Bivalve mollusks represent a taxonomically and economically significant clade within Mollusca.However,the regulatory mechanisms governing their embryonic development remain poorly characterized.The dwarf surf clam(Mul...Bivalve mollusks represent a taxonomically and economically significant clade within Mollusca.However,the regulatory mechanisms governing their embryonic development remain poorly characterized.The dwarf surf clam(Mulinia lateralis),characterized by a short generation time and high fecundity,has recently gained recognition as an ideal model system for bivalve embryological research.This study explored the epigenetic mechanisms driving embryogenesis in M.lateralis,with a particular focus on the maternal-to-zygotic transition(MZT),by integrating chromatin-state profiling and transcriptomic analysis.For the first time in this species,CUT&Tag was employed to generate high-resolution landscapes of histone modifications H3K4me1,H3K4me3,H3K27me3,and H3K27ac across key developmental stages.The resulting data revealed extensive reprogramming of histone marks,indicating dynamic shifts in chromatin architecture during early embryonic development.Integration with transcriptomic data identified the timing of MZT in M.lateralis between the morula and gastrula stages and highlighted a suite of candidate genes essential for embryogenesis.These findings provide mechanistic insight into chromatin-mediated control of bivalve embryogenesis and establish M.lateralis as a robust platform for epigenomic research in marine invertebrates,with implications for functional gene studies and aquaculture advancement.展开更多
A better understanding of genetic bases of growth regulation is essential for bivalve breeding,which is helpful to improve the yield of the commercially important bivalves.While previous studies have identified some c...A better understanding of genetic bases of growth regulation is essential for bivalve breeding,which is helpful to improve the yield of the commercially important bivalves.While previous studies have identified some candidate genes accounting for variation in growth-related traits through genotype-phenotype association analyses,seldom of them have verified the functions of these putative,growth-related genes beyond the genomic level due to the difficulty of culturing commercial bivalves under laboratory conditions.Fortunately,dwarf surf clam Mulinia lateralis can serve as a model organism for studying marine bivalves given its short generation time,the feasibility of being grown under experimental conditions and the availability of genetic and biological information.Using dwarf surf clam as a model bivalve,we characterize E2F3,a gene that has been found to account for variation in growth in scallops by a previous genome-wide association study,and verify its function in growth regulation through RNA interference(RNAi)experiments.For the first time,E2F3 in dwarf surf clam,which is termed as MulE2F3,is characterized.The results reveal that dwarf surf clams with MulE2F3 knocked down exhibit a reduction in both shell size and soft-tissue weight,indicating the functions of MulE2F3 in positively regulating bivalve growth.More importantly,we demonstrate how dwarf surf clam can be used as a model organism to investigate gene functions in commercial bivalves,shedding light on genetic causes for variation in growth to enhance the efficiency of bivalve farming.展开更多
Bivalve aquaculture plays a crucial role in the aquaculture industry due to the economic value of many bivalve species.Understanding the underlying genetic basis of bivalve growth regulation is essential for enhancing...Bivalve aquaculture plays a crucial role in the aquaculture industry due to the economic value of many bivalve species.Understanding the underlying genetic basis of bivalve growth regulation is essential for enhancing germplasm innovation and ensuring sustainable development of the industry.Though numerous candidate genes have been identified,their functional validation remains challenging.Fortunately,the dwarf surf clam(Mulinia lateralis)serves as a promising model organism for investigating genetic mechanisms underlying growth regulation in bivalves.The GWAS study in the Yesso scallop(Patinopecten yessoensis)has pinpointed the E2F3 gene as a key regulator of growth-related traits.However,the specific role of E2F3 in bivalve growth remains unclear.This study aimed to further confirm the regulatory function of the E2F3 gene in the dwarf surf clam through RNA interference experiments.Our results revealed several genes are associated with individual growth and development,including CTS7,HSP70B2,and PGLYRP3,as well as genes involved in lipid metabolism such as FABP2 and FASN.Functional enrichment analysis indicated that E2F3 primarily modulates critical processes like amino acid and lipid metabolism.These findings suggest that E2F3 likely regulates growth in the dwarf surf clam by influencing amino acid and lipid metabolism.Overall,this study advances our understanding on the function of E2F3 gene in growth regulation in bivalves,providing valuable insights for future research in this field.展开更多
The shell,a type of biological exoskeleton,is a critical feature of bivalves,serving key functions including protection,locomotion,and structural support.Although bivalve shell morphology exhibits rich and complex var...The shell,a type of biological exoskeleton,is a critical feature of bivalves,serving key functions including protection,locomotion,and structural support.Although bivalve shell morphology exhibits rich and complex variability,research on the genetic basis of this diversity remains limited.The dwarf surf clam,Mulinia lateralis,with its rapid growth and short generation interval,serves as an ideal model organism for bivalves,displaying notable shell morphology diversity.In this study,we performed high-throughput sequencing on 180 individuals,obtaining 32,318 SNPs to investigate the genetic basis of shell morphology variation in M.lateralis.The heritability of shell morphological traits was high,with values ranging from 0.439 to 0.814.Through genome-wide association study(GWAS),we identified 20 single nucleotide polymorphisms(SNPs)associated with shell morphology traits and screened 16 candidate genes,such as Lox4,AJM1-like,and Luc7l.These genes are implicated in the determination of an anteroposterior(A-P)body plan and the regulation of cytoskeletal structure and growth.Of particular interest is Lox4,which is prominently expressed during the trochophore stage and in the adult mantle tissue,playing a crucial role in shell formation in bivalves.Sanger sequencing confirmed that the SNP Chr15-22361661 located in the Lox4 gene exhibited significant dimorphism in the validation population.Individuals with the AA-genotype exhibited a diminished short-long beak length ratio(SLBR)trait alongside an upregulation of Lox4 expression(p<0.05).RNA interference(RNAi)experiments further revealed that the inhibition of Lox4 expression altered shell morphology,leading to an increase in SLBR(p<0.05).Additionally,the inhibition of Lox4 expression resulted in a downregulation of Lox2 expression,whereas the suppression of Lox2 did not affect the expression of Lox4.These results suggest the presence of a unidirectional regulatory cascade wherein Lox4 modulates Lox2 to influence shell morphology.These findings reveal genetic variations associated with shell morphology in M.lateralis and highlight the potential regulatory roles of Lox4 and homeobox clusters on bivalve shell morphology,which enhance our understanding of the genetic basis of shell morphological diversity in bivalves and provide novel insights into how they adapt to diverse lifestyles.展开更多
基金supported by the National Natural Science Foundation of China(32200667)Shandong Provincial Special Funds for Taishan Scholars(tsqn202306104)+1 种基金Hainan Province“South China Sea New Star”Science and Technology Innovation Talent Platform Project(NHXXRCXM202365)Hainan Provincial Joint Project of Sanya Yazhou Bay Science and Technology City Grant(2021JJLH0090)。
文摘Bivalve mollusks represent a taxonomically and economically significant clade within Mollusca.However,the regulatory mechanisms governing their embryonic development remain poorly characterized.The dwarf surf clam(Mulinia lateralis),characterized by a short generation time and high fecundity,has recently gained recognition as an ideal model system for bivalve embryological research.This study explored the epigenetic mechanisms driving embryogenesis in M.lateralis,with a particular focus on the maternal-to-zygotic transition(MZT),by integrating chromatin-state profiling and transcriptomic analysis.For the first time in this species,CUT&Tag was employed to generate high-resolution landscapes of histone modifications H3K4me1,H3K4me3,H3K27me3,and H3K27ac across key developmental stages.The resulting data revealed extensive reprogramming of histone marks,indicating dynamic shifts in chromatin architecture during early embryonic development.Integration with transcriptomic data identified the timing of MZT in M.lateralis between the morula and gastrula stages and highlighted a suite of candidate genes essential for embryogenesis.These findings provide mechanistic insight into chromatin-mediated control of bivalve embryogenesis and establish M.lateralis as a robust platform for epigenomic research in marine invertebrates,with implications for functional gene studies and aquaculture advancement.
基金supported by the National Natural Science Foundation of China(No.U2106231)the National Key R&D Program of China(No.2022YFD2400303)the Key R&D Project of Shandong Province(No.2022 TZXD003).
文摘A better understanding of genetic bases of growth regulation is essential for bivalve breeding,which is helpful to improve the yield of the commercially important bivalves.While previous studies have identified some candidate genes accounting for variation in growth-related traits through genotype-phenotype association analyses,seldom of them have verified the functions of these putative,growth-related genes beyond the genomic level due to the difficulty of culturing commercial bivalves under laboratory conditions.Fortunately,dwarf surf clam Mulinia lateralis can serve as a model organism for studying marine bivalves given its short generation time,the feasibility of being grown under experimental conditions and the availability of genetic and biological information.Using dwarf surf clam as a model bivalve,we characterize E2F3,a gene that has been found to account for variation in growth in scallops by a previous genome-wide association study,and verify its function in growth regulation through RNA interference(RNAi)experiments.For the first time,E2F3 in dwarf surf clam,which is termed as MulE2F3,is characterized.The results reveal that dwarf surf clams with MulE2F3 knocked down exhibit a reduction in both shell size and soft-tissue weight,indicating the functions of MulE2F3 in positively regulating bivalve growth.More importantly,we demonstrate how dwarf surf clam can be used as a model organism to investigate gene functions in commercial bivalves,shedding light on genetic causes for variation in growth to enhance the efficiency of bivalve farming.
基金funded by the National Natural Science Foundation of China (No. U2106231)the Key Research and Development Project of Shandong Province (No. 2021 ZLGX03)the National Key Research and Development Program of China (No. 2022YFD2400303)
文摘Bivalve aquaculture plays a crucial role in the aquaculture industry due to the economic value of many bivalve species.Understanding the underlying genetic basis of bivalve growth regulation is essential for enhancing germplasm innovation and ensuring sustainable development of the industry.Though numerous candidate genes have been identified,their functional validation remains challenging.Fortunately,the dwarf surf clam(Mulinia lateralis)serves as a promising model organism for investigating genetic mechanisms underlying growth regulation in bivalves.The GWAS study in the Yesso scallop(Patinopecten yessoensis)has pinpointed the E2F3 gene as a key regulator of growth-related traits.However,the specific role of E2F3 in bivalve growth remains unclear.This study aimed to further confirm the regulatory function of the E2F3 gene in the dwarf surf clam through RNA interference experiments.Our results revealed several genes are associated with individual growth and development,including CTS7,HSP70B2,and PGLYRP3,as well as genes involved in lipid metabolism such as FABP2 and FASN.Functional enrichment analysis indicated that E2F3 primarily modulates critical processes like amino acid and lipid metabolism.These findings suggest that E2F3 likely regulates growth in the dwarf surf clam by influencing amino acid and lipid metabolism.Overall,this study advances our understanding on the function of E2F3 gene in growth regulation in bivalves,providing valuable insights for future research in this field.
基金supported by the grants of the National Natural Science Foundation of China(32202898 and 32473135)Key R&D Project of Shandong Province(2021ZLGX03)the Earmarked Fund for Modern Agro-industry Technology Research System(CARS-49).
文摘The shell,a type of biological exoskeleton,is a critical feature of bivalves,serving key functions including protection,locomotion,and structural support.Although bivalve shell morphology exhibits rich and complex variability,research on the genetic basis of this diversity remains limited.The dwarf surf clam,Mulinia lateralis,with its rapid growth and short generation interval,serves as an ideal model organism for bivalves,displaying notable shell morphology diversity.In this study,we performed high-throughput sequencing on 180 individuals,obtaining 32,318 SNPs to investigate the genetic basis of shell morphology variation in M.lateralis.The heritability of shell morphological traits was high,with values ranging from 0.439 to 0.814.Through genome-wide association study(GWAS),we identified 20 single nucleotide polymorphisms(SNPs)associated with shell morphology traits and screened 16 candidate genes,such as Lox4,AJM1-like,and Luc7l.These genes are implicated in the determination of an anteroposterior(A-P)body plan and the regulation of cytoskeletal structure and growth.Of particular interest is Lox4,which is prominently expressed during the trochophore stage and in the adult mantle tissue,playing a crucial role in shell formation in bivalves.Sanger sequencing confirmed that the SNP Chr15-22361661 located in the Lox4 gene exhibited significant dimorphism in the validation population.Individuals with the AA-genotype exhibited a diminished short-long beak length ratio(SLBR)trait alongside an upregulation of Lox4 expression(p<0.05).RNA interference(RNAi)experiments further revealed that the inhibition of Lox4 expression altered shell morphology,leading to an increase in SLBR(p<0.05).Additionally,the inhibition of Lox4 expression resulted in a downregulation of Lox2 expression,whereas the suppression of Lox2 did not affect the expression of Lox4.These results suggest the presence of a unidirectional regulatory cascade wherein Lox4 modulates Lox2 to influence shell morphology.These findings reveal genetic variations associated with shell morphology in M.lateralis and highlight the potential regulatory roles of Lox4 and homeobox clusters on bivalve shell morphology,which enhance our understanding of the genetic basis of shell morphological diversity in bivalves and provide novel insights into how they adapt to diverse lifestyles.
