Pub Date : 2025-01-23DOI: 10.1016/j.ygeno.2025.111007
Lin Xian , Sunil Kumar Sahu , Xiaolin Huang , Chao Li , Yu Liang , Yan Ou-Yang , Huayang Guo , Bo Liu , Kecheng Zhu , Baosuo Liu , Nan Zhang , Tengfei Zhu , Qiye Li , Dianchang Zhang
Siganus guttatus and Siganus oramin are two major species that are naturally distributed along the Eastern Pacific coast and possess considerable ecological and economic value. Here, we present the construction and comparative analysis of the chromosome-level genomes of these two Siganus species. Employing a hybrid assembly strategy, we partitioned and independently assembled the PacBio, Illumina and Hi-C reads of S. guttatus and S. oramin, resulting in chromosome-level genomes. The assembly sizes (N50 size, BUSCO completeness) of the two genomes were 642.4 M (25.76 M, 98.26 %) and 502.8 M (16.98 M, 98.8 %) for S. guttatus and S. oramin, respectively, exhibiting high contiguity and integrity. This study marks the first successful assembly of chromosome-level genomes in Siganus species, along with an initial exploration of their dietary habits and habitats through comparative genomics analysis. These findings offer essential resources for comparative genomics and molecular evolution research.
{"title":"Chromosome-scale genomes of ecologically and economically important rabbitfish Siganus guttatus and Siganus oramin","authors":"Lin Xian , Sunil Kumar Sahu , Xiaolin Huang , Chao Li , Yu Liang , Yan Ou-Yang , Huayang Guo , Bo Liu , Kecheng Zhu , Baosuo Liu , Nan Zhang , Tengfei Zhu , Qiye Li , Dianchang Zhang","doi":"10.1016/j.ygeno.2025.111007","DOIUrl":"10.1016/j.ygeno.2025.111007","url":null,"abstract":"<div><div><em>Siganus guttatus</em> and <em>Siganus oramin</em> are two major species that are naturally distributed along the Eastern Pacific coast and possess considerable ecological and economic value. Here, we present the construction and comparative analysis of the chromosome-level genomes of these two <em>Siganus</em> species. Employing a hybrid assembly strategy, we partitioned and independently assembled the PacBio, Illumina and Hi-C reads of <em>S. guttatus</em> and <em>S. oramin,</em> resulting in chromosome-level genomes. The assembly sizes (N50 size, BUSCO completeness) of the two genomes were 642.4 M (25.76 M, 98.26 %) and 502.8 M (16.98 M, 98.8 %) for <em>S. guttatus</em> and <em>S. oramin</em>, respectively, exhibiting high contiguity and integrity. This study marks the first successful assembly of chromosome-level genomes in <em>Siganus</em> species, along with an initial exploration of their dietary habits and habitats through comparative genomics analysis. These findings offer essential resources for comparative genomics and molecular evolution research.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111007"},"PeriodicalIF":3.4,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037813","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}
Pub Date : 2025-01-23DOI: 10.1016/j.ygeno.2025.111004
Dandan Xiao , Jiahao Liu , Jing Wang , Xiaoqian Yang , Yuzhang Yang , Ruen Yu , Chun Wang , Hongbo Gao , Yanwei Wang , Yanping Liu , Dingchen Fan , Furong Lin
Gleditsia sinensis Lam. (G. sinensis) as an important species within the Leguminosae family, has been utilized in Chinese medicine for centuries, and its thorns serve as a chief medicinal ingredient. The absence of a comprehensive genome database has hindered its in-depth research. In this investigation, a chromosome-level de novo genome assembly of G. sinensis ‘Yulin No.1’ was achieved, which harbors a 786.13 Mb sized genome with 36,408 protein-coding genes and experiences two WGD events. The comparative and evolutionary analysis unveiled the close phylogenetic relationship between G. sinensis and eight other Leguminosae species. The WGCNA and gene family analysis further indicated that GsinMYB was involved in the development of thorns. This investigation offered a high-level genome of G. sinensis, facilitating comparisons in Leguminosae species evolution and functional elucidation. It also provided key insights for further research on the molecular regulation mechanisms of thorn development in plants and the molecular breeding of G. sinensis.
{"title":"Chromosome-level de novo genome unveils the evolution of Gleditsia sinensis and thorns development","authors":"Dandan Xiao , Jiahao Liu , Jing Wang , Xiaoqian Yang , Yuzhang Yang , Ruen Yu , Chun Wang , Hongbo Gao , Yanwei Wang , Yanping Liu , Dingchen Fan , Furong Lin","doi":"10.1016/j.ygeno.2025.111004","DOIUrl":"10.1016/j.ygeno.2025.111004","url":null,"abstract":"<div><div><em>Gleditsia sinensis</em> Lam. (<em>G. sinensis</em>) as an important species within the Leguminosae family, has been utilized in Chinese medicine for centuries, and its thorns serve as a chief medicinal ingredient. The absence of a comprehensive genome database has hindered its in-depth research. In this investigation, a chromosome-level de novo genome assembly of <em>G. sinensis</em> ‘Yulin No.1’ was achieved, which harbors a 786.13 Mb sized genome with 36,408 protein-coding genes and experiences two WGD events. The comparative and evolutionary analysis unveiled the close phylogenetic relationship between <em>G. sinensis</em> and eight other Leguminosae species. The WGCNA and gene family analysis further indicated that <em>GsinMYB</em> was involved in the development of thorns. This investigation offered a high-level genome of <em>G. sinensis</em>, facilitating comparisons in Leguminosae species evolution and functional elucidation. It also provided key insights for further research on the molecular regulation mechanisms of thorn development in plants and the molecular breeding of <em>G. sinensis</em>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111004"},"PeriodicalIF":3.4,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037810","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}
Pub Date : 2025-01-22DOI: 10.1016/j.ygeno.2025.110998
Jing Xu , Hao Peng , Renzhuo Kuang , Zheyu Han , Honghong Zhou , Mingyang Hu , YaPing Guo , Zhixiang Xu , Daoyuan Wang , Ruixian Ma , Daisuke Takao , Mengjin Zhu , Fenge Li , Yunxia Zhao
Intramuscular fat is an essential component of muscle tissue, and understanding its contribution to skeletal muscle fat infiltration and meat quality, together with the underlying genetic mechanisms, is a major topic in pig husbandry. However, the composition of cell types and gene expression profiles essential for this purpose remain largely unexplored. Here, we performed single-cell transcriptome analysis on muscle tissue from adult pigs and identified 15 cell types, including three previously uncharacterized types of adipocytes: Adipocyte 1, Adipocyte 2, and Aregs. Phenotypic analysis showed their proportions correlated closely with intramuscular fat content. Based on integrated analysis of ATAC-seq with RNA-seq data, Adipocyte 1 and Aregs have gene expression profiles and transcription factor (TF) motif enrichment typical of adipocytes. On the other hand, myogenic TF motifs were enriched in marker gene promoters in Adipocyte 2, suggesting that these cells originate from muscle cells. Moreover, the marker gene promoters and lineage-specific TF expression in these three adipocyte types were conserved between pigs and humans. These findings provide deep insights towards understanding the complexity of mammalian intramuscular adipocyte types and the gene regulation underlying their organization and function.
{"title":"Single-cell transcriptome reveals three types of adipocytes associated with intramuscular fat content in pigs","authors":"Jing Xu , Hao Peng , Renzhuo Kuang , Zheyu Han , Honghong Zhou , Mingyang Hu , YaPing Guo , Zhixiang Xu , Daoyuan Wang , Ruixian Ma , Daisuke Takao , Mengjin Zhu , Fenge Li , Yunxia Zhao","doi":"10.1016/j.ygeno.2025.110998","DOIUrl":"10.1016/j.ygeno.2025.110998","url":null,"abstract":"<div><div>Intramuscular fat is an essential component of muscle tissue, and understanding its contribution to skeletal muscle fat infiltration and meat quality, together with the underlying genetic mechanisms, is a major topic in pig husbandry. However, the composition of cell types and gene expression profiles essential for this purpose remain largely unexplored. Here, we performed single-cell transcriptome analysis on muscle tissue from adult pigs and identified 15 cell types, including three previously uncharacterized types of adipocytes: Adipocyte 1, Adipocyte 2, and Aregs. Phenotypic analysis showed their proportions correlated closely with intramuscular fat content. Based on integrated analysis of ATAC-seq with RNA-seq data, Adipocyte 1 and Aregs have gene expression profiles and transcription factor (TF) motif enrichment typical of adipocytes. On the other hand, myogenic TF motifs were enriched in marker gene promoters in Adipocyte 2, suggesting that these cells originate from muscle cells. Moreover, the marker gene promoters and lineage-specific TF expression in these three adipocyte types were conserved between pigs and humans. These findings provide deep insights towards understanding the complexity of mammalian intramuscular adipocyte types and the gene regulation underlying their organization and function.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110998"},"PeriodicalIF":3.4,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037821","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}
Pub Date : 2025-01-22DOI: 10.1016/j.ygeno.2025.111008
Tao Tang , Jing Zhou , Meigui Wang , Siqi Xia , Wenqiang Sun , Xianbo Jia , Jie Wang , Songjia Lai
The transition period from late pregnancy to early lactation in dairy cows involves significant metabolic changes to cope with the challenges related to energy metabolism. Muscle tissue, as the largest energy-metabolizing tissue in dairy cows, plays a crucial role in energy metabolism. Furthermore, circular RNAs (circRNAs) have been shown to play key roles in various biological events. However, the regulatory mechanisms of energy metabolism and muscle cells mediated by circRNAs in the muscle tissue of ketotic dairy cows remain unclear. Here, we identified a total of 5103 circRNAs in the muscle tissue of ketosis-affected cows. Among these, compared to healthy cows, 57 circRNAs were differentially expressed in the muscle tissue of ketosis-affected cows, with 39 upregulated and 18 downregulated. Functional enrichment analysis based on the source genes of circRNAs indicated that circ-30,628 is closely related to carbon metabolism, and circ-CoQ2 is associated with mitochondrial energy metabolism. Given the sponge effect of circRNAs on miRNAs, we further predicted the network relationships of downstream miRNAs and mRNAs of circ-30,628 and circ-CoQ2, and found that their downstream target genes are involved in signaling pathways such as MAPK, Wnt, FoxO, and autophagy, which is associated with the proliferation, differentiation, energy metabolism, oxidative stress, and mitochondrial function of muscle cells. In summary, these findings provide a theoretical basis for understanding the functions of circRNAs regulating energy metabolism in the muscle tissue of ketosis-affected cows, thereby reducing the accumulation of ketone bodies to prevent the occurrence of ketosis in dairy cows.
{"title":"Transcriptomics reveals the regulatory mechanisms of circRNA in the muscle tissue of cows with ketosis postpartum","authors":"Tao Tang , Jing Zhou , Meigui Wang , Siqi Xia , Wenqiang Sun , Xianbo Jia , Jie Wang , Songjia Lai","doi":"10.1016/j.ygeno.2025.111008","DOIUrl":"10.1016/j.ygeno.2025.111008","url":null,"abstract":"<div><div>The transition period from late pregnancy to early lactation in dairy cows involves significant metabolic changes to cope with the challenges related to energy metabolism. Muscle tissue, as the largest energy-metabolizing tissue in dairy cows, plays a crucial role in energy metabolism. Furthermore, circular RNAs (circRNAs) have been shown to play key roles in various biological events. However, the regulatory mechanisms of energy metabolism and muscle cells mediated by circRNAs in the muscle tissue of ketotic dairy cows remain unclear. Here, we identified a total of 5103 circRNAs in the muscle tissue of ketosis-affected cows. Among these, compared to healthy cows, 57 circRNAs were differentially expressed in the muscle tissue of ketosis-affected cows, with 39 upregulated and 18 downregulated. Functional enrichment analysis based on the source genes of circRNAs indicated that circ-30,628 is closely related to carbon metabolism, and circ-CoQ<sub>2</sub> is associated with mitochondrial energy metabolism. Given the sponge effect of circRNAs on miRNAs, we further predicted the network relationships of downstream miRNAs and mRNAs of circ-30,628 and circ-CoQ<sub>2</sub>, and found that their downstream target genes are involved in signaling pathways such as MAPK, Wnt, FoxO, and autophagy, which is associated with the proliferation, differentiation, energy metabolism, oxidative stress, and mitochondrial function of muscle cells. In summary, these findings provide a theoretical basis for understanding the functions of circRNAs regulating energy metabolism in the muscle tissue of ketosis-affected cows, thereby reducing the accumulation of ketone bodies to prevent the occurrence of ketosis in dairy cows.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111008"},"PeriodicalIF":3.4,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037890","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}
Pub Date : 2025-01-22DOI: 10.1016/j.ygeno.2025.111005
Binpeng Xi , Zengkui Lu , Rui Zhang , Shengguo Zhao , Jianye Li , Xuejiao An , Yaojing Yue
N6-methyladenosine (m6A) modification of RNA is a critical post-transcriptional modification, that dynamically contributes to testicular development and spermatogenesis. Nevertheless, the investigation into the role of m6A in testicular development of sheep remains insufficient. Herein, we conducted a comprehensive analysis of the m6A transcriptome landscape in the testes of F1 hybrid Southdown × Hu sheep across M0 (0 months old, newborn), M3 (3 months old, sexually immature), M6 (6 months old, sexually mature), and Y1 (1 years old, adult). By profiling the m6A signatures across the transcriptome, we observed distinct differences in m6A modification patterns during sheep testicular development. Our cross-analysis of m6A and mRNA expression revealed that the expression of 743 genes and their m6A modification were concurrent. Notably, the combined analysis of the two comparative groups, M0 vs. M6 and M0 vs. Y1, exhibited a positive correlation, with 30 candidate genes each located within the largest protein-protein interaction network. Intriguingly, eight key hub genes (VEGFA, HDAC9, ZBTB40, KDM5B, MTRR, EAPS1, TSSK3, and BMP4) were identified to be associated with the regulation of sheep testicular development and spermatogenesis. These findings contribute to a deeper understanding of the dynamic role of m6A modification in sheep testicular biology. This study to map RNA m6A modification in sheep testes at different ages, providing novel insights into m6A topology and the molecular mechanisms associated with spermatogenesis in Southdown × Hu sheep F1 hybrids and laying the foundation for further investigations of mammalian spermatogenesis.
{"title":"Comprehensive analysis of the transcriptome-wide m6A Methylome in sheep testicular development","authors":"Binpeng Xi , Zengkui Lu , Rui Zhang , Shengguo Zhao , Jianye Li , Xuejiao An , Yaojing Yue","doi":"10.1016/j.ygeno.2025.111005","DOIUrl":"10.1016/j.ygeno.2025.111005","url":null,"abstract":"<div><div>N6-methyladenosine (m6A) modification of RNA is a critical post-transcriptional modification, that dynamically contributes to testicular development and spermatogenesis. Nevertheless, the investigation into the role of m6A in testicular development of sheep remains insufficient. Herein, we conducted a comprehensive analysis of the m6A transcriptome landscape in the testes of F1 hybrid Southdown × Hu sheep across M0 (0 months old, newborn), M3 (3 months old, sexually immature), M6 (6 months old, sexually mature), and Y1 (1 years old, adult). By profiling the m6A signatures across the transcriptome, we observed distinct differences in m6A modification patterns during sheep testicular development. Our cross-analysis of m6A and mRNA expression revealed that the expression of 743 genes and their m6A modification were concurrent. Notably, the combined analysis of the two comparative groups, M0 vs. M6 and M0 vs. Y1, exhibited a positive correlation, with 30 candidate genes each located within the largest protein-protein interaction network. Intriguingly, eight key hub genes (<em>VEGFA</em>, <em>HDAC9</em>, <em>ZBTB40</em>, <em>KDM5B</em>, <em>MTRR</em>, <em>EAPS1</em>, <em>TSSK3</em>, and <em>BMP4</em>) were identified to be associated with the regulation of sheep testicular development and spermatogenesis. These findings contribute to a deeper understanding of the dynamic role of m6A modification in sheep testicular biology. This study to map RNA m6A modification in sheep testes at different ages, providing novel insights into m6A topology and the molecular mechanisms associated with spermatogenesis in Southdown × Hu sheep F1 hybrids and laying the foundation for further investigations of mammalian spermatogenesis.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111005"},"PeriodicalIF":3.4,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037762","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}
Pub Date : 2025-01-22DOI: 10.1016/j.ygeno.2025.111003
Runyang Zhou , Xi Peng , Yao Teng , Sian Liu , Yingdan Yuan
Dendrobium is divided into ornamental and medicinal varieties due to ornamental and medicinal values. However, current research mainly focuses on medicinal Dendrobium, with less study on the medicinal value of ornamental Dendrobium. We analyzed the microstructures, active components of the stems from twelve ornamental Dendrobium, and explored the biosynthetic networks of these active components based on transcriptome sequencing. This study found the Dendrobium with the highest content of polysaccharide, alkaloid, and flavonoid was Dendrobium aphyllum (53.89 %), Dendrobium thyrsiflorum (2.11 %) and Dendrobium loddigesii (7.21 %). Further research revealed 9 DEGs associated with polysaccharide biosynthesis were highly expressed in D. aphyllum; 4 DEGs related to alkaloid biosynthesis were highly expressed in D. thyrsiflorum; 8 DEGs associated with flavonoid biosynthesis were highly expressed in D. loddigesii. This study revealed the potential medicinal value of ornamental Dendrobium and the synthetic mechanisms of its medicinal components, providing a foundation for the medical applications of ornamental Dendrobium.
{"title":"Transcriptome analysis reveals potential medicinal ingredient synthesis in ornamental Dendrobium","authors":"Runyang Zhou , Xi Peng , Yao Teng , Sian Liu , Yingdan Yuan","doi":"10.1016/j.ygeno.2025.111003","DOIUrl":"10.1016/j.ygeno.2025.111003","url":null,"abstract":"<div><div><em>Dendrobium</em> is divided into ornamental and medicinal varieties due to ornamental and medicinal values. However, current research mainly focuses on medicinal <em>Dendrobium</em>, with less study on the medicinal value of ornamental <em>Dendrobium</em>. We analyzed the microstructures, active components of the stems from twelve ornamental <em>Dendrobium</em>, and explored the biosynthetic networks of these active components based on transcriptome sequencing. This study found the <em>Dendrobium</em> with the highest content of polysaccharide, alkaloid, and flavonoid was <em>Dendrobium aphyllum</em> (53.89 %), <em>Dendrobium thyrsiflorum</em> (2.11 %) and <em>Dendrobium loddigesii</em> (7.21 %). Further research revealed 9 DEGs associated with polysaccharide biosynthesis were highly expressed in <em>D. aphyllum</em>; 4 DEGs related to alkaloid biosynthesis were highly expressed in <em>D. thyrsiflorum</em>; 8 DEGs associated with flavonoid biosynthesis were highly expressed in <em>D. loddigesii</em>. This study revealed the potential medicinal value of ornamental <em>Dendrobium</em> and the synthetic mechanisms of its medicinal components, providing a foundation for the medical applications of ornamental <em>Dendrobium</em>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111003"},"PeriodicalIF":3.4,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037830","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}
Sinojackia sarcocarpa, an endangered ornamental plant endemic to China, faces germination challenges that contribute to its endangered status. The mechanisms of its seed dormancy are not well understood. This study used morphological, physiological, transcriptomic, and gene function analyses to investigate these mechanisms. Our research shows that seed dormancy in Sinojackia sarcocarpa involves both physical and physiological factors. We found that removing the hard endocarp and applying gibberellic acid can effectively break dormancy. Transcriptomic analysis identified 2218 up-regulated and 374 down-regulated genes during germination. Notably, DOG1-domain genes SsDOGL4, SsTGA9, and SsTGA10 were significantly downregulated, while SsDOG1 was not. Additionally, overexpression of SsDOGL4 in Arabidopsis endosperm was found to enhance seed dormancy. Collectively, these findings offer significant insights into the mechanisms underlying seed dormancy in this endangered plant species.
{"title":"Integrated analyses provide insights into the seed dormancy mechanisms of the endangered plant Sinojackia sarcocarpa","authors":"Yao Yang, Tingting Feng, Xianzhe Zheng, Huifang Zheng, Hao Tang, Xiaobo Yu","doi":"10.1016/j.ygeno.2025.110991","DOIUrl":"10.1016/j.ygeno.2025.110991","url":null,"abstract":"<div><div><em>Sinojackia sarcocarpa</em>, an endangered ornamental plant endemic to China, faces germination challenges that contribute to its endangered status. The mechanisms of its seed dormancy are not well understood. This study used morphological, physiological, transcriptomic, and gene function analyses to investigate these mechanisms. Our research shows that seed dormancy in <em>Sinojackia sarcocarpa</em> involves both physical and physiological factors. We found that removing the hard endocarp and applying gibberellic acid can effectively break dormancy. Transcriptomic analysis identified 2218 up-regulated and 374 down-regulated genes during germination. Notably, DOG1-domain genes <em>SsDOGL4</em>, <em>SsTGA9</em>, and <em>SsTGA10</em> were significantly downregulated, while <em>SsDOG1</em> was not. Additionally, overexpression of <em>SsDOGL4</em> in <em>Arabidopsis</em> endosperm was found to enhance seed dormancy. Collectively, these findings offer significant insights into the mechanisms underlying seed dormancy in this endangered plant species.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110991"},"PeriodicalIF":3.4,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028486","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}
Pub Date : 2025-01-21DOI: 10.1016/j.ygeno.2025.111002
Shaoyuan Xu , Dongling Hu , Yanqin Ye , Yanli Mu , Yao Xiong , Yuanzhen Zhang
Background
Current endometrial receptivity analysis is invasive, preventing embryo transfer during the biopsy cycle. This study aims to screen serum sncRNAs as non-invasive biomarkers for ERA tests.
Methods
The study included 12 infertile patients undergoing IVF-ET and ERA, whose serum samples were collected for high-energy sequencing technology to detect sncRNA expression profiles. We overexpressed and knocked down tsRNA-35:73-Asp-GTC-1 in the decidualized Immortalized Human Eutopic Endometrial Stromal Cells (HESC) model cultured in vitro to further investigate the its effect on decidualization. The predicted tsRNA-35:73-Asp-GTC-1 target gene was verified by PCR analysis.
Results
We screened 286 differentially expressed tsRNAs, 46 miRNAs, and 106 piRNAs. KEGG analysis indicated that differentially expressed tsRNAs were associated with pathways such as ‘Calcium signaling pathway,’ ‘Sphingolipid signaling pathway,’ etc. The results of RT-qPCR validation showed that the trends of four significantly differentially expressed tsRNAs in serum and endometrium were consistent with sequencing results. ROC curves demonstrated that these four tsRNAs have good predictive value for endometrial receptivity. Overexpression of tsRNA-35:73-Asp-GTC-1 affected the morphology of decidualized cells, and the decidualization indicators also showed a decreasing trend. While knocking down tsRNA-35:73-Asp-GTC-1 had the opposite effect. The RT-qPCR results showed that tsRNA-35:73-Asp-GTC-1 was associated with the Wnt3 target gene.
Conclusion
Serum sncRNA analysis shows potential for studying the molecular mechanisms of endometrial receptivity. Four serum tsRNAs can serve as novel biomarkers for non-invasive endometrial receptivity detection. TsRNA-35:73-Asp-GTC-1 may further regulate endometrial receptivity by targeting Wnt3.
{"title":"Identification of serum small non-coding RNA as biomarkers for endometrial receptivity","authors":"Shaoyuan Xu , Dongling Hu , Yanqin Ye , Yanli Mu , Yao Xiong , Yuanzhen Zhang","doi":"10.1016/j.ygeno.2025.111002","DOIUrl":"10.1016/j.ygeno.2025.111002","url":null,"abstract":"<div><h3>Background</h3><div>Current endometrial receptivity analysis is invasive, preventing embryo transfer during the biopsy cycle. This study aims to screen serum sncRNAs as non-invasive biomarkers for ERA tests.</div></div><div><h3>Methods</h3><div>The study included 12 infertile patients undergoing IVF-ET and ERA, whose serum samples were collected for high-energy sequencing technology to detect sncRNA expression profiles. We overexpressed and knocked down tsRNA-35:73-Asp-GTC-1 in the decidualized Immortalized Human Eutopic Endometrial Stromal Cells (HESC) model cultured in vitro to further investigate the its effect on decidualization. The predicted tsRNA-35:73-Asp-GTC-1 target gene was verified by PCR analysis.</div></div><div><h3>Results</h3><div>We screened 286 differentially expressed tsRNAs, 46 miRNAs, and 106 piRNAs. KEGG analysis indicated that differentially expressed tsRNAs were associated with pathways such as ‘Calcium signaling pathway,’ ‘Sphingolipid signaling pathway,’ etc. The results of RT-qPCR validation showed that the trends of four significantly differentially expressed tsRNAs in serum and endometrium were consistent with sequencing results. ROC curves demonstrated that these four tsRNAs have good predictive value for endometrial receptivity. Overexpression of tsRNA-35:73-Asp-GTC-1 affected the morphology of decidualized cells, and the decidualization indicators also showed a decreasing trend. While knocking down tsRNA-35:73-Asp-GTC-1 had the opposite effect. The RT-qPCR results showed that tsRNA-35:73-Asp-GTC-1 was associated with the Wnt3 target gene.</div></div><div><h3>Conclusion</h3><div>Serum sncRNA analysis shows potential for studying the molecular mechanisms of endometrial receptivity. Four serum tsRNAs can serve as novel biomarkers for non-invasive endometrial receptivity detection. TsRNA-35:73-Asp-GTC-1 may further regulate endometrial receptivity by targeting Wnt3.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111002"},"PeriodicalIF":3.4,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028484","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}
Pub Date : 2025-01-20DOI: 10.1016/j.ygeno.2025.111000
Yanqing Wu , Jiao Liu , Lu Zhao , Guisheng Zhou , Yuhan Tang
Sorghum is an increasingly popular topic of research in elucidating survival and adaptation approaches to augmented salinity. Nonetheless, little is known about the outcome and modulatory networks involved in the gibberellic acid (GA3)-induced salt stress alleviation in sorghum. Here, we identified 50 mg/L GA3 as the optimal concentration for sorghum (‘Jitian 3’) development under salt stress. Based on genome-wide DNA methylation analysis, CpG sites displayed the most abundant methylation statuses among all stages, with a mean value of 68.2 %, then CHG (57.9 %), and CHH (21.2 %). We identified 18,032 differentially methylated regions (DMRs) in the GA3-exposed groups. In particular, we recognized 5943 DMR genes and 269 DMR-promoter genes. Using conjoint transcriptome and DNA methylation analyses, we identified 337 important methylated-genes, which were involved in “phenylpropanoid biosynthesis”, “arginine and proline metabolism” and “tyrosine metabolism”. Together, the aforementioned data provides an in-depth understanding of the epigenetic modulation of gene expression during GA3 treatment.
{"title":"Genome-wide DNA methylation analysis of sorghum leaves following foreign GA3 exposure under salt stress","authors":"Yanqing Wu , Jiao Liu , Lu Zhao , Guisheng Zhou , Yuhan Tang","doi":"10.1016/j.ygeno.2025.111000","DOIUrl":"10.1016/j.ygeno.2025.111000","url":null,"abstract":"<div><div>Sorghum is an increasingly popular topic of research in elucidating survival and adaptation approaches to augmented salinity. Nonetheless, little is known about the outcome and modulatory networks involved in the gibberellic acid (GA3)-induced salt stress alleviation in sorghum. Here, we identified 50 mg/L GA3 as the optimal concentration for sorghum (‘Jitian 3’) development under salt stress. Based on genome-wide DNA methylation analysis, CpG sites displayed the most abundant methylation statuses among all stages, with a mean value of 68.2 %, then CHG (57.9 %), and CHH (21.2 %). We identified 18,032 differentially methylated regions (DMRs) in the GA3-exposed groups. In particular, we recognized 5943 DMR genes and 269 DMR-promoter genes. Using conjoint transcriptome and DNA methylation analyses, we identified 337 important methylated-genes, which were involved in “phenylpropanoid biosynthesis”, “arginine and proline metabolism” and “tyrosine metabolism”. Together, the aforementioned data provides an in-depth understanding of the epigenetic modulation of gene expression during GA3 treatment.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111000"},"PeriodicalIF":3.4,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143022948","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}
Pub Date : 2025-01-19DOI: 10.1016/j.ygeno.2025.111001
Gabriel Onea , Alireza Ghahramani , Xu Wang , Haider M. Hassan , Nathalie G. Bérubé , Caroline Schild-Poulter
WD-repeat containing protein 26 (WDR26) is an essential component of the CTLH E3 ligase complex. Mutations in WDR26 lead to Skraban-Deardorff, an intellectual disability syndrome with clinical features resembling other disorders arising from defects in transcriptional regulation and chromatin structure. However, the role of WDR26 and its associated CTLH complex in regulating chromatin or transcription has not been elucidated. Here, we assessed how loss of WDR26 affects chromatin accessibility and gene expression. Transcriptome analysis of WDR26 knockout HeLa cells revealed over 2000 differentially expressed genes, while ATAC-Seq analysis showed over 32,000 differentially accessible chromatin regions, the majority mapping to intergenic and intronic regions and 13 % mapping to promoters. Above all, we found that WDR26 loss affected expression of genes regulated by AP-1 and NF-1 transcription factors and resulted in dramatic changes in their chromatin accessibility. Overall, our analyses implicate WDR26 and the CTLH complex in chromatin regulation.
WD-repeat containing protein 26 （WDR26）是CTLH E3连接酶复合物的重要组成部分。WDR26突变导致Skraban-Deardorff，这是一种智力残疾综合征，其临床特征与其他由转录调控和染色质结构缺陷引起的疾病相似。然而，WDR26及其相关的CTLH复合物在调节染色质或转录中的作用尚未阐明。在这里，我们评估了WDR26缺失如何影响染色质可及性和基因表达。WDR26基因敲除的HeLa细胞转录组分析显示有超过2000个差异表达基因，而ATAC-Seq分析显示有超过32000个差异可达的染色质区域，大多数定位于基因间和内含子区域，13% %定位于启动子区域。综上所述，我们发现WDR26缺失影响了AP-1和NF-1转录因子调控基因的表达，并导致其染色质可及性发生巨大变化。总之，我们的分析表明WDR26和CTLH复合物参与染色质调控。
{"title":"WDR26 depletion alters chromatin accessibility and gene expression profiles in mammalian cells","authors":"Gabriel Onea , Alireza Ghahramani , Xu Wang , Haider M. Hassan , Nathalie G. Bérubé , Caroline Schild-Poulter","doi":"10.1016/j.ygeno.2025.111001","DOIUrl":"10.1016/j.ygeno.2025.111001","url":null,"abstract":"<div><div>WD-repeat containing protein 26 (WDR26) is an essential component of the CTLH E3 ligase complex. Mutations in <em>WDR26</em> lead to Skraban-Deardorff, an intellectual disability syndrome with clinical features resembling other disorders arising from defects in transcriptional regulation and chromatin structure. However, the role of WDR26 and its associated CTLH complex in regulating chromatin or transcription has not been elucidated. Here, we assessed how loss of WDR26 affects chromatin accessibility and gene expression. Transcriptome analysis of WDR26 knockout HeLa cells revealed over 2000 differentially expressed genes, while ATAC-Seq analysis showed over 32,000 differentially accessible chromatin regions, the majority mapping to intergenic and intronic regions and 13 % mapping to promoters. Above all, we found that WDR26 loss affected expression of genes regulated by AP-1 and NF-1 transcription factors and resulted in dramatic changes in their chromatin accessibility. Overall, our analyses implicate WDR26 and the CTLH complex in chromatin regulation.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111001"},"PeriodicalIF":3.4,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003623","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}
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