Pub Date : 2025-01-11DOI: 10.1016/j.cbd.2025.101417
Haifeng Huang , Lintao Tan , Lei Wei , Hongce Song , Wenwen Xu , Meiyun Dong , Xiaolong Chu , Xiaotong Wang
Asymmetric development, in which functional differences occur between left-right symmetrical organs, is widespread in organisms, including fish and mollusks. However, the asymmetry of symmetrical sensory structures in Haliotis discus hannai, a gastropod with a sensitive sensory system, remains unknown. This study analyzed the transcriptomes of three sensory structures (eyestalks, cephalic tentacles, and epipodial tentacles) to explore potential asymmetries in this species. RNA-seq revealed functional differences in sensory ability and sperm-egg recognition between right and left eyestalks, with cephalic tentacles displaying asymmetry in cytoskeletal organization and cell cycle regulation. Epipodial tentacles showed similar asymmetries, including immune response differences. Moreover, the cAMP-protein kinase A (PKA)-CREB-binding protein (CBP) signaling pathway responded asymmetrically, with PKA responding to activators and inhibitors on both sides and CBP showing a stronger response on the right. These findings provide insights into sensory asymmetry in mollusks and guidance for further investigations of the molecular mechanisms underlying asymmetry in symmetrical organs.
不对称发育，即左右对称器官之间的功能差异，在包括鱼类和软体动物在内的生物体中普遍存在。然而，具有敏感感觉系统的腹足动物盘足虫（halotis discus hannai）对称感觉结构的不对称性尚不清楚。本研究分析了三种感觉结构（眼柄、头端触须和下颚触须）的转录组，以探索该物种潜在的不对称性。RNA-seq揭示了左右眼柄在感觉能力和精卵识别功能上的差异，头侧触须在细胞骨架组织和细胞周期调节方面表现出不对称。下丘脑触须也表现出类似的不对称，包括免疫反应的差异。此外，cAMP-protein kinase A (PKA)-CREB-binding protein （CBP）信号通路的反应是不对称的，PKA对两侧的激活剂和抑制剂都有反应，而CBP在右侧的反应更强。这些发现为软体动物的感觉不对称提供了见解，并为进一步研究对称器官不对称的分子机制提供了指导。
{"title":"Comparative transcriptomic analysis of left-right sensory differences in Haliotis discus hannai","authors":"Haifeng Huang , Lintao Tan , Lei Wei , Hongce Song , Wenwen Xu , Meiyun Dong , Xiaolong Chu , Xiaotong Wang","doi":"10.1016/j.cbd.2025.101417","DOIUrl":"10.1016/j.cbd.2025.101417","url":null,"abstract":"<div><div>Asymmetric development, in which functional differences occur between left-right symmetrical organs, is widespread in organisms, including fish and mollusks. However, the asymmetry of symmetrical sensory structures in <em>Haliotis discus hannai</em>, a gastropod with a sensitive sensory system, remains unknown. This study analyzed the transcriptomes of three sensory structures (eyestalks, cephalic tentacles, and epipodial tentacles) to explore potential asymmetries in this species. RNA-seq revealed functional differences in sensory ability and sperm-egg recognition between right and left eyestalks, with cephalic tentacles displaying asymmetry in cytoskeletal organization and cell cycle regulation. Epipodial tentacles showed similar asymmetries, including immune response differences. Moreover, the cAMP-protein kinase A (<em>PKA</em>)-CREB-binding protein (<em>CBP</em>) signaling pathway responded asymmetrically, with <em>PKA</em> responding to activators and inhibitors on both sides and <em>CBP</em> showing a stronger response on the right. These findings provide insights into sensory asymmetry in mollusks and guidance for further investigations of the molecular mechanisms underlying asymmetry in symmetrical organs.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101417"},"PeriodicalIF":2.2,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143018384","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 : 2025-01-10DOI: 10.1016/j.cbd.2025.101418
Chao Li , Xiaoying Liu , Chaochao Hu, Jie Yan, Yanfu Qu, Hong Li, Kaiya Zhou, Peng Li
Temperature is closely linked to the life history of organisms, and thus thermoception is an important sensory mechanism. Transient receptor potential (TRP) ion channels are the key mediators of thermal sensation. In this study, we analyzed the sequence characteristics of TRPs in gecko Hemiphyllodactylus yunnanensis and compared the phylogenetic relationships of TRP family members among different Squamata species. In addition, we sequenced the transcriptome of skin and brain tissues of H. yunnanensis exposed to 12 °C (cold), 20 °C (cool), 28 °C (warm), and 36 °C (hot). The results showed that a total of 591 TRPs were identified in the genomes of 21 Squamate species, and these genes were classified into six subfamilies. Among them, 26 TRP genes were identified in H. yunnanensis and distributed on 13 chromosomes. Overall, TRP genes were conserved in squamates. Based on the transcriptome results, we found a total of 9 TRP genes expressed in the brain and skin of H. yunnanensis, of which six TRP genes were under positive selection. TRPP1L2, TRPP1L3, and TRPV1 were involved in heat-sensitive responses (> 36 °C), and TRPV3, TRPA1, and TRPM8 were involved in cold-sensitive responses (< 20 °C). TRPM8 and TRPP1L2 were important cold and heat sensors in H. yunnanensis, respectively.
{"title":"Genome-wide characterization of the TRP gene family and transcriptional expression profiles under different temperatures in gecko Hemiphyllodactylus yunnanensis","authors":"Chao Li , Xiaoying Liu , Chaochao Hu, Jie Yan, Yanfu Qu, Hong Li, Kaiya Zhou, Peng Li","doi":"10.1016/j.cbd.2025.101418","DOIUrl":"10.1016/j.cbd.2025.101418","url":null,"abstract":"<div><div>Temperature is closely linked to the life history of organisms, and thus thermoception is an important sensory mechanism. Transient receptor potential (TRP) ion channels are the key mediators of thermal sensation. In this study, we analyzed the sequence characteristics of TRPs in gecko <em>Hemiphyllodactylus yunnanensis</em> and compared the phylogenetic relationships of TRP family members among different Squamata species. In addition, we sequenced the transcriptome of skin and brain tissues of <em>H. yunnanensis</em> exposed to 12 °C (cold), 20 °C (cool), 28 °C (warm), and 36 °C (hot). The results showed that a total of 591 <em>TRPs</em> were identified in the genomes of 21 Squamate species, and these genes were classified into six subfamilies. Among them, 26 <em>TRP</em> genes were identified in <em>H. yunnanensis</em> and distributed on 13 chromosomes. Overall, <em>TRP</em> genes were conserved in squamates. Based on the transcriptome results, we found a total of 9 <em>TRP</em> genes expressed in the brain and skin of <em>H. yunnanensis</em>, of which six <em>TRP</em> genes were under positive selection. <em>TRPP1L2</em>, <em>TRPP1L3</em>, and <em>TRPV1</em> were involved in heat-sensitive responses (> 36 °C), and <em>TRPV3</em>, <em>TRPA1</em>, and <em>TRPM8</em> were involved in cold-sensitive responses (< 20 °C). TRPM8 and TRPP1L2 were important cold and heat sensors in <em>H. yunnanensis</em>, respectively.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101418"},"PeriodicalIF":2.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142985538","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 : 2025-01-10DOI: 10.1016/j.cbd.2025.101413
Fengjie Liu , Wei Li , Yanrong Wu , Zhilin Chen , Xingyang Zhao , Jie Liu , Yu Peng , Yao Zhao , Yang Zhu
Triclocarban (TCC), an emerging organic contaminant, poses a potential threat to water resources and ecosystems. The wolf spider Pardosa pseudoannulata (Araneae: Lycosidae) is a dominant predator typically inhabiting rice fields or wet habitats near water sources. However, little is known about the effects of TCC on the wolf spiders. In the present study, using environmentally relevant concentrations, we systematically investigated the toxicity of TCC on the early life stages of P. pseudoannulata at both physiological and gene expression levels. Our results indicated that TCC exposure did not significantly affect the survival and development of spiderlings. Transcriptome analysis revealed that TCC stress significantly impacted drug metabolism, cell cycle and signal transduction pathways in spiderlings. Subsequently, qRT-PCR was used to verify the expression levels of genes associated with drug metabolism and cell process, and the results were consistent with the transcriptome. These findings enhance our understanding of the toxic mechanism and ecological risk of TCC on arthropods.
{"title":"Impact of triclocarban exposure on development and gene expression in the wolf spider, Pardosa pseudoannulata (Araneae: Lycosidae)","authors":"Fengjie Liu , Wei Li , Yanrong Wu , Zhilin Chen , Xingyang Zhao , Jie Liu , Yu Peng , Yao Zhao , Yang Zhu","doi":"10.1016/j.cbd.2025.101413","DOIUrl":"10.1016/j.cbd.2025.101413","url":null,"abstract":"<div><div>Triclocarban (TCC), an emerging organic contaminant, poses a potential threat to water resources and ecosystems. The wolf spider <em>Pardosa pseudoannulata</em> (Araneae: Lycosidae) is a dominant predator typically inhabiting rice fields or wet habitats near water sources. However, little is known about the effects of TCC on the wolf spiders. In the present study, using environmentally relevant concentrations, we systematically investigated the toxicity of TCC on the early life stages of <em>P. pseudoannulata</em> at both physiological and gene expression levels. Our results indicated that TCC exposure did not significantly affect the survival and development of spiderlings. Transcriptome analysis revealed that TCC stress significantly impacted drug metabolism, cell cycle and signal transduction pathways in spiderlings. Subsequently, qRT-PCR was used to verify the expression levels of genes associated with drug metabolism and cell process, and the results were consistent with the transcriptome. These findings enhance our understanding of the toxic mechanism and ecological risk of TCC on arthropods.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101413"},"PeriodicalIF":2.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017672","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}
The formation of broodstock gametes is closely linked to the yield and quality in aquaculture production, yet molecular mechanisms underlying this process remain insufficiently understood. The noble scallop Chlamys nobilis, an economically significant dioecious bivalve species, serves as an excellent model for studying gametogenesis. In this study, the adult scallops with testis at different developmental stage were chosen for histological examination and transcriptome analysis to dig genes related gonad development. Totally, 2663 DEGs and their set modules significantly related to spermatogenesis were obtained using WGCNA, including 40 candidate genes represented by EVM713. The gene was specifically expressed in the testis. RNA interference (RNAi) of EVM713 led to impaired testis development, marked by sparse sperm cell arrangement, spermatocytes detaching from the follicle wall, and reduced spermatocyte numbers. Meanwhile, 24 h after RNAi, the expression levels of Bax, and Caspase3 significantly increased (P < 0.05), while those of Bcl2, Dmrt2 and Tssk4 were significantly decreased (P < 0.05). These results indicate that EVM713 is essential for spermatogenesis in bivalves, regulating testis development through the modulation of Dmrt2 and Tssk4 expression. This study provides the first evidence of EVM713 function in mollusks, which is conducive to better understanding molecular mechanisms underlying gametogenesis in marine invertebrates.
{"title":"Functional verification of a landmark gene EVM713 involved in spermatogenesis in the marine bivalve Chlamys nobilis","authors":"Xixi Duan , Mingfei Feng , Xiangdong Bai , Imran Rashid Rajput , Hongkuan Zhang , Huaiping Zheng","doi":"10.1016/j.cbd.2024.101412","DOIUrl":"10.1016/j.cbd.2024.101412","url":null,"abstract":"<div><div>The formation of broodstock gametes is closely linked to the yield and quality in aquaculture production, yet molecular mechanisms underlying this process remain insufficiently understood. The noble scallop <em>Chlamys nobilis</em>, an economically significant dioecious bivalve species, serves as an excellent model for studying gametogenesis. In this study, the adult scallops with testis at different developmental stage were chosen for histological examination and transcriptome analysis to dig genes related gonad development. Totally, 2663 DEGs and their set modules significantly related to spermatogenesis were obtained using WGCNA, including 40 candidate genes represented by <em>EVM713</em>. The gene was specifically expressed in the testis. RNA interference (RNAi) of <em>EVM713</em> led to impaired testis development, marked by sparse sperm cell arrangement, spermatocytes detaching from the follicle wall, and reduced spermatocyte numbers. Meanwhile, 24 h after RNAi, the expression levels of <em>Bax</em>, and <em>Caspase3</em> significantly increased (<em>P</em> < 0.05), while those of <em>Bcl2</em>, <em>Dmrt2</em> and <em>Tssk4</em> were significantly decreased (<em>P</em> < 0.05). These results indicate that <em>EVM713</em> is essential for spermatogenesis in bivalves, regulating testis development through the modulation of <em>Dmrt2</em> and <em>Tssk4</em> expression. This study provides the first evidence of <em>EVM713</em> function in mollusks, which is conducive to better understanding molecular mechanisms underlying gametogenesis in marine invertebrates.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101412"},"PeriodicalIF":2.2,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142985532","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 : 2024-12-31DOI: 10.1016/j.cbd.2024.101411
Chuangye Yang , Hailing Wu , Ruijuan Hao , Yongshan Liao , Qingheng Wang , Yuewen Deng
This study investigated the protective effect of arachidonic acid (ARA) against the allograft-induced stress response in Pinctada fucata martensii by characterizing pearl production traits and changes in genes and lipids during postoperative care. Survival and pearl production traits were higher in the ARA treatment group (ARAG) than in the control group (CG). There were 1536 differentially expressed genes (DEGs) in CG-1d vs ARAG-1d and 833 DEGs in CG-3d vs ARAG-3d. DEGs in CG-1d vs ARAG-1d were mainly enriched in “NOD-like receiver signaling pathway,” “Glycerolipid metabolism,” and “Sphingolipid metabolism.” DEGs in CG-3d vs ARAG-3d were mainly enriched in “Apoptosis” and “ARA metabolism.” Lipidomics analysis revealed 36 types of lipids. The PC, LPE (22:5), and LPE (18:0) content at 3 d after implantation was lower in the ARAG than in the CG. The PS (37,1) content was significantly higher at 3 d after implantation and the content of ceramides was significantly lower at 1 and 3 d after implantation in the ARAG than in the CG. The results indicated that ARA may alter the composition of lipids, modify the unsaturation of lipids, and regulate apoptosis, immunity, and lipid metabolism in pearl oysters, which enhances pearl production traits. These findings provide theoretical and practical basis for further alleviating the inflammatory response of pearl oysters after implantation.
{"title":"Integrated transcriptomic and lipidomic analysis reveals that arachidonic acid mediates the allograft-induced stress response in Pinctada fucata martensii","authors":"Chuangye Yang , Hailing Wu , Ruijuan Hao , Yongshan Liao , Qingheng Wang , Yuewen Deng","doi":"10.1016/j.cbd.2024.101411","DOIUrl":"10.1016/j.cbd.2024.101411","url":null,"abstract":"<div><div>This study investigated the protective effect of arachidonic acid (ARA) against the allograft-induced stress response in <em>Pinctada fucata martensii</em> by characterizing pearl production traits and changes in genes and lipids during postoperative care. Survival and pearl production traits were higher in the ARA treatment group (ARAG) than in the control group (CG). There were 1536 differentially expressed genes (DEGs) in CG-1d vs ARAG-1d and 833 DEGs in CG-3d vs ARAG-3d. DEGs in CG-1d vs ARAG-1d were mainly enriched in “NOD-like receiver signaling pathway,” “Glycerolipid metabolism,” and “Sphingolipid metabolism.” DEGs in CG-3d vs ARAG-3d were mainly enriched in “Apoptosis” and “ARA metabolism.” Lipidomics analysis revealed 36 types of lipids. The PC, LPE (22:5), and LPE (18:0) content at 3 d after implantation was lower in the ARAG than in the CG. The PS (37,1) content was significantly higher at 3 d after implantation and the content of ceramides was significantly lower at 1 and 3 d after implantation in the ARAG than in the CG. The results indicated that ARA may alter the composition of lipids, modify the unsaturation of lipids, and regulate apoptosis, immunity, and lipid metabolism in pearl oysters, which enhances pearl production traits. These findings provide theoretical and practical basis for further alleviating the inflammatory response of pearl oysters after implantation.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101411"},"PeriodicalIF":2.2,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143141657","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 : 2024-12-30DOI: 10.1016/j.cbd.2024.101403
Xiaohong Zheng , Hongfei Shang , Qifan Liu , Luao Tian , Yuzhen Yue , Shiqing Meng , Jiahui Chen , Linlin Su , Jiaxin Quan , Yi Zhang , Xiaoli Li , Kedong Xu , Xinxin Shangguan
Uridine diphosphate-glycosyltransferases (UGTs) are responsible for glycosylation by combining various small lipophilic molecules with sugars to produce water-soluble glycosides, which are crucial for the metabolism of plant secondary metabolites and detoxification in insects. This study presents a genome-wide analysis of the UGT gene family in the brown planthopper, Nilaparvata lugens, a destructive insect pest of rice in Asia. Based on the similarity to UGT homologs from other organisms, 20 putative NlUGT genes were identified in N. lugens. Sequence analysis revealed an average amino acid identity of 45.64 %; however, catalytic and sugar-binding residues, along with UGT signature motifs, were highly conserved. Phylogenetic analysis showed that the 20 NlUGTs were clustered into three main groups. The motif numbers ranged from 5 to 10, with motifs 1 and 4 being found in the functional domains of all 20 NlUGT proteins. Tandem and segmental duplication analysis identified one tandem duplication pair (UGT386K7 and UGT386K8) and two pairs of collinearity genes (UGT362C6/UGT386J4 and UGT386C2/UGT386G5) that expanded through segmental duplication within the UGT gene family of N. lugens. Combining the transcriptome and real-time quantitative PCR data showed that gut, antennae, integument, and ovaries were the tissues enriched with NlUGT gene expression. Six NlUGTs were present mainly in the gut, suggesting their putative roles in detoxification. This research provides valuable information on the molecular and genetic basis of NlUGTs, establishing a solid foundation for subsequent functional investigations of UGTs in planthopper, as well as paving the way for identifying potential targets to manage N. lugens effectively.
{"title":"Genome-wide identification and expression patterns of uridine diphosphate (UDP)-glycosyltransferase genes in the brown planthopper, Nilaparvata lugens","authors":"Xiaohong Zheng , Hongfei Shang , Qifan Liu , Luao Tian , Yuzhen Yue , Shiqing Meng , Jiahui Chen , Linlin Su , Jiaxin Quan , Yi Zhang , Xiaoli Li , Kedong Xu , Xinxin Shangguan","doi":"10.1016/j.cbd.2024.101403","DOIUrl":"10.1016/j.cbd.2024.101403","url":null,"abstract":"<div><div>Uridine diphosphate-glycosyltransferases (UGTs) are responsible for glycosylation by combining various small lipophilic molecules with sugars to produce water-soluble glycosides, which are crucial for the metabolism of plant secondary metabolites and detoxification in insects. This study presents a genome-wide analysis of the <em>UGT</em> gene family in the brown planthopper, <em>Nilaparvata lugens</em>, a destructive insect pest of rice in Asia. Based on the similarity to UGT homologs from other organisms, 20 putative <em>NlUGT</em> genes were identified in <em>N. lugens</em>. Sequence analysis revealed an average amino acid identity of 45.64 %; however, catalytic and sugar-binding residues, along with UGT signature motifs, were highly conserved. Phylogenetic analysis showed that the 20 NlUGTs were clustered into three main groups. The motif numbers ranged from 5 to 10, with motifs 1 and 4 being found in the functional domains of all 20 NlUGT proteins. Tandem and segmental duplication analysis identified one tandem duplication pair (<em>UGT386K7</em> and <em>UGT386K8</em>) and two pairs of collinearity genes (<em>UGT362C6</em>/<em>UGT386J4</em> and <em>UGT386C2</em>/<em>UGT386G5</em>) that expanded through segmental duplication within the <em>UGT</em> gene family of <em>N. lugens</em>. Combining the transcriptome and real-time quantitative PCR data showed that gut, antennae, integument, and ovaries were the tissues enriched with <em>NlUGT</em> gene expression. Six <em>NlUGTs</em> were present mainly in the gut, suggesting their putative roles in detoxification. This research provides valuable information on the molecular and genetic basis of <em>NlUGTs</em>, establishing a solid foundation for subsequent functional investigations of <em>UGT</em>s in planthopper, as well as paving the way for identifying potential targets to manage <em>N. lugens</em> effectively.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101403"},"PeriodicalIF":2.2,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142928690","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 : 2024-12-30DOI: 10.1016/j.cbd.2024.101409
Wei-Yi Lee , Chen-Hsun Liu , Bo-Hua Yu , Yung-Kuo Lee , Chiu-Hui Kuo , Cheng- Yi Huang , Chang Yu-Teng , Zi-Yan Xu , Kuohsun Chiu
This study investigated the mechanisms by which high salinity conditions stimulate adult Artemia females to produce diapaused cysts. We used a 1H NMR-based metabolomic approach to elucidate the metabolic regulation between ovoviviparity and oviparity in Artemia exposed to different salinities. At a salinity of 80 ppt, 100 % of females produced diapaused cysts, compared to 20 % at 50 ppt. Metabolic profiling revealed significant alterations in a range of metabolites, including 5,6-dihydrouracil, betaine, and malate, in females undergoing oviparity at 80 ppt compared to ovoviviparity at 30 ppt. Multivariate statistical analyses indicated clear separation between the two reproductive strategies. The up-regulated metabolites in oviparity were involved in significant metabolic pathways, such as β-alanine metabolism and the citrate cycle, highlighting substantial metabolic differences between the two reproductive strategies. These identified metabolic pathways might play crucial roles in the maternal response to high salinity, facilitating embryo protection and enhancing the survival and reproductive success of brine shrimp. These findings provide a basis for further research into the molecular mechanisms underlying Artemia adaptation to high salinity environments.
{"title":"1H NMR-based metabolomic analysis of hypersalinity-induced oviparity in brine shrimp","authors":"Wei-Yi Lee , Chen-Hsun Liu , Bo-Hua Yu , Yung-Kuo Lee , Chiu-Hui Kuo , Cheng- Yi Huang , Chang Yu-Teng , Zi-Yan Xu , Kuohsun Chiu","doi":"10.1016/j.cbd.2024.101409","DOIUrl":"10.1016/j.cbd.2024.101409","url":null,"abstract":"<div><div>This study investigated the mechanisms by which high salinity conditions stimulate adult <em>Artemia</em> females to produce diapaused cysts. We used a <sup>1</sup>H NMR-based metabolomic approach to elucidate the metabolic regulation between ovoviviparity and oviparity in <em>Artemia</em> exposed to different salinities. At a salinity of 80 ppt, 100 % of females produced diapaused cysts, compared to 20 % at 50 ppt. Metabolic profiling revealed significant alterations in a range of metabolites, including 5,6-dihydrouracil, betaine, and malate, in females undergoing oviparity at 80 ppt compared to ovoviviparity at 30 ppt. Multivariate statistical analyses indicated clear separation between the two reproductive strategies. The up-regulated metabolites in oviparity were involved in significant metabolic pathways, such as β-alanine metabolism and the citrate cycle, highlighting substantial metabolic differences between the two reproductive strategies. These identified metabolic pathways might play crucial roles in the maternal response to high salinity, facilitating embryo protection and enhancing the survival and reproductive success of brine shrimp. These findings provide a basis for further research into the molecular mechanisms underlying <em>Artemia</em> adaptation to high salinity environments.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101409"},"PeriodicalIF":2.2,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142934049","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 : 2024-12-28DOI: 10.1016/j.cbd.2024.101402
Mingyi Wang , Hui Ding , Mingjian Liu , Yurui Gao , Lin Li , Chaofan Jin , Zhenmin Bao , Bo Wang , Jingjie Hu
The Sox family genes, as a group of transcription factors, are widely expressed in vertebrates and play a critical role in reproduction and development. The present study reported that 26 sox genes were identified from the genome and transcriptome of P. leopardus. The phylogenetic tree construction, chromosome localization, and gene structure analysis were executed to verify the evolutionary relationships, gene duplication, and deletion variations of P. leopardus sox genes in evolution. The sequence alignment revealed the HMG-box domain was highly conserved throughout the Sox gene family. The expression profile showed expression levels of sox genes showed tissue specificity. The dimorphic expression pattern of most sox genes in intersex and adult gonads was also observed, suggesting an important role of sox genes for sex differentiation in P. leopardus. Notably, sox32 was specifically highly expressed in gonadal tissues and might play a novel role within the gonads. The fluorescent in situ hybridization (FISH) showed sox32 mRNA was detected in germ stem cells and oocytes of different stages, and lowly expressed in sertoli cells. In testis, sox32 was not detected in male germ cells. Our results provided new insights into the sox32 that might be involved in gonadal development and differentiation in P. leopardus. To sum up, this study comprehensively analyzed the Sox gene family of P. leopardus and provided new insights into the function of sox genes, which could potentially revolutionize our understanding of the mechanisms of sex determination, sex differentiation, and reproductive development in fish.
{"title":"Genome wide analysis of the sox32 gene in germline maintenance and differentiation in leopard coral grouper (Plectropomus leopardus)","authors":"Mingyi Wang , Hui Ding , Mingjian Liu , Yurui Gao , Lin Li , Chaofan Jin , Zhenmin Bao , Bo Wang , Jingjie Hu","doi":"10.1016/j.cbd.2024.101402","DOIUrl":"10.1016/j.cbd.2024.101402","url":null,"abstract":"<div><div>The Sox family genes, as a group of transcription factors, are widely expressed in vertebrates and play a critical role in reproduction and development. The present study reported that 26 <em>sox</em> genes were identified from the genome and transcriptome of <em>P. leopardus.</em> The phylogenetic tree construction, chromosome localization, and gene structure analysis were executed to verify the evolutionary relationships, gene duplication, and deletion variations of <em>P. leopardus sox</em> genes in evolution. The sequence alignment revealed the HMG-box domain was highly conserved throughout the Sox gene family. The expression profile showed expression levels of <em>sox</em> genes showed tissue specificity. The dimorphic expression pattern of most <em>sox</em> genes in intersex and adult gonads was also observed, suggesting an important role of <em>sox</em> genes for sex differentiation in <em>P. leopardus</em>. Notably, <em>sox32</em> was specifically highly expressed in gonadal tissues and might play a novel role within the gonads. The fluorescent in situ hybridization (FISH) showed <em>sox32</em> mRNA was detected in germ stem cells and oocytes of different stages, and lowly expressed in sertoli cells. In testis, <em>sox32</em> was not detected in male germ cells. Our results provided new insights into the <em>sox32</em> that might be involved in gonadal development and differentiation in <em>P. leopardus</em>. To sum up, this study comprehensively analyzed the Sox gene family of <em>P. leopardus</em> and provided new insights into the function of <em>sox</em> genes, which could potentially revolutionize our understanding of the mechanisms of sex determination, sex differentiation, and reproductive development in fish.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101402"},"PeriodicalIF":2.2,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916272","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 : 2024-12-23DOI: 10.1016/j.cbd.2024.101405
You Wu , Yiyun Du , Yanbin Zhang , Maolin Ye, Deshou Wang, Linyan Zhou
Myostatin (Mstn) negatively regulates muscle growth and Mstn deficiency induced “double-skeletal muscle” development in vertebrates, including tilapias. In this study, we performed a transcriptomic analysis of skeletal muscle from both wild-type and mstnb−/− males to investigate the molecular mechanisms underlying skeletal muscle hypertrophy in mstnb−/− mutants. We identified 4697 differentially expressed genes (DEGs), 113 differentially expressed long non-coding RNAs (DE lncRNAs), 211 differentially expressed circular RNAs (DE circRNAs), and 98 differentially expressed microRNAs (DE miRNAs). The DEGs were significantly enriched in proteasome and ubiquitin-mediated proteolysis pathways. Cis- and trans-targeting genes of DE lncRNAs were also notably enriched in the above two pathways. The putative host genes of DE circRNAs linked to myofibrils, contractile fibers, and so on. Additionally, DE miRNAs were associated with ubiquitin-mediated proteolysis and key signaling pathways, including AMPK, FoxO, and mTOR. Furthermore, the core competing endogenous RNA (ceRNA) network was constructed comprising 31 DEGs, 37 DE miRNAs, 14 DE circRNAs, and 45 DE lncRNAs. The key roles of ubiquitin-proteasome system were highlighted in the ceRNA network. Taken together, this study provides a novel perspective on muscle mass increase in Mstn mutants through the repression of protein degradation and facilitates our understanding of the molecular mechanisms of skeletal muscle hypertrophy in fish.
{"title":"Transcriptome-derived evidence reveals the regulatory network in the skeletal muscle of the fast-growth mstnb−/− male tilapia","authors":"You Wu , Yiyun Du , Yanbin Zhang , Maolin Ye, Deshou Wang, Linyan Zhou","doi":"10.1016/j.cbd.2024.101405","DOIUrl":"10.1016/j.cbd.2024.101405","url":null,"abstract":"<div><div>Myostatin (Mstn) negatively regulates muscle growth and Mstn deficiency induced “double-skeletal muscle” development in vertebrates, including tilapias. In this study, we performed a transcriptomic analysis of skeletal muscle from both wild-type and <em>mstnb</em><sup>−/−</sup> males to investigate the molecular mechanisms underlying skeletal muscle hypertrophy in <em>mstnb</em><sup>−/−</sup> mutants. We identified 4697 differentially expressed genes (DEGs), 113 differentially expressed long non-coding RNAs (DE lncRNAs), 211 differentially expressed circular RNAs (DE circRNAs), and 98 differentially expressed microRNAs (DE miRNAs). The DEGs were significantly enriched in proteasome and ubiquitin-mediated proteolysis pathways. Cis- and trans-targeting genes of DE lncRNAs were also notably enriched in the above two pathways. The putative host genes of DE circRNAs linked to myofibrils, contractile fibers, and so on. Additionally, DE miRNAs were associated with ubiquitin-mediated proteolysis and key signaling pathways, including AMPK, FoxO, and mTOR. Furthermore, the core competing endogenous RNA (ceRNA) network was constructed comprising 31 DEGs, 37 DE miRNAs, 14 DE circRNAs, and 45 DE lncRNAs. The key roles of ubiquitin-proteasome system were highlighted in the ceRNA network. Taken together, this study provides a novel perspective on muscle mass increase in Mstn mutants through the repression of protein degradation and facilitates our understanding of the molecular mechanisms of skeletal muscle hypertrophy in fish.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101405"},"PeriodicalIF":2.2,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142901225","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 : 2024-12-23DOI: 10.1016/j.cbd.2024.101410
Fangcheng Li , Xiangbing Cheng , Xumeng He, Gilbert Kumilamba, Jiayi Liao, Jiangwei Cao, Qigen Liu, Jiamin Sun
As a core element of the Globally Important Agricultural Heritage System (GIAHS), the Qingtian paddy field carp (Cyprinus carpio, PF-carp) has been domesticated for over 1200 years in paddy field environments. This species has successfully adapted to shallow-water conditions in paddy fields. To reveal the adaptation mechanism, we conducted transcriptome sequencing on the hepatopancreas of PF-carp under two temperature conditions (28 °C and 38 °C) and concurrently analysed RNA-seq data from hypoxic conditions in the same tissue. By analysing high-temperature transcriptome data, 3154 differentially expressed genes (DEGs) were identified. KEGG analysis indicated that DEGs involved various pathways, including protein processing in endoplasmic reticulum, circadian rhythm, and HIF-1 signaling pathway. Notably, protein processing in endoplasmic reticulum was significantly enriched with key genes such as HSP70, HSP90, HSP40, CNX, CRT, and Bip. Through concurrent analysis of RNA-seq data from hypoxic conditions, we found that PF-carp regulate their metabolism through multiple pathways and produce almost opposite metabolic regulation to adapt to high temperature and hypoxic environments. The opposite activation state observed in the HIF-1 signaling pathway is particularly intriguing. In conclusion, PF-carp appear to rely on protein processing in endoplasmic reticulum to maintain cell homeostasis at high temperatures. The HIF-1 signaling pathway may emerged as a key player in adapting PF-carps to paddy fields. This study provides valuable insights into the adaptive mechanisms of domesticated fish in paddy fields.
作为全球重要农业文化遗产系统（GIAHS）的核心组成部分，青田水田鲤鱼（Cyprinus carpio, f -carp）已经在水田环境中驯化了1200多年。这个物种已经成功地适应了水田的浅水环境。为了揭示这种适应机制，我们在两种温度条件下（28°C和38°C）对PF-carp的肝胰脏进行了转录组测序，同时分析了同一组织在缺氧条件下的RNA-seq数据。通过高温转录组数据分析，鉴定出3154个差异表达基因（DEGs）。KEGG分析表明，deg涉及多种途径，包括内质网蛋白加工、昼夜节律和HIF-1信号通路。值得注意的是，在内质网的蛋白质加工中，HSP70、HSP90、HSP40、CNX、CRT和Bip等关键基因显著富集。通过对缺氧条件下RNA-seq数据的同步分析，我们发现PF-carp通过多种途径调节其代谢，并产生几乎相反的代谢调节以适应高温和缺氧环境。在HIF-1信号通路中观察到的相反的激活状态特别有趣。综上所述，sf -鲤鱼似乎依赖于内质网的蛋白质加工来维持高温下的细胞稳态。HIF-1信号通路可能在pf -鲤适应水田的过程中发挥了关键作用。本研究对水田驯化鱼类的适应机制提供了有价值的见解。
{"title":"Molecular responses of paddy field carp (Cyprinus carpio) in the agricultural heritage to major environmental factors in paddy fields","authors":"Fangcheng Li , Xiangbing Cheng , Xumeng He, Gilbert Kumilamba, Jiayi Liao, Jiangwei Cao, Qigen Liu, Jiamin Sun","doi":"10.1016/j.cbd.2024.101410","DOIUrl":"10.1016/j.cbd.2024.101410","url":null,"abstract":"<div><div>As a core element of the Globally Important Agricultural Heritage System (GIAHS), the Qingtian paddy field carp (<em>Cyprinus carpio</em>, PF-carp) has been domesticated for over 1200 years in paddy field environments. This species has successfully adapted to shallow-water conditions in paddy fields. To reveal the adaptation mechanism, we conducted transcriptome sequencing on the hepatopancreas of PF-carp under two temperature conditions (28 °C and 38 °C) and concurrently analysed RNA-seq data from hypoxic conditions in the same tissue. By analysing high-temperature transcriptome data, 3154 differentially expressed genes (DEGs) were identified. KEGG analysis indicated that DEGs involved various pathways, including protein processing in endoplasmic reticulum, circadian rhythm, and HIF-1 signaling pathway. Notably, protein processing in endoplasmic reticulum was significantly enriched with key genes such as HSP70, HSP90, HSP40, CNX, CRT, and Bip. Through concurrent analysis of RNA-seq data from hypoxic conditions, we found that PF-carp regulate their metabolism through multiple pathways and produce almost opposite metabolic regulation to adapt to high temperature and hypoxic environments. The opposite activation state observed in the HIF-1 signaling pathway is particularly intriguing. In conclusion, PF-carp appear to rely on protein processing in endoplasmic reticulum to maintain cell homeostasis at high temperatures. The HIF-1 signaling pathway may emerged as a key player in adapting PF-carps to paddy fields. This study provides valuable insights into the adaptive mechanisms of domesticated fish in paddy fields.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101410"},"PeriodicalIF":2.2,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142903670","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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