Animal body size variation is of particular interest in evolutionary biology,but the genetic basis remains largely unknown.Previous studies have shown the presence of two parallel evolutionary genetic clusters within ...Animal body size variation is of particular interest in evolutionary biology,but the genetic basis remains largely unknown.Previous studies have shown the presence of two parallel evolutionary genetic clusters within the fish genus Epinephelus with evident divergence in body size,providing an excellent opportunity to investigate the genetic basis of body size variation in vertebrates.Herein,we performed phylotranscriptomic analysis and reconstructed the phylogeny of 13 epinephelids originating from the South China Sea.Two genetic clades with an estimated divergence time of approximately 15.4 million years ago were correlated with large and small body size,respectively.A total of 180 rapidly evolving genes and two positively selected genes were identified between the two groups.Functional enrichment analyses of these candidate genes revealed distinct enrichment categories between the two groups.These pathways and genes may play important roles in body size variation in groupers through complex regulatory networks.Based on our results,we speculate that the ancestors of the two divergent groups of groupers may have adapted to different environments through habitat selection,leading to genetic variations in metabolic patterns,organ development,and lifespan,resulting in body size divergence between the two locally adapted populations.These findings provide important insights into the genetic mechanisms underlying body size variation in groupers and species differentiation.展开更多
[Objectives]This study aimed to investigate the sequence structure and function of Myostatin(MSTN)gene in the hybrid grouper(Epinephelus fuscoguttatus,♀×Epinephelus polyphekadion,♂).[Methods]Genetic DNA samples...[Objectives]This study aimed to investigate the sequence structure and function of Myostatin(MSTN)gene in the hybrid grouper(Epinephelus fuscoguttatus,♀×Epinephelus polyphekadion,♂).[Methods]Genetic DNA samples were extracted from the caudal fins of the hybrid grouper and its parents to amplify their MSTN genes.Then,MSTN gene sequences were analyzed using bioinformatics tools to predict their protein structures and functions.[Results]The hybrid grouper and its parents shared the same MSTN gene structure,consisting of three exons and two introns.Nucleotide sequence of the gene could be translated into 376 amino acids,including an N-terminal signal peptide,a proteolytic processing site(RXXR motif),and nine conserved cysteine residues at C-terminal,which were the typical features of transforming growth factor beta(TGF-β)superfamily proteins.Alignment of protein sequence showed that MSTN was highly conserved between the hybrid grouper and its parents.Especially,exon 3,an important functional domain,exhibited a sequence similarity of 100%among them.In addition,four variable amino acid residues were detected in exon 2 at positions 141,153,185 and 186 in the hybrid grouper,but they did not affect the secondary structure of the protein.[Conclusion]These results will provide molecular information for future investigation on the growth and heterosis of hybrid grouper species,and on the roles of MSTN gene in regulating the growth traits of the hybrid grouper.展开更多
[Objective] The study aimed to evaluate the genetic variability and interspecific relationships among four species of groupers from South China Sea, including E. fario, E. merra, E. malabaricus and E. coioides. [Metho...[Objective] The study aimed to evaluate the genetic variability and interspecific relationships among four species of groupers from South China Sea, including E. fario, E. merra, E. malabaricus and E. coioides. [Method] Twenty one mircosatellite loci of groupers were selected from GenBank and eight high polymorphic loci were used to further genetic analysis. [Result] The mean number of alleles per locus （A）, effective number of alleles （Ne）, mean polymorphism information content （PIC）, observed heterozygosity （Ho） and expected heterozygosity （He） were 4.38±1.60, 3.69±0.86, 0.69±0.08, 0.67±0.08, 0.72±0.06 in E. malabaricus; 3.88±1.13, 3.55±1.04, 0.66±0.10, 0.68±0.21, 0.70±0.08 in E.coioides; 6.00±1.07, 4.68±0.65, 0.78±0.03, 0.73±0.25, 0.79±0.03 in E. fario; 5.50±1.07, 4.58±0.80, 0.76±0.05, 0.75±0.18, 0.78±0.04 in E. merra, respectively. [Conclusion] We compared the values above, the order of the genetic variability among these grouper species was E. fario E. merra E. malabaricus E. coioides. We found that the level of genetic variability of these groupers species was relatively higher than that of other marine fish, so their genetic status was good. In addition, the analyisis of genetic relationship showed that E. malabaricus and E. coioides was the closest and it was the farthest between E. merra and E. coioides.展开更多
Viral nervous necrosis （VNN） causes high mortality in marine fish, especially in the grouper, worldwide and in China. Since there is no effective vaccine or drug to deal with VNN, early detection and prevention is i...Viral nervous necrosis （VNN） causes high mortality in marine fish, especially in the grouper, worldwide and in China. Since there is no effective vaccine or drug to deal with VNN, early detection and prevention is important to block its outbreak. In this study, a reverse transcription-polymerase chain reaction （RT-PCR） was developed for the rapid, convenient, and sensitive detection of the VNN pathogen, nervous necro- sis virus （NNV）, in the grouper. The whole process was completed within 3.5 h from the RNA extraction to PCR product visualization. The detection limit of this method was 200 copies of NNV RNA standard, which corresponded to 200 copies of virus particles. This RT-PCR method was specific to the NNV detection with no cross-reactivity to other fish viral disease pathogens, such as infectious pancreatic necrosis virus （IPNV）, infectious hematopoietic necrosis virus （IHNV）, spring viraemia of carp virus （SVCV）, epizootic haematopoietic necrosis virus （EHNV）, and large yellow croaker iridovirus （LYC1V）. With this method, the orange-spotted grouper （Epinephelus coioides） fry from hatcheries with or without incidence of the VN- N epidemic in Fujian Province were detected. The results showed that all or 93% of the fry from the two hatcheries with incidence of the epidemic were diagnosed as positive, while 40% or 25% of fry from the t- wo hatcheries without the VNN epidemic were also detected as NNV positive, indicating that this RT-PCR method can be used for rapid, sensitive detection of NNV infection and applied in the VNN epidemic alert.展开更多
Leopard coral groupers belong to the Plectropomus genus of the Epinephelidae family and are important fish for coral reef ecosystems and the marine aquaculture industry. To promote future research of this species, a h...Leopard coral groupers belong to the Plectropomus genus of the Epinephelidae family and are important fish for coral reef ecosystems and the marine aquaculture industry. To promote future research of this species, a high-quality chromosome-level genome was assembled using PacBio sequencing and Hi-C technology. A 787.06 Mb genome was assembled, with 99.7%(784.57 Mb) of bases anchored to 24 chromosomes. The leopard coral grouper genome size was smaller than that of other groupers, which may be related to its ancient status among grouper species. A total of 22 317 proteincoding genes were predicted. This high-quality genome of the leopard coral grouper is the first genomic resource for Plectropomus and should provide a pivotal genetic foundation for further research. Phylogenetic analysis of the leopard coral grouper and 12 other fish species showed that this fish is closely related to the brown-marbled grouper.Expanded genes in the leopard coral grouper genome were mainly associated with immune response and movement ability, which may be related to the adaptive evolution of this species to its habitat. In addition, we also identified differentially expressed genes(DEGs) associated with carotenoid metabolism between red and brown-colored leopard coral groupers. These genes may play roles in skin color decision by regulating carotenoid content in these groupers.展开更多
基金supported by the National Natural Science Foundation of China (32273136,31872572)Agriculture Research System of China (ARS-47)+1 种基金Science and Technology Planning Project of Guangdong Province (2023B1212060023)Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) (SML2023SP201)。
文摘Animal body size variation is of particular interest in evolutionary biology,but the genetic basis remains largely unknown.Previous studies have shown the presence of two parallel evolutionary genetic clusters within the fish genus Epinephelus with evident divergence in body size,providing an excellent opportunity to investigate the genetic basis of body size variation in vertebrates.Herein,we performed phylotranscriptomic analysis and reconstructed the phylogeny of 13 epinephelids originating from the South China Sea.Two genetic clades with an estimated divergence time of approximately 15.4 million years ago were correlated with large and small body size,respectively.A total of 180 rapidly evolving genes and two positively selected genes were identified between the two groups.Functional enrichment analyses of these candidate genes revealed distinct enrichment categories between the two groups.These pathways and genes may play important roles in body size variation in groupers through complex regulatory networks.Based on our results,we speculate that the ancestors of the two divergent groups of groupers may have adapted to different environments through habitat selection,leading to genetic variations in metabolic patterns,organ development,and lifespan,resulting in body size divergence between the two locally adapted populations.These findings provide important insights into the genetic mechanisms underlying body size variation in groupers and species differentiation.
基金Supported by the Innovation Platform for Academicians of Hainan Province(YSPTZX202103)Hainan Provincial Natural Science Foundation of China(321QN263)+3 种基金National Natural Science Foundation of China(32160861)the Major Science and Technology Plan of Hainan Province(ZDKJ2021017)State Key Laboratory of Developmental Biology of Freshwater Fish(2020KF001)Scientific Research Foundation of Hainan Tropical Ocean University(RHDRC202010)。
文摘[Objectives]This study aimed to investigate the sequence structure and function of Myostatin(MSTN)gene in the hybrid grouper(Epinephelus fuscoguttatus,♀×Epinephelus polyphekadion,♂).[Methods]Genetic DNA samples were extracted from the caudal fins of the hybrid grouper and its parents to amplify their MSTN genes.Then,MSTN gene sequences were analyzed using bioinformatics tools to predict their protein structures and functions.[Results]The hybrid grouper and its parents shared the same MSTN gene structure,consisting of three exons and two introns.Nucleotide sequence of the gene could be translated into 376 amino acids,including an N-terminal signal peptide,a proteolytic processing site(RXXR motif),and nine conserved cysteine residues at C-terminal,which were the typical features of transforming growth factor beta(TGF-β)superfamily proteins.Alignment of protein sequence showed that MSTN was highly conserved between the hybrid grouper and its parents.Especially,exon 3,an important functional domain,exhibited a sequence similarity of 100%among them.In addition,four variable amino acid residues were detected in exon 2 at positions 141,153,185 and 186 in the hybrid grouper,but they did not affect the secondary structure of the protein.[Conclusion]These results will provide molecular information for future investigation on the growth and heterosis of hybrid grouper species,and on the roles of MSTN gene in regulating the growth traits of the hybrid grouper.
基金Supported by the National High Technology Research and Development Program of China(863Program,No.2007AA091404)the National Key Technology Research and Development Program(2007BAD29B03)A Project Funded by the Academic Program Development of Jiangsu Higher Education Institutions(PAPD)~~
文摘[Objective] The study aimed to evaluate the genetic variability and interspecific relationships among four species of groupers from South China Sea, including E. fario, E. merra, E. malabaricus and E. coioides. [Method] Twenty one mircosatellite loci of groupers were selected from GenBank and eight high polymorphic loci were used to further genetic analysis. [Result] The mean number of alleles per locus （A）, effective number of alleles （Ne）, mean polymorphism information content （PIC）, observed heterozygosity （Ho） and expected heterozygosity （He） were 4.38±1.60, 3.69±0.86, 0.69±0.08, 0.67±0.08, 0.72±0.06 in E. malabaricus; 3.88±1.13, 3.55±1.04, 0.66±0.10, 0.68±0.21, 0.70±0.08 in E.coioides; 6.00±1.07, 4.68±0.65, 0.78±0.03, 0.73±0.25, 0.79±0.03 in E. fario; 5.50±1.07, 4.58±0.80, 0.76±0.05, 0.75±0.18, 0.78±0.04 in E. merra, respectively. [Conclusion] We compared the values above, the order of the genetic variability among these grouper species was E. fario E. merra E. malabaricus E. coioides. We found that the level of genetic variability of these groupers species was relatively higher than that of other marine fish, so their genetic status was good. In addition, the analyisis of genetic relationship showed that E. malabaricus and E. coioides was the closest and it was the farthest between E. merra and E. coioides.
基金The National Basic Research Program under contract No.2012CB114402the National High Technology Research and Development Program of China (863 Program) under contract No.2012AA092202Scientific Research Project of Marine Public Welfare Industry of China under contract No.200905020-07
文摘Viral nervous necrosis （VNN） causes high mortality in marine fish, especially in the grouper, worldwide and in China. Since there is no effective vaccine or drug to deal with VNN, early detection and prevention is important to block its outbreak. In this study, a reverse transcription-polymerase chain reaction （RT-PCR） was developed for the rapid, convenient, and sensitive detection of the VNN pathogen, nervous necro- sis virus （NNV）, in the grouper. The whole process was completed within 3.5 h from the RNA extraction to PCR product visualization. The detection limit of this method was 200 copies of NNV RNA standard, which corresponded to 200 copies of virus particles. This RT-PCR method was specific to the NNV detection with no cross-reactivity to other fish viral disease pathogens, such as infectious pancreatic necrosis virus （IPNV）, infectious hematopoietic necrosis virus （IHNV）, spring viraemia of carp virus （SVCV）, epizootic haematopoietic necrosis virus （EHNV）, and large yellow croaker iridovirus （LYC1V）. With this method, the orange-spotted grouper （Epinephelus coioides） fry from hatcheries with or without incidence of the VN- N epidemic in Fujian Province were detected. The results showed that all or 93% of the fry from the two hatcheries with incidence of the epidemic were diagnosed as positive, while 40% or 25% of fry from the t- wo hatcheries without the VNN epidemic were also detected as NNV positive, indicating that this RT-PCR method can be used for rapid, sensitive detection of NNV infection and applied in the VNN epidemic alert.
基金the Agriculture Research System of China(ARS-47)Science and Technology Planning Project of Guangzhou(201804020013)+2 种基金National Natural Science Foundation of China(31872572,u1401213,31802266)Yang Fan Innovative&Entrepreneurial Research Team Project(No.201312H10)Program of the China-ASEAN Maritime Cooperation Fund of the Chinese Government(42000-41170002).
文摘Leopard coral groupers belong to the Plectropomus genus of the Epinephelidae family and are important fish for coral reef ecosystems and the marine aquaculture industry. To promote future research of this species, a high-quality chromosome-level genome was assembled using PacBio sequencing and Hi-C technology. A 787.06 Mb genome was assembled, with 99.7%(784.57 Mb) of bases anchored to 24 chromosomes. The leopard coral grouper genome size was smaller than that of other groupers, which may be related to its ancient status among grouper species. A total of 22 317 proteincoding genes were predicted. This high-quality genome of the leopard coral grouper is the first genomic resource for Plectropomus and should provide a pivotal genetic foundation for further research. Phylogenetic analysis of the leopard coral grouper and 12 other fish species showed that this fish is closely related to the brown-marbled grouper.Expanded genes in the leopard coral grouper genome were mainly associated with immune response and movement ability, which may be related to the adaptive evolution of this species to its habitat. In addition, we also identified differentially expressed genes(DEGs) associated with carotenoid metabolism between red and brown-colored leopard coral groupers. These genes may play roles in skin color decision by regulating carotenoid content in these groupers.
