Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters.The Jinjiang oyster(Crassostrea ariakensis)is an economic...Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters.The Jinjiang oyster(Crassostrea ariakensis)is an economically and ecologically important species in China.In the present study,RNA sequencing(RNA-seq)and assay for transposase-accessible chromatin using sequencing(ATAC-seq)were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents.Analysis identified 9483 differentially expressed genes(DEGs)and 7215 genes with significantly differential chromatin accessibility(DCAGs)were obtained,with an overlap of 2600 genes between them.Notably,a significant proportion of these genes were enriched in pathways related to glycogen metabolism,including“Glycogen metabolic process”and“Starch and sucrose metabolism”.In addition,genome-wide association study(GWAS)identified 526 single nucleotide polymorphism(SNP)loci associated with glycogen content.These loci corresponded to 241 genes,63 of which were categorized as both DEGs and DCAGs.This study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in C.ariakensis.展开更多
Quantitative real-time PCR(qRT-PCR)has been widely used for gene expression analysis,and selection of reference genes is a key point to obtain accurate results.To find out optimal reference genes for qRT-PCR in Manila...Quantitative real-time PCR(qRT-PCR)has been widely used for gene expression analysis,and selection of reference genes is a key point to obtain accurate results.To find out optimal reference genes for qRT-PCR in Manila clam Ruditapes philippinarum in response to hypoxia,different tissues were used and compared to evaluate the stability of candidate reference genes under low oxygen stress(DO 0.5mgL^(−1) and DO 2.0mgL^(−1))and normal condition(DO 7.5mgL^(−1)).Seven candidate reference genes were selected to evaluate the stability of their expression levels.The reference genes were evaluated by Delta Ct,BestKeeper,NormFinder and geNorm,and then screened by RefFinder calculation.Under hypoxic stress of 0.5mgL^(−1),the most suitable reference gene for gill and hepatopancreas was RPL31,and the optimal reference genes for axe foot and adductor muscle were TUB and HIS,respectively.For hypoxic stress of 2.0mgL^(−1),the most stable reference gene for gill and hepatopancreas was RPL31,and the optimal reference genes for axe foot and adductor muscle were RPS23 and EF1A,respectively.At the normal condition,HIS and EF1A were identified as the optimal internal reference genes in gill and hepatopancreas respectively,and GFRP2 was the best internal reference gene for axe foot and adductor muscle.The present findings will provide important basis for the selection of reference genes for qRT-PCR analysis of gene expression level in bivalves under hypoxic stress,which might be helpful for the analysis of other molluscs too.展开更多
Brine shrimp(Artemia)has existed on Earth for 400 million years and has major ecological importance in hypersaline ecosystems.As a crucial live food in aquaculture,brine shrimp cysts have become one of the most import...Brine shrimp(Artemia)has existed on Earth for 400 million years and has major ecological importance in hypersaline ecosystems.As a crucial live food in aquaculture,brine shrimp cysts have become one of the most important aquatic products traded worldwide.However,our understanding of the biodiversity,prevalence and global connectedness of viruses in brine shrimp is still very limited.A total of 143 batches of brine shrimp(belonging to seven species)cysts were collected from six continents including 21 countries and more than 100 geographic locations worldwide during 1977–2019.In total,55 novel RNA viruses were identified,which could be assigned to 18 different viral families and related clades.Eleven viruses were dsRNA viruses,16 were+ssRNA viruses,and 28 were−ssRNA viruses.Phylogenetic analyses of the RNA-directed RNA polymerase(RdRp)showed that brine shrimp viruses were often grouped with viruses isolated from other invertebrates and fungi.Remarkably,most brine shrimp viruses were related to those from different hosts that might feed on brine shrimp or share the same ecological niche.A notable case was the novel brine shrimp noda-like virus 3,which shared 79.25%(RdRp)and 63.88%(capsid proteins)amino acid identity with covert mortality nodavirus(CMNV)that may cause losses in aquaculture.In addition,both virome composition and phylogenetic analyses revealed global connectedness in certain brine shrimp viruses,particularly among Asia and Northern America.This highlights the incredible species diversity of viruses in these ancient species and provides essential data for the prevalence of RNA viruses in the global aquaculture industry.More broadly,these findings provide novel insights into the previously unrecognized RNA virosphere in hypersaline ecosystems worldwide and demonstrate that human activity might have driven the global connectedness of brine shrimp viruses.展开更多
Psychrophilic microalgae successfully survive in the extreme and highly variable polar ecosystems,which represent the energy base of most food webs and play a fundamental role in nutrient cycling.The success of microa...Psychrophilic microalgae successfully survive in the extreme and highly variable polar ecosystems,which represent the energy base of most food webs and play a fundamental role in nutrient cycling.The success of microalgae is rooted in their adaptive evolution.Revealing how they have evolved to thrive in extreme polar environments will help us better understand the origin of life in polar ecosystems.We isolated a psychrophilic unicellular green alga,Microglena sp.YARC,from Antarctic sea ice which has a huge genome.Therefore,we predicted that gene replication may play an important role in its polar adaptive evolution.We found that its protein-coding gene number significantly increased and the duplication time was dated between 37 and 48 million years ago,which is consistent with the formation of the circumpolar Southern Ocean.Most duplicated paralogous genes were enriched in pathways related to photosynthesis,DNA repair,and fatty acid metabolism.Moreover,there were a total of 657 Microglena-specific families,including collagen-like proteins.The divergence in the expression patterns of the duplicated and species-specific genes reflects sub-and neo-functionalization during stress acclimation.Overall,key findings from this study provide new information on how gene duplication and their functional novelty contributed to polar algae adaptation to the highly variable polar environmental conditions.展开更多
Aquaculture represents the fastest-growing global food production sector,as it has become an essential component of the global food supply.China has the world's largest aquaculture industry in terms of production ...Aquaculture represents the fastest-growing global food production sector,as it has become an essential component of the global food supply.China has the world's largest aquaculture industry in terms of production volume.However,the sustainable development of fish culture is hindered by several concerns,including germplasm degradation and disease outbreaks.The practice of genomic breeding,which relies heavily on genome information and genotypephenotype relationships,has significant potential for increasing the efficiency of aquaculture production.In 2014,the completion of the genome sequencing and annotation of the Chinese tongue sole signified the beginning of the fish genomics era in China.Since then,domestic researchers have made dramatic progress in functional genomic studies.To date,the genomes of more than 60 species of fish in China have been assembled and annotated.Based on these reference genomes,evolutionary,comparative,and functional genomic studies have revolutionized our understanding of a wide range of biologically and economically important traits of fishes,including growth and development,sex determination,disease resistance,metamorphosis,and pigmentation.Furthermore,genomic tools and breeding techniques such as SNP arrays,genomic selection,and genome editing have greatly accelerated genetic improvement through the incorporation of functional genomic information into breeding activities.This review aims to summarize the current status,advances,and perspectives of the genome resources,genomic study of important traits,and genomic breeding techniques of fish in China.The review will provide aquaculture researchers,fish breeders,and farmers with updated information concerning fish genomic research and breeding technology.The summary will help to promote the genetic improvement of production traits and thus will support the sustainable development of fish aquaculture.展开更多
基金supported by the National Key R&D Program of China(2022YFD2400105,2018YFD0900104)Central Publicinterest Scientific Institution Basal Research Fund,CAFS(2021XT0102,2023TD30)+2 种基金Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao)(2021QNLM050103)Key Research and Development Project of Shandong Province(2021LZGC028)National Marine Genetic Resource Center。
文摘Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters.The Jinjiang oyster(Crassostrea ariakensis)is an economically and ecologically important species in China.In the present study,RNA sequencing(RNA-seq)and assay for transposase-accessible chromatin using sequencing(ATAC-seq)were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents.Analysis identified 9483 differentially expressed genes(DEGs)and 7215 genes with significantly differential chromatin accessibility(DCAGs)were obtained,with an overlap of 2600 genes between them.Notably,a significant proportion of these genes were enriched in pathways related to glycogen metabolism,including“Glycogen metabolic process”and“Starch and sucrose metabolism”.In addition,genome-wide association study(GWAS)identified 526 single nucleotide polymorphism(SNP)loci associated with glycogen content.These loci corresponded to 241 genes,63 of which were categorized as both DEGs and DCAGs.This study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in C.ariakensis.
基金supported by research grants from the Science and Technology Innovation Program of the Laoshan Laboratory(No.LSKJ202203803)the National Natural Science Foundation of China(No.32273107)+2 种基金supported by the Central Public-Interest Scientific Institution Basal Research Fund,Yellow Sea Fisheries Research Institute,CAFS(No.20603022022001)the project of Putian Science and Technology Department(No.2021NJJ002)the Shinan District Science and Technology Plan Project(No.2022-2-026-ZH).
文摘Quantitative real-time PCR(qRT-PCR)has been widely used for gene expression analysis,and selection of reference genes is a key point to obtain accurate results.To find out optimal reference genes for qRT-PCR in Manila clam Ruditapes philippinarum in response to hypoxia,different tissues were used and compared to evaluate the stability of candidate reference genes under low oxygen stress(DO 0.5mgL^(−1) and DO 2.0mgL^(−1))and normal condition(DO 7.5mgL^(−1)).Seven candidate reference genes were selected to evaluate the stability of their expression levels.The reference genes were evaluated by Delta Ct,BestKeeper,NormFinder and geNorm,and then screened by RefFinder calculation.Under hypoxic stress of 0.5mgL^(−1),the most suitable reference gene for gill and hepatopancreas was RPL31,and the optimal reference genes for axe foot and adductor muscle were TUB and HIS,respectively.For hypoxic stress of 2.0mgL^(−1),the most stable reference gene for gill and hepatopancreas was RPL31,and the optimal reference genes for axe foot and adductor muscle were RPS23 and EF1A,respectively.At the normal condition,HIS and EF1A were identified as the optimal internal reference genes in gill and hepatopancreas respectively,and GFRP2 was the best internal reference gene for axe foot and adductor muscle.The present findings will provide important basis for the selection of reference genes for qRT-PCR analysis of gene expression level in bivalves under hypoxic stress,which might be helpful for the analysis of other molluscs too.
基金This work was supported by the National Key Research and Development Program of China(2018YFD0900501)Central Public-interest Scientific Institution Basal Research Fund,YSFRI,CAFS(20603022022005)+6 种基金Shinan District Science and Technology Foundation(Qingdao)(2022-2-027-ZH)Central Public-interest Scientific Institution Basal Research Fund,CAFS(2020TD39)China Agriculture Research System(CARS-48)C.L.was supported by the Youth Innovation Team of Shandong Higher Education Institution(2021KJ064)the National Natural Science Foundation of China(32200004)W.S.was supported by the Academic Promotion Programme of Shandong First Medical University(2019QL006)E.C.H.was funded by a National Medical Health and Research Council(Australia)Investigator Grant(GNT2017197).
文摘Brine shrimp(Artemia)has existed on Earth for 400 million years and has major ecological importance in hypersaline ecosystems.As a crucial live food in aquaculture,brine shrimp cysts have become one of the most important aquatic products traded worldwide.However,our understanding of the biodiversity,prevalence and global connectedness of viruses in brine shrimp is still very limited.A total of 143 batches of brine shrimp(belonging to seven species)cysts were collected from six continents including 21 countries and more than 100 geographic locations worldwide during 1977–2019.In total,55 novel RNA viruses were identified,which could be assigned to 18 different viral families and related clades.Eleven viruses were dsRNA viruses,16 were+ssRNA viruses,and 28 were−ssRNA viruses.Phylogenetic analyses of the RNA-directed RNA polymerase(RdRp)showed that brine shrimp viruses were often grouped with viruses isolated from other invertebrates and fungi.Remarkably,most brine shrimp viruses were related to those from different hosts that might feed on brine shrimp or share the same ecological niche.A notable case was the novel brine shrimp noda-like virus 3,which shared 79.25%(RdRp)and 63.88%(capsid proteins)amino acid identity with covert mortality nodavirus(CMNV)that may cause losses in aquaculture.In addition,both virome composition and phylogenetic analyses revealed global connectedness in certain brine shrimp viruses,particularly among Asia and Northern America.This highlights the incredible species diversity of viruses in these ancient species and provides essential data for the prevalence of RNA viruses in the global aquaculture industry.More broadly,these findings provide novel insights into the previously unrecognized RNA virosphere in hypersaline ecosystems worldwide and demonstrate that human activity might have driven the global connectedness of brine shrimp viruses.
基金supported by the National Key Research and Development Programme of China(2022YFD2400105)Laoshan Laboratory(LSKJ202203801)+4 种基金Natural Science Foundation of Shandong Province(ZR2021MD075,ZR202211110025)National Natural Science Foundation of China(41676145,32000404)Central Public-interest Scientific Institution Basal Research Fund,CAFS(2023TD28,2023TD19)China Agriculture Research System(CARS-50)the Young Taishan Scholars Program,Taishan Scholars Program.
文摘Psychrophilic microalgae successfully survive in the extreme and highly variable polar ecosystems,which represent the energy base of most food webs and play a fundamental role in nutrient cycling.The success of microalgae is rooted in their adaptive evolution.Revealing how they have evolved to thrive in extreme polar environments will help us better understand the origin of life in polar ecosystems.We isolated a psychrophilic unicellular green alga,Microglena sp.YARC,from Antarctic sea ice which has a huge genome.Therefore,we predicted that gene replication may play an important role in its polar adaptive evolution.We found that its protein-coding gene number significantly increased and the duplication time was dated between 37 and 48 million years ago,which is consistent with the formation of the circumpolar Southern Ocean.Most duplicated paralogous genes were enriched in pathways related to photosynthesis,DNA repair,and fatty acid metabolism.Moreover,there were a total of 657 Microglena-specific families,including collagen-like proteins.The divergence in the expression patterns of the duplicated and species-specific genes reflects sub-and neo-functionalization during stress acclimation.Overall,key findings from this study provide new information on how gene duplication and their functional novelty contributed to polar algae adaptation to the highly variable polar environmental conditions.
基金supported by National Natural Science Foundation of China(32230107)Agriculture Biobreeding-Major Project(2023ZD0405502)+3 种基金the Key Research and Development Project of Shandong Province(2023ZLYS02,2022CXPT002,and 2021LZGC028)Central Public-interest Scientific Institution Basal Research Fund,CAFS(2023TD20)Taishan Scholar Project(tsqn202306295)Taishan Scholar Climbing Project。
文摘Aquaculture represents the fastest-growing global food production sector,as it has become an essential component of the global food supply.China has the world's largest aquaculture industry in terms of production volume.However,the sustainable development of fish culture is hindered by several concerns,including germplasm degradation and disease outbreaks.The practice of genomic breeding,which relies heavily on genome information and genotypephenotype relationships,has significant potential for increasing the efficiency of aquaculture production.In 2014,the completion of the genome sequencing and annotation of the Chinese tongue sole signified the beginning of the fish genomics era in China.Since then,domestic researchers have made dramatic progress in functional genomic studies.To date,the genomes of more than 60 species of fish in China have been assembled and annotated.Based on these reference genomes,evolutionary,comparative,and functional genomic studies have revolutionized our understanding of a wide range of biologically and economically important traits of fishes,including growth and development,sex determination,disease resistance,metamorphosis,and pigmentation.Furthermore,genomic tools and breeding techniques such as SNP arrays,genomic selection,and genome editing have greatly accelerated genetic improvement through the incorporation of functional genomic information into breeding activities.This review aims to summarize the current status,advances,and perspectives of the genome resources,genomic study of important traits,and genomic breeding techniques of fish in China.The review will provide aquaculture researchers,fish breeders,and farmers with updated information concerning fish genomic research and breeding technology.The summary will help to promote the genetic improvement of production traits and thus will support the sustainable development of fish aquaculture.