The sirtuin (SIRT) family is a nicotine adenine dinucleotide (NAD+)-dependent class III histone deacetylase, which is widely involved in numerous physiological processes of organisms, such as metabolism, reproduction, and immunity. Here, based on the genomics database, comprehensive analysis of the SIRT gene in Nile tilapia (Oreochromis niloticus) was analyzed using bioinformatics methods and quantitative real-time PCR. The nine SIRT genes of O. niloticus (OnSIRT) were distributed on eight chromosomes. The OnSIRTs contain distinct sequences from 3 exons in OnSIRT4 to 16 exons in OnSIRT2, however, they share conserved domains and protein motifs. Phylogenetic analysis shows that the OnSIRTs belong to four subfamilies and are highly conserved in teleosts, and evolution is characterized primarily by purification selection. The OnSIRT genes showed diversified expression patterns in fourteen tissues of O. niloticus. OnSIRT2, OnSIRT3, OnSIRT3.2, OnSIRT6, and OnSIRT7 are mainly expressed in the gonads, especially in the ovary. OnSIRT1 and OnSIRT4 are mainly expressed in the kidney. OnSIRT5a is mainly expressed in the stomach, however, OnSIRT5b is mainly expressed in the liver and spleen. The results of this study provide a basis information for further exploration of the function and molecular mechanism of the SIRT gene family in teleosts.
{"title":"Genome-wide identification and expression analysis of the SIRT gene family in Nile tilapia (Oreochromis niloticus)","authors":"Jiabao Peng , Jiaqi Zou , Jinliang Zhao , Aqin Chen","doi":"10.1016/j.cbd.2025.101425","DOIUrl":"10.1016/j.cbd.2025.101425","url":null,"abstract":"<div><div>The sirtuin (SIRT) family is a nicotine adenine dinucleotide (NAD<sup>+</sup>)-dependent class III histone deacetylase, which is widely involved in numerous physiological processes of organisms, such as metabolism, reproduction, and immunity. Here, based on the genomics database, comprehensive analysis of the SIRT gene in Nile tilapia (<em>Oreochromis niloticus</em>) was analyzed using bioinformatics methods and quantitative real-time PCR. The nine <em>SIRT</em> genes of <em>O. niloticus</em> (<em>OnSIRT</em>) were distributed on eight chromosomes. The <em>OnSIRTs</em> contain distinct sequences from 3 exons in <em>OnSIRT4</em> to 16 exons in <em>OnSIRT2</em>, however, they share conserved domains and protein motifs. Phylogenetic analysis shows that the OnSIRTs belong to four subfamilies and are highly conserved in teleosts, and evolution is characterized primarily by purification selection. The <em>OnSIRT</em> genes showed diversified expression patterns in fourteen tissues of <em>O. niloticus</em>. <em>OnSIRT2</em>, <em>OnSIRT3</em>, <em>OnSIRT3.2</em>, <em>OnSIRT6</em>, and <em>OnSIRT7</em> are mainly expressed in the gonads, especially in the ovary. <em>OnSIRT1</em> and <em>OnSIRT4</em> are mainly expressed in the kidney. <em>OnSIRT5a</em> is mainly expressed in the stomach, however, <em>OnSIRT5b</em> is mainly expressed in the liver and spleen. The results of this study provide a basis information for further exploration of the function and molecular mechanism of the SIRT gene family in teleosts.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101425"},"PeriodicalIF":2.2,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076654","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 : 2025-01-19DOI: 10.1016/j.cbd.2025.101423
Chong Han , Shiyan Liu , Shuzheng Ye , Kaichun Chen , Dingxian Chen , Kaifeng Wang , Weiqian Liang , Simin Zhong , Lanyuan Liu , Sipeng Li , Weijian Chen , Qiang Li
The pax gene family is involved in the development process through its extensive effects on cell proliferation, differentiation, and apoptosis. Herein, the whole pax gene family members of mandarin fish (Siniperca chuatsi) were first identified and characterized. By comparing pax gene family members from another 13 representative animals, an expansion of pax gene family members was observed in teleosts. In mandarin fish, a total of 15 potential pax gene family members, distributed on 13 chromosomes, were found, which shared conserved synteny with other teleosts. The expression profiles revealed that members of pax gene family showed time-specific expression profiles during embryonic and gonad development in mandarin fish, which indicated they might play a specific role in organogenesis during embryonic development and the process of gonad development and differentiation. Our research will lay a good foundation for further functional investigation of pax gene family during fish embryonic and gonad development.
{"title":"Genome-wide identification, evolution and expression of pax gene family members in mandarin fish (Siniperca chuatsi)","authors":"Chong Han , Shiyan Liu , Shuzheng Ye , Kaichun Chen , Dingxian Chen , Kaifeng Wang , Weiqian Liang , Simin Zhong , Lanyuan Liu , Sipeng Li , Weijian Chen , Qiang Li","doi":"10.1016/j.cbd.2025.101423","DOIUrl":"10.1016/j.cbd.2025.101423","url":null,"abstract":"<div><div>The <em>pax</em> gene family is involved in the development process through its extensive effects on cell proliferation, differentiation, and apoptosis. Herein, the whole <em>pax</em> gene family members of mandarin fish (<em>Siniperca chuatsi</em>) were first identified and characterized. By comparing <em>pax</em> gene family members from another 13 representative animals, an expansion of <em>pax</em> gene family members was observed in teleosts. In mandarin fish, a total of 15 potential <em>pax</em> gene family members, distributed on 13 chromosomes, were found, which shared conserved synteny with other teleosts. The expression profiles revealed that members of <em>pax</em> gene family showed time-specific expression profiles during embryonic and gonad development in mandarin fish, which indicated they might play a specific role in organogenesis during embryonic development and the process of gonad development and differentiation. Our research will lay a good foundation for further functional investigation of <em>pax</em> gene family during fish embryonic and gonad development.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101423"},"PeriodicalIF":2.2,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143026064","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 : 2025-01-17DOI: 10.1016/j.cbd.2025.101422
Haiyan Li , Xin Zhang , Yangzong Zhaxi , Cheng Pan , Zhenzhen Zhang , Junru Pan , Khuram Shahzad , Fengbo Sun , Yang Zhen , Jiacuo Jinmei , Wangsheng Zhao , Tianzeng Song
The liver-gut axis is an important regulatory axis for the host's metabolic functions. The study of liver gene expression, changes in metabolic products and the regulation of gut microbial communities in plateau animals under harsh environments can reveal the mechanisms by which Tibetan goats adapt to the plateau environment. This study employs transcriptome, metabolome and metagenomic analyses to reveal the differences in genes, metabolism, and gut microbiota between Jianzhou big-eared goats (JBG) and Xizang cashmere goats (TCG), which is of significant importance for improving survival models of high-altitude ruminants. The results showed that there were 553 DEGs in the liver of JBG and TCG. Hepatic metabolomic analysis revealed significant differences in metabolic activity between the JBG and TCG groups, with notable increases in glycerophospholipid and retinol metabolic pathways. The gut microbiota, including Andreesenia, Dielma, Oscillibacter, Agrobacterium, Hyella and Thermosinus, interact with liver metabolites and can regulate the high-altitude adaptability of goats. This study reveals that TCG enhance immune regulation and energy utilization efficiency by regulating liver gene expression, modulating metabolic pathways, and improving gut microbiota, thereby helping TCG maintain healthy survival capabilities in hypoxic and high-radiation environments.
{"title":"Integrative multi-omics analysis reveals liver-gut axis adaptation in high-altitude goats","authors":"Haiyan Li , Xin Zhang , Yangzong Zhaxi , Cheng Pan , Zhenzhen Zhang , Junru Pan , Khuram Shahzad , Fengbo Sun , Yang Zhen , Jiacuo Jinmei , Wangsheng Zhao , Tianzeng Song","doi":"10.1016/j.cbd.2025.101422","DOIUrl":"10.1016/j.cbd.2025.101422","url":null,"abstract":"<div><div>The liver-gut axis is an important regulatory axis for the host's metabolic functions. The study of liver gene expression, changes in metabolic products and the regulation of gut microbial communities in plateau animals under harsh environments can reveal the mechanisms by which Tibetan goats adapt to the plateau environment. This study employs transcriptome, metabolome and metagenomic analyses to reveal the differences in genes, metabolism, and gut microbiota between Jianzhou big-eared goats (JBG) and Xizang cashmere goats (TCG), which is of significant importance for improving survival models of high-altitude ruminants. The results showed that there were 553 DEGs in the liver of JBG and TCG. Hepatic metabolomic analysis revealed significant differences in metabolic activity between the JBG and TCG groups, with notable increases in glycerophospholipid and retinol metabolic pathways. The gut microbiota, including <em>Andreesenia</em>, <em>Dielma</em>, <em>Oscillibacter</em>, <em>Agrobacterium</em>, <em>Hyella</em> and <em>Th</em>ermosinus, interact with liver metabolites and can regulate the high-altitude adaptability of goats. This study reveals that TCG enhance immune regulation and energy utilization efficiency by regulating liver gene expression, modulating metabolic pathways, and improving gut microbiota, thereby helping TCG maintain healthy survival capabilities in hypoxic and high-radiation environments.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101422"},"PeriodicalIF":2.2,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143026069","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 : 2025-01-17DOI: 10.1016/j.cbd.2025.101424
Pranoti R. Barve , Vitthal T. Barvkar , Ashok P. Giri , Hemlata M. Kotkar
Diamondback moth (Lepidoptera: Plutellidae; Plutella xylostella L.) is a specialist insect of the Brassicaceae family, damaging economically important crops, such as cabbage and cauliflower. Glucosinolates, also known as ‘mustard oil bombs' are present in all Brassicaceae members, of which sinigrin (allyl-glucosinolate or 2-propenyl-glucosinolate) is a major aliphatic compound. During herbivory, glucosinolates are converted to toxic isothiocyanates that deter insect pests. P. xylostella possesses glucosinolate sulfatases that desulfate them. Such a conversion renders them unfit for degradation to toxic products. Changes in the larval performance prompted us for RNA sequencing to understand probable adaptation mechanism under sinigrin stress. Differentially expressed genes were found to be related to larval cuticle proteins. Further, gene ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses depict genes belonging to the categories, integral component of membrane, cellular processes and those involved in biosynthesis of fatty acids. Upregulation of cuticular genes viz. larval cuticle protein-17 (LCP-17), cuticular protein-19 (2CP-19) and ATP binding cassette transporter C7 (ABCC7), ABCC16 was validated by qRT-PCR. Liquid chromatography quadrupole time of flight mass spectrometry analysis of whole larvae feeding on sinigrin and their separated cuticle, depicted abundance of fatty acids. Changes in the topography of the larval cuticle were evident by scanning electron microscopy. Expression of PxABCH1 was corroborated to its role in the transport of cuticular lipids. Notably, molecular docking of PxABCH1 with cuticular fatty acids showed favorable binding interactions. To summarize, integrated transcriptomic and metabolomic analyses suggest that in response to a diet containing a high dose of sinigrin, P. xylostella re-programs metabolic pathways related to fatty acid biosynthesis that directly influence insect development.
{"title":"High levels of sinigrin trigger synthesis of fatty acids in Plutella xylostella (L.)","authors":"Pranoti R. Barve , Vitthal T. Barvkar , Ashok P. Giri , Hemlata M. Kotkar","doi":"10.1016/j.cbd.2025.101424","DOIUrl":"10.1016/j.cbd.2025.101424","url":null,"abstract":"<div><div>Diamondback moth (Lepidoptera: Plutellidae; <em>Plutella xylostella</em> L.) is a specialist insect of the Brassicaceae family, damaging economically important crops, such as cabbage and cauliflower. Glucosinolates, also known as ‘mustard oil bombs' are present in all Brassicaceae members, of which sinigrin (allyl-glucosinolate or 2-propenyl-glucosinolate) is a major aliphatic compound. During herbivory, glucosinolates are converted to toxic isothiocyanates that deter insect pests. <em>P. xylostella</em> possesses glucosinolate sulfatases that desulfate them. Such a conversion renders them unfit for degradation to toxic products. Changes in the larval performance prompted us for RNA sequencing to understand probable adaptation mechanism under sinigrin stress. Differentially expressed genes were found to be related to larval cuticle proteins. Further, gene ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses depict genes belonging to the categories, integral component of membrane, cellular processes and those involved in biosynthesis of fatty acids. Upregulation of cuticular genes viz. larval cuticle protein-17 (<em>LCP-17)</em>, cuticular protein-19 (<em>2CP-19</em>) and ATP binding cassette transporter C7 (<em>ABCC7</em>), <em>ABCC16</em> was validated by qRT-PCR<em>.</em> Liquid chromatography quadrupole time of flight mass spectrometry analysis of whole larvae feeding on sinigrin and their separated cuticle, depicted abundance of fatty acids. Changes in the topography of the larval cuticle were evident by scanning electron microscopy. Expression of <em>PxABCH1</em> was corroborated to its role in the transport of cuticular lipids. Notably, molecular docking of <em>Px</em>ABCH1 with cuticular fatty acids showed favorable binding interactions. To summarize, integrated transcriptomic and metabolomic analyses suggest that in response to a diet containing a high dose of sinigrin, <em>P. xylostella</em> re-programs metabolic pathways related to fatty acid biosynthesis that directly influence insect development.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101424"},"PeriodicalIF":2.2,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143043244","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 : 2025-01-13DOI: 10.1016/j.cbd.2025.101414
Cheng Zhang , Shun Zhang , Guanlin Wang , Xiang Huang , Shanliang Xu , Danli Wang , Chunyang Guo , Yajun Wang
Pampus argenteus, a species distributed throughout the Indo-West Pacific, plays a significant role in the yield of aquaculture species. However, cultured P. argenteus has always been characterised by unbalanced growth synchronisation among individuals, slow growth rate, and lack of excellent germplasm resources. Therefore, we conducted mass selection for fast-growing strain P. argenteus for several consecutive years. Various genetic improvement programs have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In the present study, we combined bulked segregant analysis and transcriptome sequencing to identify candidate single nucleotide polymorphisms (SNPs) and key genes for growth-related traits in P. argenteus. A total of 7,280,936 SNPs and 2,212,379 insertions/deletions were identified in the extreme phenotypes of the fast-growing and slow-growing groups. Based on the examination of SNP frequency differences and sliding-window analysis, 42 SNPs were identified as candidate markers. Moreover, 14 of the 42 SNPs linked to growth-related traits were confirmed to be credible SNPs, and eight growth-related genes were screened, namely myb-binding protein 1 A, insulin A/B chains, α-1B adrenoceptor, engulfment and cell motility protein 3, myosin light chain kinase family member 4, insulin receptor located, unconventional myosin-9b, and matrilin-1. An optimal three-factor model (SNP4&SNP12&SNP14) was constructed using the generalized multifactor dimensionality reduction method, and its accuracy was verified as 67.72 %. These results may benefit genetic studies and accelerate genetic improvement of fast-growing strains of P. argenteus.
{"title":"Genomics and transcriptomics identify quantitative trait loci affecting growth-related traits in silver pomfret (Pampus argenteus)","authors":"Cheng Zhang , Shun Zhang , Guanlin Wang , Xiang Huang , Shanliang Xu , Danli Wang , Chunyang Guo , Yajun Wang","doi":"10.1016/j.cbd.2025.101414","DOIUrl":"10.1016/j.cbd.2025.101414","url":null,"abstract":"<div><div><em>Pampus argenteus</em>, a species distributed throughout the Indo-West Pacific, plays a significant role in the yield of aquaculture species. However, cultured <em>P. argenteus</em> has always been characterised by unbalanced growth synchronisation among individuals, slow growth rate, and lack of excellent germplasm resources. Therefore, we conducted mass selection for fast-growing strain <em>P. argenteus</em> for several consecutive years. Various genetic improvement programs have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In the present study, we combined bulked segregant analysis and transcriptome sequencing to identify candidate single nucleotide polymorphisms (SNPs) and key genes for growth-related traits in <em>P. argenteus</em>. A total of 7,280,936 SNPs and 2,212,379 insertions/deletions were identified in the extreme phenotypes of the fast-growing and slow-growing groups. Based on the examination of SNP frequency differences and sliding-window analysis, 42 SNPs were identified as candidate markers. Moreover, 14 of the 42 SNPs linked to growth-related traits were confirmed to be credible SNPs, and eight growth-related genes were screened, namely myb-binding protein 1 A, insulin A/B chains, α-1B adrenoceptor, engulfment and cell motility protein 3, myosin light chain kinase family member 4, insulin receptor located, unconventional myosin-9b, and matrilin-1. An optimal three-factor model (SNP4&SNP12&SNP14) was constructed using the generalized multifactor dimensionality reduction method, and its accuracy was verified as 67.72 %. These results may benefit genetic studies and accelerate genetic improvement of fast-growing strains of <em>P. argenteus</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101414"},"PeriodicalIF":2.2,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143018387","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 : 2025-01-13DOI: 10.1016/j.cbd.2025.101421
Huimin Duan , Yazhuo Zhang , Jia Liu , Gehui Ren , Zhentong Li , Yongsheng Tian
Vibrio anguillarum acts as an infectious agent in the aquaculture industry that causes a fatal hemolytic septicaemic disease in fish and shellfish. Viral nervous necrosis (VNN) disease seriously impacts the healthy development of the aquaculture industry. While the detrimental effects of V. anguillarum and NNV have been widely researched on freshwater and marine fish, whether they affect DNA replication in fish is unclear. In this study, we used Jinhu grouper as a model to investigate the influence of V. anguillarum and NNV on their DNA replication. By RNA-seq analysis in conjunction with gene set enrichment analysis, we found a significant upregulation of genes related to DNA replication in the liver and spleen of the Jinhu grouper after V. anguillarum infection while a prominent downregulation of genes related to DNA replication in the brain of the Jinhu grouper after NNV infection. We identified 27, 29 and 18 key genes involved in DNA replication that may respond to V. anguillarum and NNV infection and selected and identified six DNA replication genes (pole, pole2, pold1, pola1, pcna and mcm2). In addition, our results indicated that these genes exhibit tissue-specific expression patterns, with an increasing pattern of expression when V. anguillarum infected and a decreasing pattern when NNV infected. These results may provide valuable understanding on the underlying mechanisms of V. anguillarum and NNV infection in fish.
{"title":"Transcriptome analysis reveals the DNA replication genes response to Vibrio anguillarum and NNV infection in Jinhu grouper (Epinephelus fuscoguttatus♀ × Epinephelus tukulal♂)","authors":"Huimin Duan , Yazhuo Zhang , Jia Liu , Gehui Ren , Zhentong Li , Yongsheng Tian","doi":"10.1016/j.cbd.2025.101421","DOIUrl":"10.1016/j.cbd.2025.101421","url":null,"abstract":"<div><div><em>Vibrio anguillarum</em> acts as an infectious agent in the aquaculture industry that causes a fatal hemolytic septicaemic disease in fish and shellfish. Viral nervous necrosis (VNN) disease seriously impacts the healthy development of the aquaculture industry. While the detrimental effects of <em>V. anguillarum</em> and NNV have been widely researched on freshwater and marine fish, whether they affect DNA replication in fish is unclear. In this study, we used Jinhu grouper as a model to investigate the influence of <em>V. anguillarum</em> and NNV on their DNA replication. By RNA-seq analysis in conjunction with gene set enrichment analysis, we found a significant upregulation of genes related to DNA replication in the liver and spleen of the Jinhu grouper after <em>V. anguillarum</em> infection while a prominent downregulation of genes related to DNA replication in the brain of the Jinhu grouper after NNV infection. We identified 27, 29 and 18 key genes involved in DNA replication that may respond to <em>V. anguillarum</em> and NNV infection and selected and identified six DNA replication genes (<em>pole</em>, <em>pole2</em>, <em>pold1</em>, <em>pola1</em>, <em>pcna</em> and <em>mcm2</em>). In addition, our results indicated that these genes exhibit tissue-specific expression patterns, with an increasing pattern of expression when <em>V. anguillarum</em> infected and a decreasing pattern when NNV infected. These results may provide valuable understanding on the underlying mechanisms of <em>V. anguillarum</em> and NNV infection in fish.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101421"},"PeriodicalIF":2.2,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017864","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 : 2025-01-12DOI: 10.1016/j.cbd.2025.101419
Ru Zhang , Jiayue Liang , Zhaomin Liu , Jiale Chang , Junjie Zhang , Zhanxiong Zhang , Rui Li , Wei Zhao , Yongyuan Deng , Hongmei Xiao
As a widely epigenetic modification, m6A (N6-methyladenosine, m6A) can regulate the degradation, translation, and other biological functions of circRNAs through dynamic reversible processes. It plays an important role in regulating the life activities of biological organisms, particularly in cell differentiation, apoptosis, embryonic development, stress response, and innate immunity. In this study, bioinformatics analysis, qRT-PCR identification, FISH subcellular localization, and ceRNA network construction were performed on m6A modified circRNAs regulating the apoptosis of secondary hair follicle cells of Inner Mongolia Albas white cashmere goats based on the skin m6A sequencing data of secondary hair follicles in anagen and catagen. The results showed that 8 m6A modified circRNAs regulating the cell apoptosis of secondary hair follicles, namely circRNA_2130, circRNA_0013, circRNA_1203, circRNA_1462, circRNA_1242, circRNA_2308, circRNA_2654 and circRNA_1442 were identified, and they are respectively derived from ANGEL2, APP, GKAP1, HNRNPC, PTBP3, NUCB1, SNRK and ZNF609 genes. Among them, circRNA_0013, circRNA_1442 and circRNA_1462 were located in the cytoplasm of the secondary hair follicle papilla, while circRNA_1203, circRNA_1242, circRNA_2130, circRNA_2308 and circRNA_2654 were located in the nucleus. There are complex and diverse regulatory relationships among 8 circRNAs, with each circRNA targeting one or more miRNAs, revealing that each m6A circRNA can exert regulatory effects through multiple potential miRNA-mRNA axes, to regulate the apoptosis of secondary hair follicle cells of cashmere goats during the growth cycles. This result provides a direction for further elucidating the regulatory mechanism of m6A modified circRNAs in cashmere growth and exploring biomarkers.
{"title":"MeRIP-seq data analysis and validation reveal the regulatory role of m6A modified circRNAs in the apoptosis of secondary hair follicle cells in Inner Mongolia cashmere goats","authors":"Ru Zhang , Jiayue Liang , Zhaomin Liu , Jiale Chang , Junjie Zhang , Zhanxiong Zhang , Rui Li , Wei Zhao , Yongyuan Deng , Hongmei Xiao","doi":"10.1016/j.cbd.2025.101419","DOIUrl":"10.1016/j.cbd.2025.101419","url":null,"abstract":"<div><div>As a widely epigenetic modification, m<sup>6</sup>A (N<sup>6</sup>-methyladenosine, m<sup>6</sup>A) can regulate the degradation, translation, and other biological functions of circRNAs through dynamic reversible processes. It plays an important role in regulating the life activities of biological organisms, particularly in cell differentiation, apoptosis, embryonic development, stress response, and innate immunity. In this study, bioinformatics analysis, qRT-PCR identification, FISH subcellular localization, and ceRNA network construction were performed on m<sup>6</sup>A modified circRNAs regulating the apoptosis of secondary hair follicle cells of Inner Mongolia Albas white cashmere goats based on the skin m<sup>6</sup>A sequencing data of secondary hair follicles in anagen and catagen. The results showed that 8 m<sup>6</sup>A modified circRNAs regulating the cell apoptosis of secondary hair follicles, namely circRNA_2130, circRNA_0013, circRNA_1203, circRNA_1462, circRNA_1242, circRNA_2308, circRNA_2654 and circRNA_1442 were identified, and they are respectively derived from <em>ANGEL2</em>, <em>APP</em>, <em>GKAP1</em>, <em>HNRNPC</em>, <em>PTBP3</em>, <em>NUCB1</em>, <em>SNRK</em> and <em>ZNF609</em> genes. Among them, circRNA_0013, circRNA_1442 and circRNA_1462 were located in the cytoplasm of the secondary hair follicle papilla, while circRNA_1203, circRNA_1242, circRNA_2130, circRNA_2308 and circRNA_2654 were located in the nucleus. There are complex and diverse regulatory relationships among 8 circRNAs, with each circRNA targeting one or more miRNAs, revealing that each m<sup>6</sup>A circRNA can exert regulatory effects through multiple potential miRNA-mRNA axes, to regulate the apoptosis of secondary hair follicle cells of cashmere goats during the growth cycles. This result provides a direction for further elucidating the regulatory mechanism of m<sup>6</sup>A modified circRNAs in cashmere growth and exploring biomarkers.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101419"},"PeriodicalIF":2.2,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017874","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 : 2025-01-12DOI: 10.1016/j.cbd.2025.101416
Yaling Zhang , Muhammad Farhan , Hanjing Yang , Jun Zhao , Xiaoyan Ma , Shuai Zhang
Glutathione S-transferase (GST) plays a critical role in detoxifying various chemical compounds and is essential for host adaptation and pesticide resistance in insects. To understand the genetic structure of the GST family and the expression patterns among three haplotypes of Aphis gossypii, we conducted studies using genome annotation files and RNA-seq data. We identified 11 GSTs in A. gossypii, which include 2 microsomal GSTs, 2 in the Theta class, 2 in the Delta class, 3 in the Sigma class (one of which contains a probable pseudogene), 1 in the Omega class, and 1 belonging to a GST C-terminal domain-containing protein. These GSTs are distributed on autosomes, with the two Delta class GSTs and two Theta class GSTs clustered on a chromosome. AgosGSTCD3 is evolutionarily conserved in aphids, encoding 550 amino acids with the C-terminal region containing a methyltransferase domain. AgosGSTo4 exhibits alternative splicing, resulting in the formation of three isoforms. GSTs show conservation among Hap1, Hap3, and Hap4, except for AgosGSTm9, which demonstrates noticeable variations in the protein-coding regions and surrounding areas among the three haplotypes of A. gossypii. The expression profiles of GSTs were observed in the three haplotypes of A. gossypii, most showing different expression levels. These findings provide a valuable resource for further investigations into population differentiation and pesticide resistance evolution.
谷胱甘肽s -转移酶（GST）在多种化学物质的解毒过程中起着重要作用，对昆虫的寄主适应和抗性具有重要作用。为了了解棉蚜GST家族的遗传结构和三种单倍型的表达模式，我们利用基因组注释文件和RNA-seq数据进行了研究。我们在棉籽棉中鉴定了11个GST，其中包括2个微粒体GST， 2个在Theta类，2个在Delta类，3个在Sigma类（其中一个可能含有假基因），1个在Omega类，1个属于GST c -末端结构域蛋白。这些gst分布在常染色体上，两个Delta类gst和两个Theta类gst聚集在一条染色体上。AgosGSTCD3在蚜虫中具有进化保守性，编码550个氨基酸，其c端区域含有甲基转移酶结构域。AgosGSTo4表现出选择性剪接，导致形成三个同工异构体。除AgosGSTm9外，GSTs在Hap1、Hap3和ha4中均表现出保守性，其蛋白编码区和周围区域在棉棉三种单倍型中存在明显差异。GSTs在棉蚜三种单倍型中的表达谱均有差异，且多数表现出不同的表达水平。这些发现为进一步深入研究昆虫种群分化和抗药性演变提供了宝贵的资源。
{"title":"Genome-wide analyses of glutathione S-transferase gene family and expression profiling among three haplotypes Aphis gossypii","authors":"Yaling Zhang , Muhammad Farhan , Hanjing Yang , Jun Zhao , Xiaoyan Ma , Shuai Zhang","doi":"10.1016/j.cbd.2025.101416","DOIUrl":"10.1016/j.cbd.2025.101416","url":null,"abstract":"<div><div>Glutathione S-transferase (GST) plays a critical role in detoxifying various chemical compounds and is essential for host adaptation and pesticide resistance in insects. To understand the genetic structure of the GST family and the expression patterns among three haplotypes of <em>Aphis gossypii</em>, we conducted studies using genome annotation files and RNA-seq data. We identified 11 <em>GSTs</em> in <em>A. gossypii</em>, which include 2 microsomal <em>GSTs</em>, 2 in the Theta class, 2 in the Delta class, 3 in the Sigma class (one of which contains a probable pseudogene), 1 in the Omega class, and 1 belonging to a GST C-terminal domain-containing protein. These <em>GSTs</em> are distributed on autosomes, with the two Delta class GSTs and two Theta class GSTs clustered on a chromosome. <em>AgosGSTCD3</em> is evolutionarily conserved in aphids, encoding 550 amino acids with the C-terminal region containing a methyltransferase domain. <em>AgosGSTo4</em> exhibits alternative splicing, resulting in the formation of three isoforms. <em>GSTs</em> show conservation among Hap1, Hap3, and Hap4, except for <em>AgosGSTm9</em>, which demonstrates noticeable variations in the protein-coding regions and surrounding areas among the three haplotypes of <em>A. gossypii</em>. The expression profiles of <em>GSTs</em> were observed in the three haplotypes of <em>A. gossypii</em>, most showing different expression levels. These findings provide a valuable resource for further investigations into population differentiation and pesticide resistance evolution.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101416"},"PeriodicalIF":2.2,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143018385","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 : 2025-01-12DOI: 10.1016/j.cbd.2025.101415
Minxin Liang , Jinping Xie , Yiwei Huang , Qingheng Wang , Ronglian Huang , Yongshan Liao , Yuewen Deng , Chuangye Yang , Zhe Zheng
Biomineralization to fabricate diverse morphology shell is typical character of bivalve species and ectopic calcification to form is the production of defense. Long non-coding RNAs (LncRNAs) plays critical roles in multiple cellular biological processes in invertebrate and vertebrate. However, LncRNAs remain poorly understood about expression and regulation roles in bivalve biomineralization studies. In this research, we systematically identified lncRNAs that functioned in differentiated mantle regions for fabricating two phenotypes of CaCO3 crystal shell, along with pearl sac depositing pearls for ectopic calcification by CaCO3. A total of 48,555 non-coding transcripts were obtained. 229 differentially expressed lncRNAs in mantle tissue as well as 401 differentially expressed lncRNAs in the comparison of mantle center to pearl sac were identified. By cis- and trans-regulation ways, these DELs could be involved in provisioning and metabolism such as chitin, glycosaminoglycan, ECM/shell matrix protein, Ca2+ and HCO3− offering, and also affecting related signaling pathways. In addition, lncRNAs were found to crosstalk with miRNAs not only as primary competing endogenous RNAs but as the primary miRNAs. Our studies provided insight into non-coding RNA regulation of epigenetic regulation in biomineralization in bivalve species.
{"title":"Identification of long non-coding RNAs and their multiple regulation mechanism in shell deposition of pearl oyster","authors":"Minxin Liang , Jinping Xie , Yiwei Huang , Qingheng Wang , Ronglian Huang , Yongshan Liao , Yuewen Deng , Chuangye Yang , Zhe Zheng","doi":"10.1016/j.cbd.2025.101415","DOIUrl":"10.1016/j.cbd.2025.101415","url":null,"abstract":"<div><div>Biomineralization to fabricate diverse morphology shell is typical character of bivalve species and ectopic calcification to form is the production of defense. Long non-coding RNAs (LncRNAs) plays critical roles in multiple cellular biological processes in invertebrate and vertebrate. However, LncRNAs remain poorly understood about expression and regulation roles in bivalve biomineralization studies. In this research, we systematically identified lncRNAs that functioned in differentiated mantle regions for fabricating two phenotypes of CaCO<sub>3</sub> crystal shell, along with pearl sac depositing pearls for ectopic calcification by CaCO<sub>3</sub>. A total of 48,555 non-coding transcripts were obtained. 229 differentially expressed lncRNAs in mantle tissue as well as 401 differentially expressed lncRNAs in the comparison of mantle center to pearl sac were identified. By cis- and trans-regulation ways, these DELs could be involved in provisioning and metabolism such as chitin, glycosaminoglycan, ECM/shell matrix protein, Ca<sup>2+</sup> and HCO<sub>3</sub><sup>−</sup> offering, and also affecting related signaling pathways. In addition, lncRNAs were found to crosstalk with miRNAs not only as primary competing endogenous RNAs but as the primary miRNAs. Our studies provided insight into non-coding RNA regulation of epigenetic regulation in biomineralization in bivalve species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101415"},"PeriodicalIF":2.2,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017627","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 : 2025-01-11DOI: 10.1016/j.cbd.2025.101420
Jihang Gong , Xiao Han , Lu Qi , Lingfeng Kong , Qi Li
Trochoidea is the richest and most diverse group within Vetigastropoda, serving as one of the main focuses on studies of marine ecology and systematics. Both morphological and molecular studies have sought to resolve the phylogenetic framework of Trochoidea; however, the phylogenetic relationships among some lineages remain controversial. In order to explore the phylogenetic relationships within Trochoidea, we sequenced the mitochondrial genomes of 9 trochoids and analyzed them with data from 38 previously published mitochondrial genomes and 27 transcriptomic data representing 11 families within this group. The mitochondrial genomes of all Trochidae exhibited a consistent gene arrangement and showed conserved genome size and nucleotide composition; however, Colloniidae and Phasianellidae showed higher levels of gene order rearrangement. Furthermore, three-nucleotide insertions were observed in the cox1 gene of Colloniidae and nad4L gene of Phasianellidae, while three-nucleotide deletions were detected in nad4 gene of Trochidae. Both maximum likelihood and Bayesian inference analyses supported the monophyly of all families within the Trochoidea, except Tegulidae, and placed Liotiidae as sister to the rest of Trochoidea with poor to moderate support. Areneidae was recovered as the sister group to a clade including Phasianellidae and Colloniidae. These findings challenge the traditional classification of this family based on both morphological and molecular data. Our study provides new insights into the phylogeny of Trochoidea, especially with the incorporation of micromolluscs taxa, and highlight the significance of incorporating microgastropoda taxa into molecular phylogenetic reconstructions of gastropod subgroups.
{"title":"Incorporation of microgastropoda species provides novel insights into phylogeny of Trochoidea (Gastropoda: Vetigastropoda)","authors":"Jihang Gong , Xiao Han , Lu Qi , Lingfeng Kong , Qi Li","doi":"10.1016/j.cbd.2025.101420","DOIUrl":"10.1016/j.cbd.2025.101420","url":null,"abstract":"<div><div>Trochoidea is the richest and most diverse group within Vetigastropoda, serving as one of the main focuses on studies of marine ecology and systematics. Both morphological and molecular studies have sought to resolve the phylogenetic framework of Trochoidea; however, the phylogenetic relationships among some lineages remain controversial. In order to explore the phylogenetic relationships within Trochoidea, we sequenced the mitochondrial genomes of 9 trochoids and analyzed them with data from 38 previously published mitochondrial genomes and 27 transcriptomic data representing 11 families within this group. The mitochondrial genomes of all Trochidae exhibited a consistent gene arrangement and showed conserved genome size and nucleotide composition; however, Colloniidae and Phasianellidae showed higher levels of gene order rearrangement. Furthermore, three-nucleotide insertions were observed in the <em>cox1</em> gene of Colloniidae and <em>nad4L</em> gene of Phasianellidae, while three-nucleotide deletions were detected in <em>nad4</em> gene of Trochidae. Both maximum likelihood and Bayesian inference analyses supported the monophyly of all families within the Trochoidea, except Tegulidae, and placed Liotiidae as sister to the rest of Trochoidea with poor to moderate support. Areneidae was recovered as the sister group to a clade including Phasianellidae and Colloniidae. These findings challenge the traditional classification of this family based on both morphological and molecular data. Our study provides new insights into the phylogeny of Trochoidea, especially with the incorporation of micromolluscs taxa, and highlight the significance of incorporating microgastropoda taxa into molecular phylogenetic reconstructions of gastropod subgroups.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101420"},"PeriodicalIF":2.2,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017944","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}
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