Pub Date : 2025-02-12DOI: 10.1016/j.ygeno.2025.111015
K. Sai Timmarao , Naresh Ponnam , D.C. Lakshmanareddy , M. Krishna Reddy , V. Venkataravanappa , P. Roshini , Mahebub Shaik , B.P. Manoj , K. Madhavi Reddy
Chilli leaf curl virus (ChLCV), caused by whiteflies transmitted begomoviruses, poses a significant threat to chilli cultivation and production all over the world. Exploring host plant resistance and identification of associated molecular markers will accelerate resistance breeding. QTL-seq analysis was employed in the IHR4615(R) × IHR2451(S) F2 population to identify QTLs associated with ChLCV-Raichur isolate resistance. A significant QTL was mapped on chromosome 6 associated with ChLCV-Raichur isolate resistance. Defense-related genes were predicted within the identified locus. Further refining of the identified locus with simple sequence repeats (SSR) markers led to the identification of two SSR markers IHR-LCV-SSR-76 and IHR-LCV-SSR-165 associated with the ChLCV-Raichur isolate resistance with 89.50 and 72.50 % prediction efficacy, respectively in IHR4615(R) × IHR2451(S) F2 population. These markers are located at 7 cM and 17.65 cM genetic distances from the resistant gene. These markers were further validated in another resistant source-based F2 population of IHR4392(S) × IHR4597(R). The developed and validated molecular markers can be explored in marker-assisted breeding programs aiming at developing resistant cultivars/ F1 hybrids of chilli.
{"title":"Molecular mapping and development of SSR markers associated with Chilli leaf curl virus resistance in chilli (Capsicum annuum L.)","authors":"K. Sai Timmarao , Naresh Ponnam , D.C. Lakshmanareddy , M. Krishna Reddy , V. Venkataravanappa , P. Roshini , Mahebub Shaik , B.P. Manoj , K. Madhavi Reddy","doi":"10.1016/j.ygeno.2025.111015","DOIUrl":"10.1016/j.ygeno.2025.111015","url":null,"abstract":"<div><div>Chilli leaf curl virus (ChLCV), caused by whiteflies transmitted begomoviruses, poses a significant threat to chilli cultivation and production all over the world. Exploring host plant resistance and identification of associated molecular markers will accelerate resistance breeding. QTL-seq analysis was employed in the IHR4615(R) × IHR2451(S) F<sub>2</sub> population to identify QTLs associated with ChLCV-Raichur isolate resistance. A significant QTL was mapped on chromosome 6 associated with ChLCV-Raichur isolate resistance. Defense-related genes were predicted within the identified locus. Further refining of the identified locus with simple sequence repeats (SSR) markers led to the identification of two SSR markers IHR-LCV-SSR-76 and IHR-LCV-SSR-165 associated with the ChLCV-Raichur isolate resistance with 89.50 and 72.50 % prediction efficacy, respectively in IHR4615(R) × IHR2451(S) F<sub>2</sub> population. These markers are located at 7 cM and 17.65 cM genetic distances from the resistant gene. These markers were further validated in another resistant source-based F<sub>2</sub> population of IHR4392(S) × IHR4597(R). The developed and validated molecular markers can be explored in marker-assisted breeding programs aiming at developing resistant cultivars/ F<sub>1</sub> hybrids of chilli.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111015"},"PeriodicalIF":3.4,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143425250","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 : 2025-02-04DOI: 10.1016/j.ygeno.2025.111012
Chunwei Wang , Liqiang Chen , Sijia Ma , Ruixue Bai , Quanzhong Xu , Rui Feng , Chao Bian , Liguo Zhang , Xiaohu Su
Baicalin is a natural flavonoid compound with a wide range of biological activities, including anti-oxidant and anti-inflammatory properties. Previous we found that the abundance of baicalin in bovine serum is significantly higher than in ovine serum at mid-lactation. It suggests that baicalin may play a role in the regulation of lactation performance. Here, the biological effects of baicalin on proliferative, oxidative stress response, synthesis capacities of major milk components of ovine mammary epithelial cells (OMECs) were investigated. And the transcriptomic analysis was utilized to explore the possible regulatory mechanism. Results showed that 25 μg/mL baicalin can significantly enhance the proliferation, antioxidant, triglyceride and lactose synthesis capacities of OMECs. In transcriptomic analysis, 150 differentially expressed genes (DEGs) were screened between 25 μM baicalin treated (Baicalin) and 0 μM baicalin treated (NT) groups. Functional analysis of DEGs showed that lipid metabolic process, response to oxidative stress, biosynthesis of fat and saccharide pathways were enriched. qRT-PCR result showed that antioxidation-related negative regulatory gene MPO was significantly down-regulated and milk fat biosynthesis related genes PLA2G12A, GPCPD1, LPIN1, FASN and lactose biosynthesis related genes MGEA5, RHOQ were significantly up-regulated in baicalin treated OMECs (P < 0.01). In summarize, 25 μM baicalin can significantly enhance the proliferation, antioxidant and biosynthesis of milk fat and lactose capacities through lipid metabolic process, response to oxidative stress, biosynthesis of fat and saccharide pathways related genes regulation in OMECs. The study would provide a theoretical basis for the improvement of lactation performance and the exploration of lactation regulation theory of dairy sheep.
{"title":"Biological effects of baicalin on the ovine mammary cells and regulatory mechanism study by transcriptomic analysis","authors":"Chunwei Wang , Liqiang Chen , Sijia Ma , Ruixue Bai , Quanzhong Xu , Rui Feng , Chao Bian , Liguo Zhang , Xiaohu Su","doi":"10.1016/j.ygeno.2025.111012","DOIUrl":"10.1016/j.ygeno.2025.111012","url":null,"abstract":"<div><div>Baicalin is a natural flavonoid compound with a wide range of biological activities, including anti-oxidant and anti-inflammatory properties. Previous we found that the abundance of baicalin in bovine serum is significantly higher than in ovine serum at mid-lactation. It suggests that baicalin may play a role in the regulation of lactation performance. Here, the biological effects of baicalin on proliferative, oxidative stress response, synthesis capacities of major milk components of ovine mammary epithelial cells (OMECs) were investigated. And the transcriptomic analysis was utilized to explore the possible regulatory mechanism. Results showed that 25 μg/mL baicalin can significantly enhance the proliferation, antioxidant, triglyceride and lactose synthesis capacities of OMECs. In transcriptomic analysis, 150 differentially expressed genes (DEGs) were screened between 25 μM baicalin treated (Baicalin) and 0 μM baicalin treated (NT) groups. Functional analysis of DEGs showed that lipid metabolic process, response to oxidative stress, biosynthesis of fat and saccharide pathways were enriched. qRT-PCR result showed that antioxidation-related negative regulatory gene <em>MPO</em> was significantly down-regulated and milk fat biosynthesis related genes <em>PLA2G12A</em>, <em>GPCPD1</em>, <em>LPIN1</em>, <em>FASN</em> and lactose biosynthesis related genes <em>MGEA5</em>, <em>RHOQ</em> were significantly up-regulated in baicalin treated OMECs (<em>P</em> < 0.01). In summarize, 25 μM baicalin can significantly enhance the proliferation, antioxidant and biosynthesis of milk fat and lactose capacities through lipid metabolic process, response to oxidative stress, biosynthesis of fat and saccharide pathways related genes regulation in OMECs. The study would provide a theoretical basis for the improvement of lactation performance and the exploration of lactation regulation theory of dairy sheep.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111012"},"PeriodicalIF":3.4,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143255140","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 : 2025-02-04DOI: 10.1016/j.ygeno.2025.111013
Zhipeng Zheng , Huimin Lu , Xiaowen Wang , Zhiyuan Yang , Yubin Zhang , Kaiyuan Li , Cheng Shen , Zhifeng Yin , Min Sha , Jun Ye , Li Zhu
Atherosclerosis is a chronic inflammatory disease characterized by lipid accumulation in arterial walls. The role of the interplay between mitochondrial dysfunction and immune inflammation in atherosclerosis is still unclear. This study aimed to investigate the molecular characteristics and immune landscape of mitochondrial hub genes involved in atherosclerosis. Based on bioinformatics analysis, three hub Mitochondria-related DEGs (MitoDEGs), including OXCT1, UCP2, and CPT1B, were screened out and showed good diagnostic performance in identifying atherosclerosis patients and controls. Immune analysis demonstrated strong correlations between hub MitoDEGs and immune cells, such as macrophages and T cells. Additionally, the predicted transcription factors of these hub MitoDEGs were significantly enriched in Th17, Th1 and Th2 cell differentiation signaling pathways. Both cell and animal experiments confirmed the expression trends of OXCT1 and CPT1B observed in the bioinformatics analysis. These hub MitoDEGs may play an important role in coordinating mitochondrial metabolism in the immune inflammation of atherosclerosis.
{"title":"Integrative analysis of genes provides insights into the molecular and immune characteristics of mitochondria-related genes in atherosclerosis","authors":"Zhipeng Zheng , Huimin Lu , Xiaowen Wang , Zhiyuan Yang , Yubin Zhang , Kaiyuan Li , Cheng Shen , Zhifeng Yin , Min Sha , Jun Ye , Li Zhu","doi":"10.1016/j.ygeno.2025.111013","DOIUrl":"10.1016/j.ygeno.2025.111013","url":null,"abstract":"<div><div>Atherosclerosis is a chronic inflammatory disease characterized by lipid accumulation in arterial walls. The role of the interplay between mitochondrial dysfunction and immune inflammation in atherosclerosis is still unclear. This study aimed to investigate the molecular characteristics and immune landscape of mitochondrial hub genes involved in atherosclerosis. Based on bioinformatics analysis, three hub Mitochondria-related DEGs (MitoDEGs), including OXCT1, UCP2, and CPT1B, were screened out and showed good diagnostic performance in identifying atherosclerosis patients and controls. Immune analysis demonstrated strong correlations between hub MitoDEGs and immune cells, such as macrophages and T cells. Additionally, the predicted transcription factors of these hub MitoDEGs were significantly enriched in Th17, Th1 and Th2 cell differentiation signaling pathways. Both cell and animal experiments confirmed the expression trends of OXCT1 and CPT1B observed in the bioinformatics analysis. These hub MitoDEGs may play an important role in coordinating mitochondrial metabolism in the immune inflammation of atherosclerosis.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111013"},"PeriodicalIF":3.4,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143340801","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 : 2025-01-31DOI: 10.1016/j.ygeno.2025.111011
Yadan Yan , Yafeng Wen , Zejun Zhang , Jun Zhang , Xingtong Wu , Chuncheng Wang , Yanghui Zhao
Fruit coloration results from a complex process. Maire yew (Taxus mairei) is an evergreen tree with red, purple, and yellow fruits (arils). While significant progress has been made in understanding pigment biosynthesis in arils, the role of chromatin accessibility in color development remains less well understood. To gain deeper insights into the genetic and epigenetic factors involved, we employed RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin sequencing (ATAC-seq). By integrating the results, we identified 723 differentially expressed genes (DEGs) with chromatin changes in P vs. R, including 312 up- and 411 down-regulated genes. In Y vs. R, we found 159 DEGs, with 97 up- and 62 down-regulated. KEGG enrichment analysis highlighted the flavonoid and carotenoid pathways as major contributors to color variation. When the arils turned purple, the expression levels of C4H, CHS, C3’H, F3’H, F3H, DFR, PSY, PDS, β-OHase, CYP97A3, and LUT1 were significantly up-regulated, while ZDS was down-regulated. The transition to yellow arils was characterized by the up-regulation of F3H, DFR, ZDS, CYP97A3, β-OHase, and LUT1, accompanied by the down-regulation of C4H, CHS, PSY, and PDS. Additionally, 27 transcription factors (TFs) were identified, including MYB, bHLH, and bZIP. These TFs may potentially influence variation in aril color by regulating downstream genes. In total, eight genes were selected for qRT-PCR validation, indicating the reliability of the transcriptome sequencing data. Our results provide in-depth information regarding the coloration of the arils in Maire yew. The study could provide insights for further genetic improvement in Taxus.
{"title":"Integrating ATAC-seq and RNA-seq to reveal the dynamics of chromatin accessibility and gene expression in regulating aril coloration of Taxus mairei","authors":"Yadan Yan , Yafeng Wen , Zejun Zhang , Jun Zhang , Xingtong Wu , Chuncheng Wang , Yanghui Zhao","doi":"10.1016/j.ygeno.2025.111011","DOIUrl":"10.1016/j.ygeno.2025.111011","url":null,"abstract":"<div><div>Fruit coloration results from a complex process. Maire yew (<em>Taxus mairei</em>) is an evergreen tree with red, purple, and yellow fruits (arils). While significant progress has been made in understanding pigment biosynthesis in arils, the role of chromatin accessibility in color development remains less well understood. To gain deeper insights into the genetic and epigenetic factors involved, we employed RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin sequencing (ATAC-seq). By integrating the results, we identified 723 differentially expressed genes (DEGs) with chromatin changes in P vs. R, including 312 up- and 411 down-regulated genes. In Y vs. R, we found 159 DEGs, with 97 up- and 62 down-regulated. KEGG enrichment analysis highlighted the flavonoid and carotenoid pathways as major contributors to color variation. When the arils turned purple, the expression levels of <em>C4H</em>, <em>CHS</em>, <em>C3’H</em>, <em>F3’H</em>, <em>F3H</em>, <em>DFR</em>, <em>PSY</em>, <em>PDS</em>, <em>β-OHase</em>, <em>CYP97A3</em>, and <em>LUT1</em> were significantly up-regulated, while ZDS was down-regulated. The transition to yellow arils was characterized by the up-regulation of <em>F3H</em>, <em>DFR</em>, <em>ZDS</em>, <em>CYP97A3</em>, <em>β-OHase</em>, and <em>LUT1</em>, accompanied by the down-regulation of <em>C4H</em>, <em>CHS</em>, <em>PSY</em>, and <em>PDS</em>. Additionally, 27 transcription factors (TFs) were identified, including MYB, bHLH, and bZIP. These TFs may potentially influence variation in aril color by regulating downstream genes. In total, eight genes were selected for qRT-PCR validation, indicating the reliability of the transcriptome sequencing data. Our results provide in-depth information regarding the coloration of the arils in Maire yew. The study could provide insights for further genetic improvement in <em>Taxus</em>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111011"},"PeriodicalIF":3.4,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143079282","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 : 2025-01-27DOI: 10.1016/j.ygeno.2025.111009
Pan Tongtong , Shen Yujuan , Li Ting , Yi Fangfang , Wu Shijia , Huang Yilun , Zhang Huadong , Zhang Qiongying , Chen Yongping , Chen Dazhi
Background
Ferroptosis is associated with alcoholic hepatitis (AH); however, the underlying mechanisms remain unclear.
Methods
Changes in iron content and oxidative stress in AH patients and in vivo and in vitro models were analyzed. Iron homeostasis pathways in the livers of patients with AH were investigated using RNA sequencing. AH-associated ferroptosis-related genes (FRGs) were identified using weighted gene co-expression network analysis. Hub genes were identified using machine learning methods, and their diagnostic potential for AH was assessed. The correlation between FRGs and the immune microenvironment was analyzed, and the underlying regulatory mechanism was explored. FRG expression was validated in clinical samples and in vitro and in vivo models. The role of FRGs in AH-related ferroptosis was explored through gene-silencing experiments.
Results
Significant iron deposits and oxidative stress were detected in clinical samples and in vivo and in vitro AH models. Bioinformatics identified GCLC, NQO1, and ULK1 as key FRGs linked to the immune microenvironment and AH-related pathogenic genes. A nomogram based on these FRGs accurately assessed AH risk, as validated using the calibration curve. A regulatory network involving 154 miRNAs and 136 transcription factors was mapped for FRGs. In AH patients, NQO1 was upregulated in the liver, whereas GCLC and ULK1 were downregulated. Silencing GCLC and ULK1 reduced cell viability and increased oxidative stress and ferroptosis, whereas silencing NQO1 had the opposite effect.
Conclusions
Therefore, GCLC, NQO1, and ULK1 are key AH-related FRGs, potentially serving as targets for diagnosing and treating AH.
{"title":"Decoding ferroptosis in alcoholic hepatitis: A bioinformatics approach to hub gene identification","authors":"Pan Tongtong , Shen Yujuan , Li Ting , Yi Fangfang , Wu Shijia , Huang Yilun , Zhang Huadong , Zhang Qiongying , Chen Yongping , Chen Dazhi","doi":"10.1016/j.ygeno.2025.111009","DOIUrl":"10.1016/j.ygeno.2025.111009","url":null,"abstract":"<div><h3>Background</h3><div>Ferroptosis is associated with alcoholic hepatitis (AH); however, the underlying mechanisms remain unclear.</div></div><div><h3>Methods</h3><div>Changes in iron content and oxidative stress in AH patients and in vivo and in vitro models were analyzed. Iron homeostasis pathways in the livers of patients with AH were investigated using RNA sequencing. AH-associated ferroptosis-related genes (FRGs) were identified using weighted gene co-expression network analysis. Hub genes were identified using machine learning methods, and their diagnostic potential for AH was assessed. The correlation between FRGs and the immune microenvironment was analyzed, and the underlying regulatory mechanism was explored. FRG expression was validated in clinical samples and in vitro and in vivo models. The role of FRGs in AH-related ferroptosis was explored through gene-silencing experiments.</div></div><div><h3>Results</h3><div>Significant iron deposits and oxidative stress were detected in clinical samples and in vivo and in vitro AH models. Bioinformatics identified <em>GCLC</em>, <em>NQO1</em>, and <em>ULK1</em> as key FRGs linked to the immune microenvironment and AH-related pathogenic genes. A nomogram based on these FRGs accurately assessed AH risk, as validated using the calibration curve. A regulatory network involving 154 miRNAs and 136 transcription factors was mapped for FRGs. In AH patients, <em>NQO1</em> was upregulated in the liver, whereas <em>GCLC</em> and <em>ULK1</em> were downregulated. Silencing <em>GCLC</em> and <em>ULK1</em> reduced cell viability and increased oxidative stress and ferroptosis, whereas silencing <em>NQO1</em> had the opposite effect.</div></div><div><h3>Conclusions</h3><div>Therefore, <em>GCLC</em>, <em>NQO1</em>, and <em>ULK1</em> are key AH-related FRGs, potentially serving as targets for diagnosing and treating AH.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111009"},"PeriodicalIF":3.4,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143046195","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 : 2025-01-27DOI: 10.1016/j.ygeno.2025.111010
Li Ren , Li Deng , Minjie Guo , Wenzhao Dong , Yuanjin Fang , Xiangyu Tian , Yang Li , Junhua Yin , Jianli Miao , Zheng Zheng , Shaowei Li , Junping Hu , Wenhao Liu , Bingyan Huang , Xinyou Zhang
High-oleic peanuts are increasingly valued in agricultural production and consumer markets. Nevertheless, limited genomic information hinders the integration of genetic analyses and modern breeding strategies. This study details a chromosome-level genome assembly of Kaixuan 016, a high-oleic peanut variety developed through gamma-radiation-assisted breeding, exhibiting enhanced agronomic traits. Utilizing PacBio long-read sequencing and Hi-C technology, the assembly encompasses 2532.9 Mb, with a contig N50 of 11.48 Mb, structured into 20 pseudochromosomes. Repetitive elements comprise 72.26 % of the genome. Of the 69,845 protein-coding genes, 97 % are annotated in public databases. Phylogenetic analysis reveals divergence times of approximately 0.3 million years ago (Mya) for the A subgenome and 0.2 Mya for the B subgenome, with their initial divergence occurring around 2.6 Mya. Additionally, our study includes enrichment analyses on species-specific genes, along with expanded, contracted, and positively selected gene families engaged in vital metabolic and biosynthetic pathways such as photosynthesis, linoleic acid metabolism, and fatty acid elongation—key processes for oleic acid accumulation in developing seeds. Comparative genomic analysis with the AT1–1 parent genome suggests that γ-radiation primarily induces structural variations in Kaixuan 016. Population analysis further differentiated Kaixuan 016 and its derivatives into two distinct clusters—Kainong and Jihua accessions, highlighting their superior agronomic traits. This high-quality genome assembly provides a vital resource for comparative genomic studies and facilitates the advancement of accelerated, genome-guided breeding efforts in high-oleic peanuts.
{"title":"Chromosome-level genome assembly and characterization of Kaixuan 016: A high-oleic peanut variety with improved agronomic traits developed through gamma-radiation-assisted breeding","authors":"Li Ren , Li Deng , Minjie Guo , Wenzhao Dong , Yuanjin Fang , Xiangyu Tian , Yang Li , Junhua Yin , Jianli Miao , Zheng Zheng , Shaowei Li , Junping Hu , Wenhao Liu , Bingyan Huang , Xinyou Zhang","doi":"10.1016/j.ygeno.2025.111010","DOIUrl":"10.1016/j.ygeno.2025.111010","url":null,"abstract":"<div><div>High-oleic peanuts are increasingly valued in agricultural production and consumer markets. Nevertheless, limited genomic information hinders the integration of genetic analyses and modern breeding strategies. This study details a chromosome-level genome assembly of Kaixuan 016, a high-oleic peanut variety developed through gamma-radiation-assisted breeding, exhibiting enhanced agronomic traits. Utilizing PacBio long-read sequencing and Hi-C technology, the assembly encompasses 2532.9 Mb, with a contig N50 of 11.48 Mb, structured into 20 pseudochromosomes. Repetitive elements comprise 72.26 % of the genome. Of the 69,845 protein-coding genes, 97 % are annotated in public databases. Phylogenetic analysis reveals divergence times of approximately 0.3 million years ago (Mya) for the A subgenome and 0.2 Mya for the B subgenome, with their initial divergence occurring around 2.6 Mya. Additionally, our study includes enrichment analyses on species-specific genes, along with expanded, contracted, and positively selected gene families engaged in vital metabolic and biosynthetic pathways such as photosynthesis, linoleic acid metabolism, and fatty acid elongation<strong>—</strong>key processes for oleic acid accumulation in developing seeds. Comparative genomic analysis with the AT1–1 parent genome suggests that γ-radiation primarily induces structural variations in Kaixuan 016. Population analysis further differentiated Kaixuan 016 and its derivatives into two distinct clusters<strong>—</strong>Kainong and Jihua accessions, highlighting their superior agronomic traits. This high-quality genome assembly provides a vital resource for comparative genomic studies and facilitates the advancement of accelerated, genome-guided breeding efforts in high-oleic peanuts.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111010"},"PeriodicalIF":3.4,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143065041","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 : 2025-01-26DOI: 10.1016/j.ygeno.2025.111006
Hongming Ma , Ying Lu , Wei Chen , Zhendong Gao, Dongwang Wu, Yuqing Chong, Jiao Wu, Dongmei Xi, Weidong Deng, Jieyun Hong
The differentiation and lipid metabolism of preadipocytes are crucial processes in IMF deposition. Studies have demonstrated that SIRT4 plays essential roles in energy metabolism and redox homeostasis, with its expression being coordinately regulated by multiple transcription factors associated with energy and lipid metabolism. In this study, the findings of multiple omics analysis reveal that SIRT4 significantly up-regulates the expression of genes involved in adipogenesis and enhances the differentiation and lipid deposition of bovine preadipocytes. Furthermore, SIRT4 profoundly influences the expression pattern of metabolites by increasing the abundance of substances involved in lipid synthesis while decreasing those that promote lipid oxidative decomposition. Additionally, SIRT4 broadly up-regulates the expression levels of various lipid classes, including glycerolipids, glycerophospholipids, sphingolipids, and sterol lipids. These findings not only provide a theoretical basis for molecular breeding and genetic improvement in beef cattle, but also offer potential therapeutic approaches for energy homeostasis disorders and obesity.
{"title":"Multiple omics analysis reveals the regulation of SIRT4 on lipid deposition and metabolism during the differentiation of bovine preadipocytes","authors":"Hongming Ma , Ying Lu , Wei Chen , Zhendong Gao, Dongwang Wu, Yuqing Chong, Jiao Wu, Dongmei Xi, Weidong Deng, Jieyun Hong","doi":"10.1016/j.ygeno.2025.111006","DOIUrl":"10.1016/j.ygeno.2025.111006","url":null,"abstract":"<div><div>The differentiation and lipid metabolism of preadipocytes are crucial processes in IMF deposition. Studies have demonstrated that <em>SIRT4</em> plays essential roles in energy metabolism and redox homeostasis, with its expression being coordinately regulated by multiple transcription factors associated with energy and lipid metabolism. In this study, the findings of multiple omics analysis reveal that <em>SIRT4</em> significantly up-regulates the expression of genes involved in adipogenesis and enhances the differentiation and lipid deposition of bovine preadipocytes. Furthermore, <em>SIRT4</em> profoundly influences the expression pattern of metabolites by increasing the abundance of substances involved in lipid synthesis while decreasing those that promote lipid oxidative decomposition. Additionally, <em>SIRT4</em> broadly up-regulates the expression levels of various lipid classes, including glycerolipids, glycerophospholipids, sphingolipids, and sterol lipids. These findings not only provide a theoretical basis for molecular breeding and genetic improvement in beef cattle, but also offer potential therapeutic approaches for energy homeostasis disorders and obesity.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111006"},"PeriodicalIF":3.4,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058717","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.2025.110999
Feng Yuan , Yongchang Tang , Hao Liang , Mingbo Cao , Yupeng Ren , Yuxuan Li , Gaoyuan Yang , Zhaozhong Zhong , Zhiyong Xiong , Zhiwei He , Meihai Deng , Zhicheng Yao
Introduction
Resistance to lenvatinib limits the effectiveness of the targeted treatments for HCC. However, the exact mechanism behind this resistance remains elusive. Current research suggests that circular RNA (circRNA) is pivotal in mediating drug resistance during targeted treatments.
Objectives
To investigate the influence of circRNA on HCC progression and its resistance to lenvatinib.
Methods
We identified the crucial circRNA hsa_circ_0005711 (circPIK3C3) through bioinformatics. Study (in-vitro and in-vivo) on the expression of circPIK3C3 (measured by qRT-PCR) and its association with progress of HCC patients including lenvatinib resistance were performed. Techniques such as dual-luciferase reporter assays, RNA FISH, RAP, and AGO2-RIP were employed for discerning circPIK3C3's specific mechanisms related to progression of HCC and its lenvatinib resistance.
Results
Study (in-vitro and in-vivo) revealed that circPIK3C3 exhibited reduced expression and lenvatinib resistance in HCC, which was intimately tied to patient outcomes. Moreover, circPIK3C3 elevated SOX15 expression while suppressing the signaling pathway related to Wnt/β-catenin via inhibition of miR-452-5p through a competitive endogenous RNA (ceRNA) network. This, in turn, mitigated HCC progression and its resistance to lenvatinib.
Conclusion
CircPIK3C3 is instrumental in the disease progression and resistance to Lenvatinib in HCC. It presents a potential therapeutic avenue for patients with lenvatinib-resistant HCC and could serve as a valuable molecular marker for forecasting lenvatinib resistance in HCC patients.
{"title":"CircPIK3C3 inhibits hepatocellular carcinoma progression and lenvatinib resistance by suppressing the Wnt/β-catenin pathway via the miR-452-5p/SOX15 axis","authors":"Feng Yuan , Yongchang Tang , Hao Liang , Mingbo Cao , Yupeng Ren , Yuxuan Li , Gaoyuan Yang , Zhaozhong Zhong , Zhiyong Xiong , Zhiwei He , Meihai Deng , Zhicheng Yao","doi":"10.1016/j.ygeno.2025.110999","DOIUrl":"10.1016/j.ygeno.2025.110999","url":null,"abstract":"<div><h3>Introduction</h3><div>Resistance to lenvatinib limits the effectiveness of the targeted treatments for HCC. However, the exact mechanism behind this resistance remains elusive. Current research suggests that circular RNA (circRNA) is pivotal in mediating drug resistance during targeted treatments.</div></div><div><h3>Objectives</h3><div>To investigate the influence of circRNA on HCC progression and its resistance to lenvatinib.</div></div><div><h3>Methods</h3><div>We identified the crucial circRNA hsa_circ_0005711 (circPIK3C3) through bioinformatics. Study (in-vitro <em>and</em> in-vivo) on the expression of circPIK3C3 (measured by qRT-PCR) and its association with progress of HCC patients including lenvatinib resistance were performed. Techniques such as dual-luciferase reporter assays, RNA FISH, RAP, and AGO2-RIP were employed for discerning circPIK3C3's specific mechanisms related to progression of HCC and its lenvatinib resistance.</div></div><div><h3>Results</h3><div>Study (in-vitro <em>and</em> in-vivo) revealed that circPIK3C3 exhibited reduced expression and lenvatinib resistance in HCC, which was intimately tied to patient outcomes. Moreover, circPIK3C3 elevated SOX15 expression while suppressing the signaling pathway related to Wnt/β-catenin via inhibition of miR-452-5p through a competitive endogenous RNA (ceRNA) network. This, in turn, mitigated HCC progression and its resistance to lenvatinib.</div></div><div><h3>Conclusion</h3><div>CircPIK3C3 is instrumental in the disease progression and resistance to Lenvatinib in HCC. It presents a potential therapeutic avenue for patients with lenvatinib-resistant HCC and could serve as a valuable molecular marker for forecasting lenvatinib resistance in HCC patients.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110999"},"PeriodicalIF":3.4,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037758","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.2025.111007
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}
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