Genomics最新文献

{"title":"Deciphering common bean (Phaseolus Vulgaris L.) microbiome assemblages reveal mechanistic insights into host-pathogen-microbiome interactions","authors":"Aggrey Keya Osogo ,&nbsp;Francis Muyekho ,&nbsp;Hassan Were ,&nbsp;Patrick Okoth","doi":"10.1016/j.ygeno.2025.111064","DOIUrl":"10.1016/j.ygeno.2025.111064","url":null,"abstract":"<div><div>Common bean (<em>Phaseolus vulgaris L</em>.) is the primary source of proteins and nutrients in most households in sub-Saharan Africa. However, production of this crop is constrained by several biotic factors. While research on common bean plant-pathogen interactions has predominantly focused on binary relationships, the diversity of microbes naturally inhabiting plant tissues and their interactions has often been overlooked. Recent findings, however, show that these resident microbes actively contribute to plant defense mechanisms, rather than merely acting as passive bystanders. This study aimed to document and explore potential interactions within the common bean microbiome assemblages through field investigations in selected locations across the western regions of Kenya. Common bean leaf samples were collected from farmer's fields along motorable roads 3–5 km apart. Shotgun metagenomic analysis identified a diverse range of microorganisms, including bacteria, fungi, yeast, phytoplasmas, viruses, and bacteriophages, across multiple taxonomic levels—spanning 4 Kingdoms, 136 Phyla, 168 Classes, 360 Orders, 792 Families, 2039 Genera, and 6130 Species—both epiphytic and endophytic, and pathogenic or non-pathogenic. Pseudomonadota consistently showed the highest taxonomic annotation for antimicrobial-resistant organisms, highlighting its central role in resistance across the studied area. The sequences obtained were mapped to the EggNOG, CAZy, and KEGG databases to explore, assign, and predict gene functions. The EggNOG database emphasized the importance of “Replication, recombination, and repair” processes in maintaining genomic stability, along with amino acid transport, energy production, and metabolism. CAZy analysis revealed a significant presence of glycosyltransferases, particularly from GT1 and GT32 families, and noted the role of enzymes like Glycoside Hydrolases in plant defense against pathogens. KEGG pathway analysis underscored the central role of metabolic processes such as energy metabolism, translation, and carbohydrate metabolism. Key pathways linked to plant defense and resilience, including 2-oxocarboxylic acid metabolism, amino acid biosynthesis, and secondary metabolite biosynthesis, were identified. These findings underscore the role of metabolic and enzymatic processes in strengthening plant defenses and stress tolerance while laying the groundwork for multidisciplinary research to advance sustainable agriculture and food safety.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111064"},"PeriodicalIF":3.4,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144198808","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":"Ancient genomes reveal complex population interactions in the middle Yellow River basin during the Late Neolithic period","authors":"Zishuai Huang ,&nbsp;Jiaqi Gao ,&nbsp;Mingzhi Ma ,&nbsp;Wengao Hu ,&nbsp;Xin Xiao ,&nbsp;Hui Li","doi":"10.1016/j.ygeno.2025.111061","DOIUrl":"10.1016/j.ygeno.2025.111061","url":null,"abstract":"<div><div>The middle reaches of the Yellow River in the Late Neolithic period were the frontier of cultural communication between the Central Plains and the northern steppe. The remarkable sites that emerged during this period, such as Taosi, Shimao, and Lushanmao, played important roles in the formation of early Chinese civilization. Here we report ancient genomic data from 8 individuals from the three sites. Population genetics analysis revealed that the ancestries of these individuals were mainly related to the Yangshao culture populations from the Central Plains, supplemented by Northeast Asian ancestry. We also found an individual who was a genetic outlier at the Lushanmao site who carried excess Northeast Asian ancestry and harbored a genetic background similar to that of the Hongshan culture population. These findings provide a more detailed picture of genetic interactions and population migrations in northern China of Late Neolithic period and suggest potential cross-regional population interactions.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111061"},"PeriodicalIF":3.4,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144185407","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":"Integrating multi-omics analysis unveils the key mechanisms of PQS-enhanced Algicidal activity in Enterobacter hormaechei F2","authors":"Bin Zhang,&nbsp;Meiqi Yang,&nbsp;Wei Liu","doi":"10.1016/j.ygeno.2025.111060","DOIUrl":"10.1016/j.ygeno.2025.111060","url":null,"abstract":"<div><div>Quorum sensing, as a pivotal bacterial signaling pathway, exhibits substantial potential for regulating algicidal activity. This study pioneers the integration of multi-omics analyses (transcriptomics, proteomics, metabolomics) with phenotypic profiling to systematically unravel the molecular mechanisms underlying Pseudomonas Quinolone Signal (2-heptyl-3-hydroxy-4(1H)-quinolinone, PQS)-enhanced algicidal activity in <em>Enterobacter hormaechei</em> F2. Co-cultivation with PQS triggered marked reductions in algal biomass and chlorophyll-a levels, outperforming traditional approaches. Fourier-transform infrared spectroscopy (FTIR) revealed PQS-induced metabolic disruption and membrane degradation in algal cells. Transcriptomic profiling identified novel regulatory hubs, including upregulated glycolysis (<em>tktA</em>, transketolase), fatty acid degradation (<em>fadE</em>, acyl-CoA dehydrogenase), and chemotaxis (<em>malE</em>, maltose-binding protein) pathways. Proteomics confirmed PQS-driven enrichment of terpenoid precursors, notably DXS synthase (1-deoxy-D-xylulose-5-phosphate synthase), and quorum sensing effectors. Metabolomics highlighted amino acid derivatives (e.g., L-glutamate) and heterocyclic antibiotics as dominant algicidal metabolites. Crucially, multi-omics integration delineated a core network of 46 key nodes (e.g., ribose transporter <em>rbsB</em>, L-glutamate) coordinating energy metabolism, motility, and algicide synthesis. Fatty acid degradation enzymes (e.g., FadE) and flagellar assembly regulators (e.g., FlgK) emerged as previously unrecognized targets, with PQS significantly enhancing bacterial swarming motility (<em>p &lt;</em> 0.01) and biofilm formation. These findings establish the first mechanistic framework linking PQS signaling to algicidal process, demonstrating its role in synchronizing metabolic flux toward terpenoid synthesis while optimizing bacterial-algal interactions. Key pathways—including chemotaxis (<em>malE</em>) and terpenoid biosynthesis (DXS synthase)—provide actionable targets for engineering bioaugmented consortia or precision algicidal formulations. This work advances quorum sensing-driven strategies for sustainable harmful algal bloom (HAB) mitigation, offering scalable solutions for aquaculture and eutrophic water remediation with minimal ecological disruption. By bridging molecular mechanisms to field applications, the study underscores the translational potential of this approach in global water security initiatives.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111060"},"PeriodicalIF":3.4,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144180123","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":"LUC7L-201 is an important regulator of skeletal muscle growth and development in goats identified through integration of nanopore and Illumina sequencing","authors":"Aishao Shangguan,&nbsp;Juan Yang,&nbsp;Nian Zhang,&nbsp;Hu Tao,&nbsp;Feng Zhang,&nbsp;Tian Xu,&nbsp;Mingxin Chen,&nbsp;Qi Xiong","doi":"10.1016/j.ygeno.2025.111059","DOIUrl":"10.1016/j.ygeno.2025.111059","url":null,"abstract":"<div><div>Alternative splicing (AS) plays a crucial role in the post-transcriptional regulation of gene expression, influencing skeletal muscle growth and development. However, research into transcriptomic landscape of AS and its key isoforms associated with skeletal muscle in goats is comparatively limited compared with other livestock species such as pigs. In this study, longissimus dorsi muscles from 4 Macheng black goats and 4 Boer goats were used to perform Oxford Nanopore Technologies full-length sequencing and Illumina RNA-seq. A total of 91,874 unique full-length non-chimeric sequences and 10,955 novel isoforms were identified. Subsequently, we detected 13,866 AS events and 1702 novel long non-coding RNAs (lncRNAs), with exon skipping (4024, 29.02 %) being the most prevalent AS event. In addition, a total of 2267 differentially expressed isoforms (DEIs) were identified between Macheng black and Boer goats. Among these DEIs, 1301 isoforms were up-regulated and 966 were down-regulated in Macheng black goats. Functional enrichment analyses revealed that these DEIs were predominantly associated with pathways related to skeletal muscle development, cellular metabolic processes, and genetic information processing. Notably, we identified LUC7L-201 as an important isoform that negatively regulates cell proliferation and differentiation in goat primary myoblasts, as demonstrated by overexpression experiments. Overall, this study enhances our understanding of the transcriptomic diversity underlying skeletal muscle growth and development in goats, providing valuable insights for future research and potential applications in livestock management.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111059"},"PeriodicalIF":3.4,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144131889","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":"An updated Gallus gallus genome annotation through multi-tissue transcriptome analysis","authors":"Andressa O. de Lima ,&nbsp;Theros T. Ng ,&nbsp;Brandi Sparling ,&nbsp;Lisa M. Griggs ,&nbsp;Kenneth Lai ,&nbsp;Yvonne Drechsler ,&nbsp;R. David Hawkins","doi":"10.1016/j.ygeno.2025.111056","DOIUrl":"10.1016/j.ygeno.2025.111056","url":null,"abstract":"<div><div>This study presents an updated <em>Gallus gallus</em> genome annotation through a comprehensive multi-tissue transcriptome analysis aimed at enhancing the Functional Annotation of Animal Genomes (FAANG) efforts. Generating RNA sequencing data from 20 different chicken tissues and cell types allowed for the identification of 110,930 transcript isoforms, including approximately 37,000 unannotated transcripts. This expanded resource significantly enhances transcript diversity and functional annotation. We analyzed allele-specific expression (ASE) across tissues, revealing 11,530 unique ASE genes. Our findings elucidate the intricate landscape of gene expression patterns and allelic imbalances. Notably, tissue-specific isoforms and differentially expressed genes, particularly in reproductive and muscle tissues, showcase their relevance for traits like fertility and meat quality. The identification of novel lncRNAs and protein-coding genes underscores the necessity of continued genomic improvements. This work contributes valuable resources for breeding strategies focused on disease resistance and productivity enhancement, addressing global agricultural challenges and the evolving needs of poultry science.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111056"},"PeriodicalIF":3.4,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144093296","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":"A comprehensive approach for identifying filaggrin mutations and copy number variants by long-read sequencing","authors":"Akane Yuda ,&nbsp;Takako Nakamura ,&nbsp;Sakura Momose ,&nbsp;Sena Ishii ,&nbsp;Hiromu Tanaka ,&nbsp;Kiwako Yamamoto-Hanada ,&nbsp;Tatsuki Fukuie ,&nbsp;Yukihiro Ohya ,&nbsp;Toshifumi Nomura ,&nbsp;Emiko Noguchi","doi":"10.1016/j.ygeno.2025.111055","DOIUrl":"10.1016/j.ygeno.2025.111055","url":null,"abstract":"<div><div>Filaggrin (FLG) is essential for skin barrier function, but has highly diverse and complex mutations linked to various allergic and dermatological diseases. Current genotyping methods often fail to capture the full range of <em>FLG</em> variants, especially in regions with high sequence homology. To overcome this limitation, we developed a singleplex PCR method that amplifies <em>FLG</em> exon 3 using <em>FLG</em>-specific primers tailed with barcodes for sample identification, followed by long-read sequencing on the PacBio Sequel IIe system. After demultiplexing with the barcode sequences, pbmm2 and GATK HaplotypeCaller were used for alignment and variant calling, respectively. This method successfully identified single nucleotide variants, insertion-deletion variants, and copy number variations (CNVs), including several loss-of-function mutations. We also determined the <em>FLG</em> copy number in each allele, which ranged from 7 to 20 repeats. This comprehensive, convenient genotyping approach could significantly enhance diagnostic accuracy and personalized treatment strategies for allergy- and skin-related conditions.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111055"},"PeriodicalIF":3.4,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143977971","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":"Trichaptum biforme (Pallidohirschioporus biformis) genome decoding provides insights into carbohydrate degradation and polysaccharide synthesis","authors":"Xiuchao Xie ,&nbsp;Rong-Xin Chen ,&nbsp;Yu Song ,&nbsp;Chao Lin ,&nbsp;Ming Zhang ,&nbsp;Minglei Li ,&nbsp;Jianzhao Qi","doi":"10.1016/j.ygeno.2025.111057","DOIUrl":"10.1016/j.ygeno.2025.111057","url":null,"abstract":"<div><div><em>Trichaptum biforme</em> is a white-rot fungus that plays a key role in the process of cellulose degradation. In this study, we employed a suite of techniques to sequence the genome of <em>T. biforme</em>, and achieved high-quality assembly and detailed annotation. The genome spans 50.71 Mb, comprises 13 chromosomal pseudomolecules, and encodes 15,302 predicted genes, exhibiting a BUSCO completeness of 96.30 %. Comparative genomic analysis has elucidated the similarities in gene composition and the differences in evolutionary pressure between <em>T. biforme</em> and <em>T. abietinum</em>. Phylogenetic analysis revealed the evolutionary position of <em>T. abietinum</em> and indicates that their divergence time is 21.20 million years ago (MYAs). Bioinformatic analysis revealed 375 genes encoding carbohydrate-active enzymes (CAZymes), of which 144 CAZymes were predicted to interact with 18 polysaccharide synthases. In conclusion, this work reports for the first time the genome of <em>T. biforme</em>, providing a comprehensive understanding of its complex functions, and elucidating the genetic basis of its ability to degrade lignocellulose.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111057"},"PeriodicalIF":3.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143985934","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":"Long-term exposure to 17β-estradiol of the Manila clam (Ruditapes philippinarum): Shifts of gender ratio and changes of gene expression","authors":"Zhongming Huo ,&nbsp;Jiaxin Xiao ,&nbsp;Yang Liu ,&nbsp;Lei Fang ,&nbsp;Jiaxi Li ,&nbsp;Dongdong Li ,&nbsp;Wenwen Yang ,&nbsp;Qidi Wu ,&nbsp;Zhuang Li ,&nbsp;Jing Gu ,&nbsp;Yanjie Qin ,&nbsp;Xiwu Yan","doi":"10.1016/j.ygeno.2025.111052","DOIUrl":"10.1016/j.ygeno.2025.111052","url":null,"abstract":"<div><div>Estrogen is widely distributed in the aquatic environment, causing feminization, changes of gender ratio and reduced fecundity in aquatic organisms. 17β-estradiol is a potent estrogen with strong estrogenic activity and pseudo-persistence, which poses significant risks to global aquatic ecosystems. In this study, effects of long-term exposure to 17β-estradiol in the Manila clam (<em>Ruditapes philippinarum</em>) were investigated. The clams were treated with 17β-estradiol (10 μg/L) for 2 months and then subjected to dissection. Gonadal tissue sections were prepared for observation, and the sex ratio was calculated. The results showed that the female male ratio of clams in the control group was 0.93, which was close to 1. Nevertheless, the female male ratio of the 17β-estradiol-treated clams was 1.39, which was nearly 50 % higher than that in the control group. Furthermore, for clams in the control group, no hermaphrodites were observed. However, for clams treated with 17β-estradiol, 2 % of them were hermaphroditic, which was higher than that in natural environment (approximately one thousandth). It implies that long-term exposure to 17β-estradiol might affect sexual differentiation as well as sexual reversal in <em>R. Philippinarum</em>, promoting male individuals to reverse into female individuals. Comparative transcriptomics was conducted to identify genes related to sex differentiation in <em>R. Philippinarum</em>. Gene expression profiles of the estrogen-treated females (EF) were compared with those of the estrogen-treated males (EM), and 3751 differentially expressed genes (DEGs) were identified, among which 1512 were up-regulated in females, whereas 2239 were up-regulated in males. Meanwhile, the transcriptome profiles of females (DF) and males (DM) in the control group were compared, and 1718 differentially expressed genes (DEGs) were identified, of which 601 were upregulated in females and 1117 were upregulated in males. GO (gene ontology) and KEGG (Kyoto encyclopedia of genes and genomes) analyses showed that the above mentioned DEGs identified in both the estrogen treatment group and the control group were enriched in the ubiquitination pathway, ribosome, phagosome, and cytochrome P450 metabolic pathways. It is noteworthy that some of the gender-related DEGs identified in the comparison combination of DF vs DM were enriched in ubiquitination. In conculsion, the results indicate that exogenous estradiol treatment might influence sex differentiation in <em>R. Philippinarum</em>, enriching the knowledge on molecular mechanisms underlying sex differentiation in mollusks</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111052"},"PeriodicalIF":3.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143923860","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":"Study on the anticancer function and mechanism of cathelicidin-DM in liver cancer","authors":"Huang Hu ,&nbsp;Jingjing Tai ,&nbsp;Ruiyun Zhang ,&nbsp;Hong Zhang","doi":"10.1016/j.ygeno.2025.111049","DOIUrl":"10.1016/j.ygeno.2025.111049","url":null,"abstract":"<div><h3>Background</h3><div>Previous studies have shown that bioactive molecules secreted by toad skin possess anticancer properties. Cathelicidin-DM (C-DM) is a bioactive peptide secreted by toad skin, but its effects on tumor cells and the underlying molecular mechanisms remain unknown.</div></div><div><h3>Methods</h3><div>The impact of varying amphibian peptides on the viability of various tumor cells was determined by CCK-8. The influence of C-DM on liver cancer (LC) cell function was investigated using colony formation, flow cytometry, and Transwell. The anti-tumor activity of C-DM was evaluated by xenograft models. RNA-seq was done to confirm differentially expressed genes (DEGs), which were subject to GSEA. Cellular experiments were performed to verify the molecular regulatory mechanism of C-DM in LC.</div></div><div><h3>Results</h3><div>C-DM (100 μg/mL) had a significant repressive impact on the proliferation, migration, invasion, and cell cycle progression of HepG2 and Hep3B cells, and facilitated apoptosis. <em>In vivo</em> experiments validated the anti-tumor impact of C-DM, while its toxicity was low. DEG DHRS3 was enriched in the JAK-STAT pathway. Overexpression of DHRS3 fostered the malignant phenotype of LC cells and activated the JAK-STAT pathway. However, the addition of C-DM weakened the oncogenic properties of DHRS3 and repressed the JAK-STAT pathway.</div></div><div><h3>Conclusion</h3><div>C-DM exerted an anti-LC effect by downregulating DHRS3 and mediating the JAK-STAT pathway, indicating that C-DM may be a promising candidate drug for LC treatment.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111049"},"PeriodicalIF":3.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143895796","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":"Validation of male-specific markers confirmed an XY/XX-type sex determination system in Chinese dark sleeper (Odontobutis sinensis)","authors":"Xiaocan Li ,&nbsp;Jiaxiang Liu ,&nbsp;Qi Hong ,&nbsp;Xilan Ma ,&nbsp;Le Wang ,&nbsp;Zhenzhen Xie","doi":"10.1016/j.ygeno.2025.111053","DOIUrl":"10.1016/j.ygeno.2025.111053","url":null,"abstract":"<div><div>Next generation sequencing (NGS) method has been successfully used to identify sex-specific markers in many fish species. The Chinese dark sleeper (<em>Odontobutis sinensis</em>) is a commercially important aquaculture species in China. Here, by conducting whole genome sequencing of three females, three males and one female mixed pool, we initially identified 658 male-specific sequences and 242 female-specific sequences of Chinese dark sleeper. Based on polymerase chain reaction (PCR) confirmation, three markers showed 100 % male-specific amplification in 16 female and 16 male individuals from the Wuhan population, and this result was further validated using an additional 16 females and 16 males from the Guangdong population, demonstrating the reliability of these markers across multiple populations. These findings suggest a male heterogametic sex determination system in Chinese dark sleeper. Moreover, male-specific genes including <em>high mobility group box 3</em> (<em>hmgxb3</em>) and <em>insulin-like growth factor 2b</em> (<em>igf2b</em>) were identified through NR annotation, which might be candidate sex-determining genes in Chinese dark sleeper. Generally, these validated male-specific markers first demonstrated the existence of an XY-type sex determination system in Chinese dark sleeper and would make a significant contribution to the development of all-male breeding and understanding of sex determination mechanisms.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111053"},"PeriodicalIF":3.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143929179","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}