Pub Date : 2025-03-01DOI: 10.1016/j.ygeno.2025.111024
Jinmu Kim , Hyeon Jin Kim , Eunkyung Choi , Jung Jun Park , Minjoo Cho , Soyun Choi , Hyejin Kim , Jung Sick Lee , Hyun Park
Arsenic is a widespread environmental contaminant recognized for its high mobility and potential toxicity. Arsenic levels at Suncheon Bay, one of the primary Tegillarca granosa culturation sites in South Korea, were identified as higher than the habitat's threshold effect level (TEL). After 12 and 48 h of arsenic exposure, a total of 939 and 842 DEGs were identified in the gill and mantle, respectively. Detoxification genes were identified based on DEG analysis, and out of 10 ABCA3 genes in T. granosa, seven ABCA3 genes in total were up- and/or downregulated in two tissues. The metabolic and the cell adhesion molecules KEGG pathways were the most enriched among the commonly identified up- and downregulated genes. The ‘metabolic process’ gene ontology term was highly enriched with upregulated DEGs. We then identified 74 ATP-binding cassette (ABC) genes in the T. granosa genome, which has seven subfamilies (A to G), with gene expansion found in the ABCC and ABCA subfamilies. Although the precise mechanisms of arsenic-induced gene dysregulation remain unknown, our findings suggest that ABCA3 genes might participate in arsenic active transport and play an important role in arsenic detoxification.
{"title":"Genome-wide identification of Tegillarca granosa ATP-binding cassette (ABC) transporter family related to arsenic toxicity","authors":"Jinmu Kim , Hyeon Jin Kim , Eunkyung Choi , Jung Jun Park , Minjoo Cho , Soyun Choi , Hyejin Kim , Jung Sick Lee , Hyun Park","doi":"10.1016/j.ygeno.2025.111024","DOIUrl":"10.1016/j.ygeno.2025.111024","url":null,"abstract":"<div><div>Arsenic is a widespread environmental contaminant recognized for its high mobility and potential toxicity. Arsenic levels at Suncheon Bay, one of the primary <em>Tegillarca granosa</em> culturation sites in South Korea, were identified as higher than the habitat's threshold effect level (TEL). After 12 and 48 h of arsenic exposure, a total of 939 and 842 DEGs were identified in the gill and mantle, respectively. Detoxification genes were identified based on DEG analysis, and out of 10 ABCA3 genes in <em>T. granosa</em>, seven ABCA3 genes in total were up- and/or downregulated in two tissues. The metabolic and the cell adhesion molecules KEGG pathways were the most enriched among the commonly identified up- and downregulated genes. The ‘metabolic process’ gene ontology term was highly enriched with upregulated DEGs. We then identified 74 ATP-binding cassette (ABC) genes in the <em>T. granosa</em> genome, which has seven subfamilies (A to G), with gene expansion found in the ABCC and ABCA subfamilies. Although the precise mechanisms of arsenic-induced gene dysregulation remain unknown, our findings suggest that ABCA3 genes might participate in arsenic active transport and play an important role in arsenic detoxification.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111024"},"PeriodicalIF":3.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143520339","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}
This study investigates the regulatory effects of methylation in the promoter region of the bovine MEF2A gene on its transcription levels and the impact on bovine myoblasts. Transcription levels and promoter methylation status of MEF2A in the same tissues of calves and adult cattle were assessed using qRT-PCR and BSP methods. The results indicated that MEF2A expression levels in calves were significantly lower than those in adult cattle (P < 0.05), while the methylation rate of MEF2A was significantly higher in calves (P < 0.05), suggesting a correlation between high methylation levels and reduced gene expression. Subsequently, MEF2A overexpression and interference vectors were transfected into bovine myoblasts to examine the effects of altered MEF2A expression on its promoter methylation status. The findings revealed that MEF2A overexpression significantly reduced the methylation rate (P < 0.01), whereas MEF2A interference increased the methylation rate (P < 0.01), aligning with the expression trends of DNMT1. Furthermore, bovine myoblasts were treated with varying concentrations of the methylation inhibitor 5-Aza-dC to evaluate changes in MEF2A promoter methylation and mRNA levels. The effects on cell cycle progression, apoptosis, and other growth parameters were assessed using flow cytometry, ELISA, and qRT-PCR. Results showed that a concentration of 1 μM 5-Aza-dC effectively reduced MEF2A promoter methylation and significantly upregulated MEF2A expression, leading to accelerated cell cycle progression and increased secretion levels of GH and INS, all differences being statistically significant (P < 0.01). Additionally, 1 μM of 5-Aza-dC promoted apoptosis, with qRT-PCR results for relevant genes supporting this finding. In conclusion, methylation of the MEF2A promoter negatively regulates its mRNA transcription levels, thereby impacting the growth and development of Guanling cattle myoblasts. These results provide valuable insights for the genetic improvement of cattle through marker-assisted selection.
{"title":"MEF2A promoter methylation negatively regulates mRNA transcription and affects myoblast physiological function in cattle","authors":"Jinkui Sun , Xiang Chen , Yong Ruan , Jiali Xu , Houqiang Xu","doi":"10.1016/j.ygeno.2025.111016","DOIUrl":"10.1016/j.ygeno.2025.111016","url":null,"abstract":"<div><div>This study investigates the regulatory effects of methylation in the promoter region of the bovine MEF2A gene on its transcription levels and the impact on bovine myoblasts. Transcription levels and promoter methylation status of MEF2A in the same tissues of calves and adult cattle were assessed using qRT-PCR and BSP methods. The results indicated that MEF2A expression levels in calves were significantly lower than those in adult cattle (<em>P</em> < 0.05), while the methylation rate of MEF2A was significantly higher in calves (<em>P</em> < 0.05), suggesting a correlation between high methylation levels and reduced gene expression. Subsequently, MEF2A overexpression and interference vectors were transfected into bovine myoblasts to examine the effects of altered MEF2A expression on its promoter methylation status. The findings revealed that MEF2A overexpression significantly reduced the methylation rate (<em>P</em> < 0.01), whereas MEF2A interference increased the methylation rate (<em>P</em> < 0.01), aligning with the expression trends of DNMT1. Furthermore, bovine myoblasts were treated with varying concentrations of the methylation inhibitor 5-Aza-dC to evaluate changes in MEF2A promoter methylation and mRNA levels. The effects on cell cycle progression, apoptosis, and other growth parameters were assessed using flow cytometry, ELISA, and qRT-PCR. Results showed that a concentration of 1 μM 5-Aza-dC effectively reduced MEF2A promoter methylation and significantly upregulated MEF2A expression, leading to accelerated cell cycle progression and increased secretion levels of GH and INS, all differences being statistically significant (<em>P</em> < 0.01). Additionally, 1 μM of 5-Aza-dC promoted apoptosis, with qRT-PCR results for relevant genes supporting this finding. In conclusion, methylation of the MEF2A promoter negatively regulates its mRNA transcription levels, thereby impacting the growth and development of Guanling cattle myoblasts. These results provide valuable insights for the genetic improvement of cattle through marker-assisted selection.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111016"},"PeriodicalIF":3.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537063","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 : 2025-03-01DOI: 10.1016/j.ygeno.2025.111023
Cunxia Ma, Yuzhu Guo, Tongtong Tu, Shuangshuang Cui, Jintao Zhong, Yunhai Zhang, Ning Song, Hongyu Liu
E74-like factor 5 (ELF5) is an Ets transcription factor of epithelial development, while the function of ELF5 gene in goat milk fat synthesis remains to be elucidated. In goat mammary epithelial cells, we performed RNA sequencing and analyzed differentially expressed genes (DEGs) after ELF5 gene overexpression. ELF5 gene significantly up-regulated the synthesis of triglyceride, total cholesterol, free fatty acid, and lipid droplets. We obtained 929 DEGs after ELF5 gene overexpression in GMECs. Among the DEGs, SPP1, ELOVL1, PNPLA2, FOXO1, PTGS2, SEMA6A, ACSL5, and GPNMB genes that are related to lipid metabolism were identified. Enrichment analysis showed MAPK and FoxO signaling pathways were up-regulated by ELF5 gene overexpression in GMECs. These findings offer evidence that ELF5 gene could be a candidate gene for the regulation of milk lipid synthesis in goats, and provide molecular targets for the breeding of goats with high milk fat.
{"title":"ELF5 gene promotes milk lipid synthesis in goat mammary epithelial cells by transcriptomic analysis","authors":"Cunxia Ma, Yuzhu Guo, Tongtong Tu, Shuangshuang Cui, Jintao Zhong, Yunhai Zhang, Ning Song, Hongyu Liu","doi":"10.1016/j.ygeno.2025.111023","DOIUrl":"10.1016/j.ygeno.2025.111023","url":null,"abstract":"<div><div>E74-like factor 5 (ELF5) is an Ets transcription factor of epithelial development, while the function of <em>ELF5</em> gene in goat milk fat synthesis remains to be elucidated. In goat mammary epithelial cells, we performed RNA sequencing and analyzed differentially expressed genes (DEGs) after <em>ELF5</em> gene overexpression. <em>ELF5</em> gene significantly up-regulated the synthesis of triglyceride, total cholesterol, free fatty acid, and lipid droplets. We obtained 929 DEGs after <em>ELF5</em> gene overexpression in GMECs. Among the DEGs, <em>SPP1</em>, <em>ELOVL1</em>, <em>PNPLA2</em>, <em>FOXO1</em>, <em>PTGS2</em>, <em>SEMA6A</em>, <em>ACSL5</em>, and <em>GPNMB</em> genes that are related to lipid metabolism were identified. Enrichment analysis showed MAPK and FoxO signaling pathways were up-regulated by <em>ELF5</em> gene overexpression in GMECs. These findings offer evidence that <em>ELF5</em> gene could be a candidate gene for the regulation of milk lipid synthesis in goats, and provide molecular targets for the breeding of goats with high milk fat.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111023"},"PeriodicalIF":3.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143512240","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 : 2025-03-01DOI: 10.1016/j.ygeno.2025.111022
Fanyi Meng , Mengqiu Ma , Shanshan Li , Pan Liang , Yunfei Liang , Hongyan Shi , Shudi Huang , Huai Su , Yilin Deng , Muhammad Asif Akram , Xiaoxia Shen , Ru Feng , Xiangqiang Zhan , Fang Ma
Light-harvesting chlorophyll a/b-binding (LHC) proteins, as the antenna complex, collect and transfer light energy to the reaction centers of PSII. They are crucial for abiotic stress responses, especially in the photoprotection under cold stress. However, members of the LHC gene family in tomato (Solanum lycopersicum L.) have not yet been identified. In this study, a total of 39 SlLHC proteins containing the chlorophyll a/b binding domain or light-harvesting-like domain were identified, and classified into four subfamilies: Lhc, Lil, PsbS, and FCII. Further qRT-PCR analysis showed SlLhcb1.11 was inhibited and SlELIP1 was induced at low temperature (4 °C). Subsequently, the result of VIGS experiment showed that silencing SlLhcb1.11 or SlELIP1 genes resulted in lighter leaf color, reduced chlorophyll content, compromised photosynthesis, and decreased cold tolerance in tomato plants. These findings offer novel insights into the structure and function of SlLHC genes, thereby contributing to genetic resources for the development of cold-tolerant tomato germplasm.
{"title":"Genome-wide identification of light-harvesting chlorophyll a/b-binding (LHC) gene family in tomato and functional analysis of SlLhcb1.11 and SlELIP1 under cold stress","authors":"Fanyi Meng , Mengqiu Ma , Shanshan Li , Pan Liang , Yunfei Liang , Hongyan Shi , Shudi Huang , Huai Su , Yilin Deng , Muhammad Asif Akram , Xiaoxia Shen , Ru Feng , Xiangqiang Zhan , Fang Ma","doi":"10.1016/j.ygeno.2025.111022","DOIUrl":"10.1016/j.ygeno.2025.111022","url":null,"abstract":"<div><div>Light-harvesting chlorophyll a/b-binding (LHC) proteins, as the antenna complex, collect and transfer light energy to the reaction centers of PSII. They are crucial for abiotic stress responses, especially in the photoprotection under cold stress. However, members of the <em>LHC</em> gene family in tomato (<em>Solanum lycopersicum</em> L.) have not yet been identified. In this study, a total of 39 SlLHC proteins containing the chlorophyll a/b binding domain or light-harvesting-like domain were identified, and classified into four subfamilies: Lhc, Lil, PsbS, and FCII. Further qRT-PCR analysis showed <em>SlLhcb1.11</em> was inhibited and <em>SlELIP1</em> was induced at low temperature (4 °C). Subsequently, the result of VIGS experiment showed that silencing <em>SlLhcb1.11</em> or <em>SlELIP1</em> genes resulted in lighter leaf color, reduced chlorophyll content, compromised photosynthesis, and decreased cold tolerance in tomato plants. These findings offer novel insights into the structure and function of <em>SlLHC</em> genes, thereby contributing to genetic resources for the development of cold-tolerant tomato germplasm.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111022"},"PeriodicalIF":3.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531302","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 : 2025-02-22DOI: 10.1016/j.ygeno.2025.111018
Jiepeng Huang, Di Zhang, Shiting Yang, Yanyu Liu, Jurong Ma, Maojuan Zhou, Yunhong Tan, Yu Song
The tropical genus Cryptocarya is known for its valuable timber and its constituents show potential for medicinal properties. However, the phylogenetic relationships among species in Asia remain unclear. Here, we report the first mitochondrial genome assembly for Cryptocarya kwangtungensis, consisting of 758,020 bp, including 43 protein-coding genes, 23 tRNA genes and three rRNA genes, with 234 simple sequence repeats, and 1346 dispersed repeats, 35 homologous DNA fragments between the mitogenome and the plastome. Comparative genomic analysis indicated frequent recombination events among the sequences of five magnoliids mitogenomes and only five conserved clustered genes. Further phylogenetic analyses based on 91 mitochondrial regions and nuclear ribosomal cistron sequences of 21 species compound three well-resolved congruent groups for the Cryptocarya species in Asia, both of which support the genus divide into three clades, suggesting that the mitogenome sequence can provide strongly supported relationships within the genus in the family Lauraceae.
{"title":"Genomic insights and phylogenetics of the mitochondrial genome of Cryptocarya.","authors":"Jiepeng Huang, Di Zhang, Shiting Yang, Yanyu Liu, Jurong Ma, Maojuan Zhou, Yunhong Tan, Yu Song","doi":"10.1016/j.ygeno.2025.111018","DOIUrl":"https://doi.org/10.1016/j.ygeno.2025.111018","url":null,"abstract":"<p><p>The tropical genus Cryptocarya is known for its valuable timber and its constituents show potential for medicinal properties. However, the phylogenetic relationships among species in Asia remain unclear. Here, we report the first mitochondrial genome assembly for Cryptocarya kwangtungensis, consisting of 758,020 bp, including 43 protein-coding genes, 23 tRNA genes and three rRNA genes, with 234 simple sequence repeats, and 1346 dispersed repeats, 35 homologous DNA fragments between the mitogenome and the plastome. Comparative genomic analysis indicated frequent recombination events among the sequences of five magnoliids mitogenomes and only five conserved clustered genes. Further phylogenetic analyses based on 91 mitochondrial regions and nuclear ribosomal cistron sequences of 21 species compound three well-resolved congruent groups for the Cryptocarya species in Asia, both of which support the genus divide into three clades, suggesting that the mitogenome sequence can provide strongly supported relationships within the genus in the family Lauraceae.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111018"},"PeriodicalIF":3.4,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143491642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-13DOI: 10.1016/j.ygeno.2025.111014
Julieta G. Hamze , Josep M. Cambra , Sergio Navarro-Serna , Cristina A. Martinez-Serrano
Gene editing technologies, particularly CRISPR/Cas9, have emerged as transformative tools in genetic modification, significantly advancing the use of porcine embryos in biomedical and agricultural research. This review comprehensively examines the various methodologies for gene editing and delivery methods, such as somatic cell nuclear transfer (SCNT), microinjection, electroporation, and lipofection. This review, focuses on the advantages or limitations of using different biological sources (in vivo- vs. in vitro oocytes/embryos). Male germ cell manipulation using sperm-mediated gene transfer (SMGT) and testis-mediated gene transfer (TMGT) represent innovative approaches for producing genetically modified animals. Although these technologies have revolutionized the genetic engineering field, all these strategies face challenges, including high rates of off-target events and mosaicism. This review emphasizes the need to refine these methods, with a focus on reducing mosaicism and improving editing accuracy. Further advancements are essential to unlocking the full potential of gene editing for both agricultural applications and biomedical innovations.
{"title":"Navigating gene editing in porcine embryos: Methods, challenges, and future perspectives","authors":"Julieta G. Hamze , Josep M. Cambra , Sergio Navarro-Serna , Cristina A. Martinez-Serrano","doi":"10.1016/j.ygeno.2025.111014","DOIUrl":"10.1016/j.ygeno.2025.111014","url":null,"abstract":"<div><div>Gene editing technologies, particularly CRISPR/Cas9, have emerged as transformative tools in genetic modification, significantly advancing the use of porcine embryos in biomedical and agricultural research. This review comprehensively examines the various methodologies for gene editing and delivery methods, such as somatic cell nuclear transfer (SCNT), microinjection, electroporation, and lipofection. This review, focuses on the advantages or limitations of using different biological sources (<em>in vivo- vs. in vitro</em> oocytes/embryos). Male germ cell manipulation using sperm-mediated gene transfer (SMGT) and testis-mediated gene transfer (TMGT) represent innovative approaches for producing genetically modified animals. Although these technologies have revolutionized the genetic engineering field, all these strategies face challenges, including high rates of off-target events and mosaicism. This review emphasizes the need to refine these methods, with a focus on reducing mosaicism and improving editing accuracy. Further advancements are essential to unlocking the full potential of gene editing for both agricultural applications and biomedical innovations.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111014"},"PeriodicalIF":3.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143422675","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 : 2025-02-12DOI: 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}
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