GenomicsPub Date : 2025-05-21DOI: 10.1016/j.ygeno.2025.111059
Aishao Shangguan, Juan Yang, Nian Zhang, Hu Tao, Feng Zhang, Tian Xu, Mingxin Chen, Qi Xiong
{"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, Juan Yang, Nian Zhang, Hu Tao, Feng Zhang, Tian Xu, Mingxin Chen, 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}
GenomicsPub Date : 2025-05-16DOI: 10.1016/j.ygeno.2025.111056
Andressa O. de Lima , Theros T. Ng , Brandi Sparling , Lisa M. Griggs , Kenneth Lai , Yvonne Drechsler , R. David Hawkins
{"title":"An updated Gallus gallus genome annotation through multi-tissue transcriptome analysis","authors":"Andressa O. de Lima , Theros T. Ng , Brandi Sparling , Lisa M. Griggs , Kenneth Lai , Yvonne Drechsler , 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 , Takako Nakamura , Sakura Momose , Sena Ishii , Hiromu Tanaka , Kiwako Yamamoto-Hanada , Tatsuki Fukuie , Yukihiro Ohya , Toshifumi Nomura , 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}
GenomicsPub Date : 2025-05-01DOI: 10.1016/j.ygeno.2025.111052
Zhongming Huo , Jiaxin Xiao , Yang Liu , Lei Fang , Jiaxi Li , Dongdong Li , Wenwen Yang , Qidi Wu , Zhuang Li , Jing Gu , Yanjie Qin , Xiwu Yan
{"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 , Jiaxin Xiao , Yang Liu , Lei Fang , Jiaxi Li , Dongdong Li , Wenwen Yang , Qidi Wu , Zhuang Li , Jing Gu , Yanjie Qin , 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}
GenomicsPub Date : 2025-05-01DOI: 10.1016/j.ygeno.2025.111057
Xiuchao Xie , Rong-Xin Chen , Yu Song , Chao Lin , Ming Zhang , Minglei Li , Jianzhao Qi
{"title":"Trichaptum biforme (Pallidohirschioporus biformis) genome decoding provides insights into carbohydrate degradation and polysaccharide synthesis","authors":"Xiuchao Xie , Rong-Xin Chen , Yu Song , Chao Lin , Ming Zhang , Minglei Li , 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}
GenomicsPub Date : 2025-05-01DOI: 10.1016/j.ygeno.2025.111049
Huang Hu , Jingjing Tai , Ruiyun Zhang , Hong Zhang
{"title":"Study on the anticancer function and mechanism of cathelicidin-DM in liver cancer","authors":"Huang Hu , Jingjing Tai , Ruiyun Zhang , 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}
GenomicsPub Date : 2025-05-01DOI: 10.1016/j.ygeno.2025.111053
Xiaocan Li , Jiaxiang Liu , Qi Hong , Xilan Ma , Le Wang , Zhenzhen Xie
{"title":"Validation of male-specific markers confirmed an XY/XX-type sex determination system in Chinese dark sleeper (Odontobutis sinensis)","authors":"Xiaocan Li , Jiaxiang Liu , Qi Hong , Xilan Ma , Le Wang , 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}
GenomicsPub Date : 2025-05-01DOI: 10.1016/j.ygeno.2025.111050
Siriluck Ponsuksili , Shuaichen Li , Puntita Siengdee , Frieder Hadlich , Nares Trakooljul , Michael Oster , Henry Reyer , Klaus Wimmers
{"title":"DNA methylation in adipocyte differentiation of porcine mesenchymal stem cells and the impact of the donor metabolic type","authors":"Siriluck Ponsuksili , Shuaichen Li , Puntita Siengdee , Frieder Hadlich , Nares Trakooljul , Michael Oster , Henry Reyer , Klaus Wimmers","doi":"10.1016/j.ygeno.2025.111050","DOIUrl":"10.1016/j.ygeno.2025.111050","url":null,"abstract":"<div><div>The impact of metabolic donor mesenchymal stem cells (MSCs) on DNA methylation, a critical epigenetic mechanism, significantly regulates adipogenesis. In this study, we investigated epigenetic changes during differentiation of synovial MSCs (SMSCs) from two pig breeds differing in metabolic performance (German Landrace (DL) and Angeln Saddleback (AS)). Stimulation of SMSCs to differentiate into adipocytes in vitro revealed several differentially methylated loci and regions, particularly on gene promoter regions, at day 7 and 14. AS breeds, known for higher fat deposition, exhibited more hypermethylation compared to DL. Furthermore, we utilized differentially methylated regions associated with the adipogenic process and breed, especially those in promoter regions, for predicting transcription factor motifs. This study provides insights into the DNA methylation landscape during adipogenesis in pigs of different metabolic types, revealing its role in regulating cell fate and donor memory retention in culture.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111050"},"PeriodicalIF":3.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143887943","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}
GenomicsPub Date : 2025-05-01DOI: 10.1016/j.ygeno.2025.111054
Yanling Ding , Yanfeng Zhang , Xiaonan Zhou , Chenglong Li , Zonghua Su , Junjie Xu , Yuangang Shi , Yun Ma , Cong-Jun Li , Xiaolong Kang
{"title":"miR-144 regulates bovine skeletal muscle satellite cell proliferation and differentiation by targeting the NACC1 gene","authors":"Yanling Ding , Yanfeng Zhang , Xiaonan Zhou , Chenglong Li , Zonghua Su , Junjie Xu , Yuangang Shi , Yun Ma , Cong-Jun Li , Xiaolong Kang","doi":"10.1016/j.ygeno.2025.111054","DOIUrl":"10.1016/j.ygeno.2025.111054","url":null,"abstract":"<div><div>MicroRNAs (miRNAs) are small, non-coding RNAs encoded by eukaryotic genomes that exhibit tissue-specific and temporal expression patterns. They play multifaceted roles in regulating gene expression across various tissues and developmental stages through several regulatory pathways. miR-144 has been implicated in cellular development in multiple species. However, its specific role in bovine skeletal muscle satellite cells (BSMSCs) remains unclear. The study aimed to elucidate the function of miR-144 in BSMSC development. The findings indicate that miR-144 inhibits BSMSC proliferation while promoting its differentiation. miR-144 overexpression led to the identification of 476 differentially expressed genes (DEGs) through RNA sequencing (RNA-seq), which were primarily involved in adrenergic, MAPK, and PI3K-AKT signaling pathways. Dual luciferase reporter assays confirmed that <em>NACC1</em> is a target of bta-miR-144. Further analysis revealed that <em>NACC1</em> promotes BSMSC proliferation and suppresses its differentiation. Collectively, these results suggest that miR-144 modulates BSMSC development by negatively regulating the <em>NACC1</em> gene.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111054"},"PeriodicalIF":3.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143923861","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}
GenomicsPub Date : 2025-05-01DOI: 10.1016/j.ygeno.2025.111051
Huaxi Huang , Chunfeng Tang , Fanglin Liu , Yong Ren , Siren Cheng , Yude Peng , Rong Chen , Qin Liu
{"title":"Comparative nutrient profiling of three Murraya species through combined metabolomic and transcriptomic analyses","authors":"Huaxi Huang , Chunfeng Tang , Fanglin Liu , Yong Ren , Siren Cheng , Yude Peng , Rong Chen , Qin Liu","doi":"10.1016/j.ygeno.2025.111051","DOIUrl":"10.1016/j.ygeno.2025.111051","url":null,"abstract":"<div><div><em>Murraya</em>, a valuable plant resource, plays a critical role in medicine, industry, and landscaping. Despite its significance, research on <em>Murraya</em>, as well as its development and utilization, remains limited. Therefore, investigating the metabolites and metabolic pathways within its germplasm is of considerable importance. In this study, we utilized LC-MS to comprehensively profile amino acids, nucleotides, saccharides, and vitamins in the leaves of three <em>Murraya</em> materials. In parallel, transcriptome analysis was conducted to unravel the metabolic pathways associated with key metabolites and to identify candidate genes. Our metabolomic profiling identified a total of 215 metabolites, including 95 saccharides, 85 amino acids, 25 nucleotides, and 10 vitamins. Among these, D-(+)-Maltose Monohydrate, L(+)-Arabinose, and DL-Xylose were identified as pivotal candidate metabolites contributing to the distinct characteristics of <em>Murraya</em> materials through differential metabolite analysis. Furthermore, transcriptome and qPCR analysis revealed 11 differentially expressed genes, which are proposed as potential regulators influencing the differential accumulation of these key metabolites. Our study reveals that among the three materials examined, <em>Murraya tetramera</em> exhibits heightened potential for medicinal and industrial applications. This research significantly advances our comprehension of the metabolic regulatory mechanisms at play within <em>Murraya</em> species. Furthermore, it lays a vital scientific groundwork that is instrumental for the advancement of medicinal resources, the enhancement of plant varieties, the expansion of industrial utilization, and the promotion of sustainable agricultural practices for <em>Murraya</em>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111051"},"PeriodicalIF":3.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143918344","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}