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
In the present study,we successfully assembled a high-quality genome of Planiliza haematocheila(redlip mullet)based on Oxford Nanopore long read,single-tube long fragment read(stLFR),and Hi-C chromatin interaction seq...In the present study,we successfully assembled a high-quality genome of Planiliza haematocheila(redlip mullet)based on Oxford Nanopore long read,single-tube long fragment read(stLFR),and Hi-C chromatin interaction sequencing.The size of the P.haematocheila genome was 652.91 Mb.More than 93.8%of BUSCO genes were detected,and the N50 lengths of contigs and scaffolds reached 7.21 Mb and 28.01 Mb,respectively,thus demonstrating outstanding genome completeness and sequence continuity.A total of 21045 protein-coding genes were predicted in the assembled genome,and 99.77%of those genes were functionally annotated.Comparative genomic and phylogenetic analyses revealed the adaptability of P.haematocheila to complex living environments at the genomic level,highlighting its broad adaptability and resistance to multiple stresses as an important economic fish.The high-quality reference chromosome-level genome of P.haematocheila provides a powerful genomic resource for further systematic study of Mugilidae.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This study was supported by the Special Funding for Modern Agricultural Industrial Technology System(CARS-47-Z01)。
文摘In the present study,we successfully assembled a high-quality genome of Planiliza haematocheila(redlip mullet)based on Oxford Nanopore long read,single-tube long fragment read(stLFR),and Hi-C chromatin interaction sequencing.The size of the P.haematocheila genome was 652.91 Mb.More than 93.8%of BUSCO genes were detected,and the N50 lengths of contigs and scaffolds reached 7.21 Mb and 28.01 Mb,respectively,thus demonstrating outstanding genome completeness and sequence continuity.A total of 21045 protein-coding genes were predicted in the assembled genome,and 99.77%of those genes were functionally annotated.Comparative genomic and phylogenetic analyses revealed the adaptability of P.haematocheila to complex living environments at the genomic level,highlighting its broad adaptability and resistance to multiple stresses as an important economic fish.The high-quality reference chromosome-level genome of P.haematocheila provides a powerful genomic resource for further systematic study of Mugilidae.