , Hang Yang , Chai Luv , Guanglong Chen , Weijie Zhao , Zikun Wu , Shijun Xu , Jie Ma , Kangdong Liu , Zhi Li
Background
Typical cases of familial adenomatous polyposis (FAP) exhibit variants in the coding sequence of adenomatous polyposis coli (APC) gene coding sequence. Families without detectable APC variants can't benefit from genetic testing.
Methods
We investigated a FAP family with APC variant negativity using exome sequencing, genome sequencing. Quantitative real-time PCR, single nucleotide polymorphism analysis, sanger sequencing, and organoid drug sensitivity assays.
Results
We discovered a novel deletion spanning about 100 kb upstream of the APC transcription start site, covering the entire APC 1B promoter, in all affected members of the FAP family. The proband's blood RNA revealed the silencing of one APC allele, linked to this deletion. This deletion suppressed APC gene transcription. Additionally, this family exhibited unique extracolonic manifestations, and their response to FAP treatment drugs was similar to that of typical FAP cases. Despite this, conventional anticancer treatments led to favorable outcomes for the patients.
Conclusion
These findings indicated that APC exon variant-negative FAP patients may have deletions in the promoter region, particularly the 1B region. Their clinical features and treatment responses differ from other FAP cases, emphasizing the importance of personalized management strategies tailored to their variant profile.
{"title":"Identifying and characterizing a novel APC promoter 1B deletion in a Chinese family with familial adenomatous polyposis","authors":"Huihan Ai , Hang Yang , Chai Luv , Guanglong Chen , Weijie Zhao , Zikun Wu , Shijun Xu , Jie Ma , Kangdong Liu , Zhi Li","doi":"10.1016/j.ygeno.2025.111119","DOIUrl":"10.1016/j.ygeno.2025.111119","url":null,"abstract":"<div><h3>Background</h3><div>Typical cases of familial adenomatous polyposis (FAP) exhibit variants in the coding sequence of adenomatous polyposis coli (<em>APC</em>) gene coding sequence. Families without detectable APC variants can't benefit from genetic testing.</div></div><div><h3>Methods</h3><div>We investigated a FAP family with APC variant negativity using exome sequencing, genome sequencing. Quantitative real-time PCR, single nucleotide polymorphism analysis, sanger sequencing, and organoid drug sensitivity assays.</div></div><div><h3>Results</h3><div>We discovered a novel deletion spanning about 100 kb upstream of the APC transcription start site, covering the entire <em>APC</em> 1B promoter, in all affected members of the FAP family. The proband's blood RNA revealed the silencing of one APC allele, linked to this deletion. This deletion suppressed <em>APC</em> gene transcription. Additionally, this family exhibited unique extracolonic manifestations, and their response to FAP treatment drugs was similar to that of typical FAP cases. Despite this, conventional anticancer treatments led to favorable outcomes for the patients.</div></div><div><h3>Conclusion</h3><div>These findings indicated that <em>APC</em> exon variant-negative FAP patients may have deletions in the promoter region, particularly the 1B region. Their clinical features and treatment responses differ from other FAP cases, emphasizing the importance of personalized management strategies tailored to their variant profile.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111119"},"PeriodicalIF":3.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212400","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}
Pub Date : 2025-09-30DOI: 10.1016/j.ygeno.2025.111128
Shanshan Gao , Mengyi Guo , Enlu Zhang , Zupei Yi , Kui Liu , Shuang Xue , Ruimin Li , Kunpeng Zhang
Aldehyde oxidase in insects participates in the degradation of various aldehyde insecticides and toxic plant-derived aldehydes, increasing the resistance of pests to these agents. However, the specific mechanism underlying this resistance remains unclear. In this study, we examined the differentially expressed genes in Tribolium castaneum, a global stored-grain pest, before and after knockdown of aldehyde oxidase TcAOX3. We found decreased expression levels of chymotrypsin-like proteinase 5B precursor and serine protease P40, which are involved in immunity and digestion, indicating that TcAOX3 may be involved in immune and digestive functions of larvae. Reduction of TcAOX3 expression also significantly decreased the resistance of T. castaneum larvae to benzaldehyde, with an increase of about 20 % in the killing effect of benzaldehyde against T. castaneum. Molecular docking and isothermal titration calorimetry results showed that benzaldehyde bound to TcAOX3 via Val761, Tyr558, Met562, Ile559, Gln557, Arg763, and Arg762, with a binding energy of ΔG = −24.23 kJ/mol. These results provide a theoretical basis for analysis of the detoxification mechanism of aldehyde oxidase in insects and offer a reference for screening of green insecticides targeting aldehyde oxidase.
{"title":"RNA-seq analysis combined with insecticidal efficacy assays reveal the insecticidal molecular mechanism of benzaldehyde against Tribolium castaneum","authors":"Shanshan Gao , Mengyi Guo , Enlu Zhang , Zupei Yi , Kui Liu , Shuang Xue , Ruimin Li , Kunpeng Zhang","doi":"10.1016/j.ygeno.2025.111128","DOIUrl":"10.1016/j.ygeno.2025.111128","url":null,"abstract":"<div><div>Aldehyde oxidase in insects participates in the degradation of various aldehyde insecticides and toxic plant-derived aldehydes, increasing the resistance of pests to these agents. However, the specific mechanism underlying this resistance remains unclear. In this study, we examined the differentially expressed genes in <em>Tribolium castaneum</em>, a global stored-grain pest, before and after knockdown of aldehyde oxidase <em>TcAOX3</em>. We found decreased expression levels of chymotrypsin-like proteinase 5B precursor and serine protease P40, which are involved in immunity and digestion, indicating that <em>TcAOX3</em> may be involved in immune and digestive functions of larvae. Reduction of <em>TcAOX3</em> expression also significantly decreased the resistance of <em>T. castaneum</em> larvae to benzaldehyde, with an increase of about 20 % in the killing effect of benzaldehyde against <em>T. castaneum</em>. Molecular docking and isothermal titration calorimetry results showed that benzaldehyde bound to TcAOX3 via Val761, Tyr558, Met562, Ile559, Gln557, Arg763, and Arg762, with a binding energy of ΔG = −24.23 kJ/mol. These results provide a theoretical basis for analysis of the detoxification mechanism of aldehyde oxidase in insects and offer a reference for screening of green insecticides targeting aldehyde oxidase.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111128"},"PeriodicalIF":3.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212381","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}
Pub Date : 2025-09-30DOI: 10.1016/j.ygeno.2025.111116
Pengwei Hu , Jixiang Xing , Wuritu Yang , Hongxia Chi , Yongqiang Xing , Yongchun Zuo
Alternative splicing (AS) in single cell is crucial for cell heterogeneity, gene expression and transcriptome diversity. However, given the complexity of AS analysis in single-cell RNA sequencing (scRNA-seq), employing a continuous and iterative process to refine data and uncover relevant latent information is crucial. While several tools have been developed to address various aspects of scRNA-seq AS analysis, a versatile and user-friendly web application that can perform all essential steps of AS analysis on scRNA-seq data is still lacking. Here, we made significant advancements in improving the usability and functionality of MARVEL. Firstly, we developed a Python package that can easily and efficiently generate input files, reducing the technical barrier. Secondly, we developed a Shiny-based R package that extends MARVEL's analysis capabilities to multiple cell populations, enabling interactive, code-free ex-ploration of AS and gene expression dynamics at single-cell level. The package, named ScASplicer (Single-Cell Alternative Splicing Shiny Explorer), provides a user-friendly platform for more efficient and comprehensive single-cell AS analysis.
单细胞的选择性剪接（AS）对细胞异质性、基因表达和转录组多样性至关重要。然而，考虑到单细胞RNA测序（scRNA-seq）中AS分析的复杂性，采用连续迭代的过程来完善数据并发现相关的潜在信息至关重要。虽然已经开发了一些工具来解决scRNA-seq AS分析的各个方面，但仍然缺乏一个通用的、用户友好的web应用程序，可以在scRNA-seq数据上执行AS分析的所有基本步骤。在这里，我们在提高MARVEL的可用性和功能方面取得了重大进展。首先，我们开发了一个Python包，它可以轻松有效地生成输入文件，减少了技术障碍。其次，我们开发了一个基于shine的R包，将MARVEL的分析能力扩展到多个细胞群体，从而实现了在单细胞水平上对AS和基因表达动态的交互式、无代码探索。该软件包名为ScASplicer (Single-Cell Alternative Splicing Shiny Explorer)，为更高效和全面的单细胞AS分析提供了一个用户友好的平台。
{"title":"ScASplicer: An interactive shiny/R application for alternative splicing analysis of single-cell sequencing","authors":"Pengwei Hu , Jixiang Xing , Wuritu Yang , Hongxia Chi , Yongqiang Xing , Yongchun Zuo","doi":"10.1016/j.ygeno.2025.111116","DOIUrl":"10.1016/j.ygeno.2025.111116","url":null,"abstract":"<div><div>Alternative splicing (AS) in single cell is crucial for cell heterogeneity, gene expression and transcriptome diversity. However, given the complexity of AS analysis in single-cell RNA sequencing (scRNA-seq), employing a continuous and iterative process to refine data and uncover relevant latent information is crucial. While several tools have been developed to address various aspects of scRNA-seq AS analysis, a versatile and user-friendly web application that can perform all essential steps of AS analysis on scRNA-seq data is still lacking. Here, we made significant advancements in improving the usability and functionality of MARVEL. Firstly, we developed a Python package that can easily and efficiently generate input files, reducing the technical barrier. Secondly, we developed a Shiny-based R package that extends MARVEL's analysis capabilities to multiple cell populations, enabling interactive, code-free ex-ploration of AS and gene expression dynamics at single-cell level. The package, named ScASplicer (Single-Cell Alternative Splicing Shiny Explorer), provides a user-friendly platform for more efficient and comprehensive single-cell AS analysis.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111116"},"PeriodicalIF":3.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212398","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}
Pub Date : 2025-09-30DOI: 10.1016/j.ygeno.2025.111117
Qian Liu , Jianghui Yu , Xinjie Ai , Huiying Xu , Zijian Qiu , Liming Xu , Jinfeng Ma , Jin Zhou , Chenxi Liu , Qingbo Zhao , Pinghua Li , Ruihua Huang
The carcass backfat thickness (BFT) provides a valuable indication of fat deposition and carcass leanness, which are essential for the determination of carcass grading and pricing. Identifying genetic loci and crucial genes related to BFT using integrated multi-omics methods offers significant contributions to the genetic advancement of pig. In the present study, 418 Chinese Suhuai pigs were slaughtered, and carcass BFT were subsequently measure. We conducted a genome-wide association study (GWAS) based on SNP chip data and imputed whole-genome sequencing data (iWGS), respectively. Significant quantitative trait loci (QTL) correlated with carcass BFT were identified on Sus scrofa chromosome (SSC) 2, SSC4, and SSC14, with the most significant single-nucleotide polymorphisms (SNPs) explaining 6.58 %–9.91 % of the phenotypic variance. Bayesian fine mapping validated two previously reported quantitative trait loci (QTLs), narrowing the most refined confidence interval to 3 kb (SSC2, 37.337–37.340 Mb and SSC4, 75.407–77.006 Mb), while identifying two novel QTLs (SSC14, 137.086–138.863 Mb and SSC4, 95.237–96.894 Mb) associated with carcass BFT. Furthermore, transcriptome analysis identified 322 differentially expressed genes (DEGs) and several critical regulatory pathways related to lipid and energy metabolism, including fatty acid and pyruvate metabolism. The integration of genomic and transcriptomic data identified three pivotal candidate genes, S100A12, XKR4 and PENK, which are typically associated with BFT. Transcriptome-wide association study (TWAS) and Phenome-wide association study (PheWAS) provided further evidence that these three genes were significantly associated with BFT and fatty acid composition. This study uncovers novel insights into the important genes and molecular markers related to carcass BFT in pig.
{"title":"Integrated genomic and transcriptomic analysis identifies novel candidate genes affecting carcass backfat thickness in pigs","authors":"Qian Liu , Jianghui Yu , Xinjie Ai , Huiying Xu , Zijian Qiu , Liming Xu , Jinfeng Ma , Jin Zhou , Chenxi Liu , Qingbo Zhao , Pinghua Li , Ruihua Huang","doi":"10.1016/j.ygeno.2025.111117","DOIUrl":"10.1016/j.ygeno.2025.111117","url":null,"abstract":"<div><div>The carcass backfat thickness (BFT) provides a valuable indication of fat deposition and carcass leanness, which are essential for the determination of carcass grading and pricing. Identifying genetic loci and crucial genes related to BFT using integrated multi-omics methods offers significant contributions to the genetic advancement of pig. In the present study, 418 Chinese Suhuai pigs were slaughtered, and carcass BFT were subsequently measure. We conducted a genome-wide association study (GWAS) based on SNP chip data and imputed whole-genome sequencing data (iWGS), respectively. Significant quantitative trait loci (QTL) correlated with carcass BFT were identified on <em>Sus scrofa</em> chromosome (SSC) 2, SSC4, and SSC14, with the most significant single-nucleotide polymorphisms (SNPs) explaining 6.58 %–9.91 % of the phenotypic variance. Bayesian fine mapping validated two previously reported quantitative trait loci (QTLs), narrowing the most refined confidence interval to 3 kb (SSC2, 37.337–37.340 Mb and SSC4, 75.407–77.006 Mb), while identifying two novel QTLs (SSC14, 137.086–138.863 Mb and SSC4, 95.237–96.894 Mb) associated with carcass BFT. Furthermore, transcriptome analysis identified 322 differentially expressed genes (DEGs) and several critical regulatory pathways related to lipid and energy metabolism, including fatty acid and pyruvate metabolism. The integration of genomic and transcriptomic data identified three pivotal candidate genes, <em>S100A12</em>, <em>XKR4</em> and <em>PENK</em>, which are typically associated with BFT. Transcriptome-wide association study (TWAS) and Phenome-wide association study (PheWAS) provided further evidence that these three genes were significantly associated with BFT and fatty acid composition. This study uncovers novel insights into the important genes and molecular markers related to carcass BFT in pig.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111117"},"PeriodicalIF":3.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212461","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}
Penaeus japonicus is an economically important marine shrimp species, but its sand-diving habit affects the further improvement of their culture yield. To investigate the molecular response to the restriction of sand-diving behavior, we designed three culture systems: the sandy group, the sandless group, and the sandless stress group (transfer the individuals to a sandless pond after a week in the sandy group). First, we analyzed the expression differences of stress-related (HSP60) and circadian rhythm genes (period, timeless) at different time points after stress induction, identifying 6 h post-transition as the timepoint with the most significant stress response (p < 0.05). A total of 25,371 highly expressed genes were detected across cell clusters, which were further classified into 13 distinct cell subpopulations. Manual annotation categorized these into granular cells (GCs), semi-granular cells (SGCs), hyaline cells (HCs), prohemocyte-like cells, and functional cells. qRT-PCR analysis confirmed the expression profiles of 13 highly expressed genes in GCs, SGCs, and HCs of P. japonicus. RNA in situ hybridization localized pxt, IGSF10, and IFI30 to GCs, HCs, and SGCs, respectively, validating the accuracy of cell clusters classification based on marker genes. Single-cell transcriptome differential expression analysis revealed significant gene expression differences among the three groups (p < 0.05), with most differentially expressed genes (DEGs) concentrated in cluster 2 (GCs) and cluster 8 (HCs), suggesting their close association with burrowing behavior regulation. qRT-PCR analysis of these DEGs in hemocytes from P. japonicus reared under different substrate conditions yielded results consistent with the scRNA-seq data, confirming the reliability of the transcriptomic findings. Furthermore, comparative analysis between groups identified key candidate DEGs, including trpa1, trpm, and the cut protein family, that may play pivotal roles in the response to environmental change and the restriction of natural behavior, though their specific functions require further validation. This study provides a theoretical foundation for understanding the molecular stress response to substrate deprivation in P. japonicus and identifies candidate genes for future functional studies on behavioral regulation.
{"title":"scRNA-seq of Penaeus japonicus hemocytes under environmentally-induced restriction of sand-diving behavior","authors":"Huimin Zhang , Xinyu Zhou , Yang Zhang , Jiahan Yu , Junjie Qi , Jing Xu , Panpan Wang , Fei Yu , Jianxin Zhang , Huan Gao","doi":"10.1016/j.ygeno.2025.111125","DOIUrl":"10.1016/j.ygeno.2025.111125","url":null,"abstract":"<div><div><em>Penaeus japonicus</em> is an economically important marine shrimp species, but its sand-diving habit affects the further improvement of their culture yield. To investigate the molecular response to the restriction of sand-diving behavior, we designed three culture systems: the sandy group, the sandless group, and the sandless stress group (transfer the individuals to a sandless pond after a week in the sandy group). First, we analyzed the expression differences of stress-related (<em>HSP60</em>) and circadian rhythm genes (<em>period</em>, <em>timeless</em>) at different time points after stress induction, identifying 6 h post-transition as the timepoint with the most significant stress response (<em>p < 0.05</em>). A total of 25,371 highly expressed genes were detected across cell clusters, which were further classified into 13 distinct cell subpopulations. Manual annotation categorized these into granular cells (GCs), semi-granular cells (SGCs), hyaline cells (HCs), prohemocyte-like cells, and functional cells. qRT-PCR analysis confirmed the expression profiles of 13 highly expressed genes in GCs, SGCs, and HCs of <em>P. japonicus.</em> RNA in situ hybridization localized <em>pxt</em>, <em>IGSF10</em>, and <em>IFI30</em> to GCs, HCs, and SGCs, respectively, validating the accuracy of cell clusters classification based on marker genes. Single-cell transcriptome differential expression analysis revealed significant gene expression differences among the three groups (<em>p < 0.05</em>), with most differentially expressed genes (DEGs) concentrated in cluster 2 (GCs) and cluster 8 (HCs), suggesting their close association with burrowing behavior regulation. qRT-PCR analysis of these DEGs in hemocytes from <em>P. japonicus</em> reared under different substrate conditions yielded results consistent with the scRNA-seq data, confirming the reliability of the transcriptomic findings. Furthermore, comparative analysis between groups identified key candidate DEGs, including <em>trpa1</em>, <em>trpm</em>, and the cut protein family, that may play pivotal roles in the response to environmental change and the restriction of natural behavior, though their specific functions require further validation. This study provides a theoretical foundation for understanding the molecular stress response to substrate deprivation in <em>P. japonicus</em> and identifies candidate genes for future functional studies on behavioral regulation.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111125"},"PeriodicalIF":3.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212372","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}
Pub Date : 2025-09-30DOI: 10.1016/j.ygeno.2025.111121
Delong Guan , Yingcan Qin , Jing Song , Yue Qin , Shihao Zhang , Lei Xin , Xiaodong Li
Understanding insect molecular responses to different insecticides is essential for sustainable pest management. This study presents a comprehensive transcriptomic analysis of Phthonandria atrilineata exposed to insecticides with distinct modes of action. RNA sequencing was performed on larvae treated with organophosphates (trichlorfon, malathion, and trichlorfon-malathion mixture) and mitochondrial inhibitors (methoxyfenozide and chlorfenapyr). Our analysis revealed both mechanism-specific responses and conserved xenobiotic defense programs. We identified 180 commonly upregulated genes involved in detoxification and sensory perception pathways, and 357 commonly downregulated genes indicating suppression of carbohydrate metabolism and developmental processes under chemical stress. Fuzzy clustering revealed nine distinct expression modules, with organophosphates primarily affecting neuronal functions while mitochondrial inhibitors triggered metabolic reprogramming centered on energy balance and protein homeostasis. Additionally, the trichlorfon-malathion mixture produced synergistic effects on endocrine signaling pathways. These findings illuminate the molecular architecture of insecticide responses, providing valuable insights for pest management strategies and resistance monitoring in agricultural settings.
{"title":"Comparative transcriptomics reveal universal and compound-specific mechanisms of insecticide response in the mulberry looper (Phthonandria atrilineata)","authors":"Delong Guan , Yingcan Qin , Jing Song , Yue Qin , Shihao Zhang , Lei Xin , Xiaodong Li","doi":"10.1016/j.ygeno.2025.111121","DOIUrl":"10.1016/j.ygeno.2025.111121","url":null,"abstract":"<div><div>Understanding insect molecular responses to different insecticides is essential for sustainable pest management. This study presents a comprehensive transcriptomic analysis of <em>Phthonandria atrilineata</em> exposed to insecticides with distinct modes of action. RNA sequencing was performed on larvae treated with organophosphates (trichlorfon, malathion, and trichlorfon-malathion mixture) and mitochondrial inhibitors (methoxyfenozide and chlorfenapyr). Our analysis revealed both mechanism-specific responses and conserved xenobiotic defense programs. We identified 180 commonly upregulated genes involved in detoxification and sensory perception pathways, and 357 commonly downregulated genes indicating suppression of carbohydrate metabolism and developmental processes under chemical stress. Fuzzy clustering revealed nine distinct expression modules, with organophosphates primarily affecting neuronal functions while mitochondrial inhibitors triggered metabolic reprogramming centered on energy balance and protein homeostasis. Additionally, the trichlorfon-malathion mixture produced synergistic effects on endocrine signaling pathways. These findings illuminate the molecular architecture of insecticide responses, providing valuable insights for pest management strategies and resistance monitoring in agricultural settings.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111121"},"PeriodicalIF":3.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212429","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}
Pub Date : 2025-09-30DOI: 10.1016/j.ygeno.2025.111124
H.A.C.R. Hanchapola , Po Gong , Gaeun Kim , D.S. Liyanage , W.K.M. Omeka , Jeongeun Kim , Yasara Kavindi Kodagoda , M.A.H. Dilshan , D.C.G. Rodrigo , G.A.N. Piyumika Ganepola , Cecile Massault , Dean R. Jerry , Jihun Lee , Jehee Lee
Acute and chronic high-temperature stress negatively impact olive flounder (Paralichthys olivaceus) aquaculture, weakening immune function and increasing mortality. This study conducted a genome-wide association study (GWAS) to identify genetic markers linked to thermal stress resilience. A total of 384 fish were exposed to acute stress (29 °C for 30 min and 1 h) and chronic stress (19.8–30 °C for 16 days). Genomic DNA from 329 deceased and 55 surviving fish was genotyped using a 70 K SNP chip, yielding 57,638 SNPs from 376 fish after quality filtering. GWAS identified 34 SNPs associated with both acute and chronic thermal stress on chromosomes 4, 10, 11, 15, 18, 19, and 23, surpassing the suggestive (p < 1 × 10−4) and Bonferroni-corrected (p < 8.6 × 10−7) thresholds. Genes myhc, nlrc5, hydin, and gfod1 were linked to thermal stress. These findings may support marker-assisted selection for thermal stress resilience strains, promoting sustainable aquaculture.
{"title":"Genome-wide association study identifies novel candidate genes linked to acute and chronic thermal stress resilience in olive flounder (Paralichthys olivaceus)","authors":"H.A.C.R. Hanchapola , Po Gong , Gaeun Kim , D.S. Liyanage , W.K.M. Omeka , Jeongeun Kim , Yasara Kavindi Kodagoda , M.A.H. Dilshan , D.C.G. Rodrigo , G.A.N. Piyumika Ganepola , Cecile Massault , Dean R. Jerry , Jihun Lee , Jehee Lee","doi":"10.1016/j.ygeno.2025.111124","DOIUrl":"10.1016/j.ygeno.2025.111124","url":null,"abstract":"<div><div>Acute and chronic high-temperature stress negatively impact olive flounder (<em>Paralichthys olivaceus</em>) aquaculture, weakening immune function and increasing mortality. This study conducted a genome-wide association study (GWAS) to identify genetic markers linked to thermal stress resilience. A total of 384 fish were exposed to acute stress (29 °C for 30 min and 1 h) and chronic stress (19.8–30 °C for 16 days). Genomic DNA from 329 deceased and 55 surviving fish was genotyped using a 70 K SNP chip, yielding 57,638 SNPs from 376 fish after quality filtering. GWAS identified 34 SNPs associated with both acute and chronic thermal stress on chromosomes 4, 10, 11, 15, 18, 19, and 23, surpassing the suggestive (<em>p</em> < 1 × 10<sup>−4</sup>) and Bonferroni-corrected (<em>p</em> < 8.6 × 10<sup>−7</sup>) thresholds. Genes <em>myhc</em>, <em>nlrc5</em>, <em>hydin</em>, and <em>gfod1</em> were linked to thermal stress. These findings may support marker-assisted selection for thermal stress resilience strains, promoting sustainable aquaculture.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111124"},"PeriodicalIF":3.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212379","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}
Pub Date : 2025-09-30DOI: 10.1016/j.ygeno.2025.111127
Fengcheng Song , Chen Gao , Yufei Zan , Yu Sun , Tingting Wang , Zhepei Zhang , Lupei Zhang , Zhengrong Yuan , Tianliu Zhang , Xue Gao
The F-box only protein (FBXO) family plays a critical role in protein ubiquitination, but the absence of research on the FBXO family in cattle (Bos taurus) persists.
In this study, 38 FBXO family members in cattle were identified and analyzed for the first time. Phylogenetic analysis demonstrated evolutionary conservation of FBXO members across Bovinae and model species, suggesting conserved biological functions. Using transcriptomic data, three muscle-specific FBXO genes (FBXO31, FBXO32, FBXO40) were identified. Importantly, silencing these genes in bovine skeletal muscle satellite cells affected the expression of genes involved in cell proliferation and differentiation. Furthermore, EdU staining and CCK8 assays revealed that silencing FBXO32 and FBXO40 accelerated cell proliferation. These findings indicate that these FBXO genes may influence myogenesis.
Collectively, the present study identified and analyzed the FBXO family members in cattle and revealed their potential effects on cattle muscle development, offering new insights for improving beef yield and quality.
{"title":"F-box only protein (FBXO) family genes in cattle (Bos taurus): Genome-wide identification and functions in the skeletal muscle development","authors":"Fengcheng Song , Chen Gao , Yufei Zan , Yu Sun , Tingting Wang , Zhepei Zhang , Lupei Zhang , Zhengrong Yuan , Tianliu Zhang , Xue Gao","doi":"10.1016/j.ygeno.2025.111127","DOIUrl":"10.1016/j.ygeno.2025.111127","url":null,"abstract":"<div><div>The F-box only protein (FBXO) family plays a critical role in protein ubiquitination, but the absence of research on the FBXO family in cattle (<em>Bos taurus</em>) persists.</div><div>In this study, 38 FBXO family members in cattle were identified and analyzed for the first time. Phylogenetic analysis demonstrated evolutionary conservation of FBXO members across Bovinae and model species, suggesting conserved biological functions. Using transcriptomic data, three muscle-specific FBXO genes (<em>FBXO31</em>, <em>FBXO32</em>, <em>FBXO40)</em> were identified. Importantly, silencing these genes in bovine skeletal muscle satellite cells affected the expression of genes involved in cell proliferation and differentiation. Furthermore, EdU staining and CCK8 assays revealed that silencing <em>FBXO32</em> and <em>FBXO40</em> accelerated cell proliferation. These findings indicate that these FBXO genes may influence myogenesis.</div><div>Collectively, the present study identified and analyzed the FBXO family members in cattle and revealed their potential effects on cattle muscle development, offering new insights for improving beef yield and quality.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111127"},"PeriodicalIF":3.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212469","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}
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