Coilia nasus,a migratory fish species found in the middle and lower reaches of the Yangtze River and along offshore areas of China,possesses considerable aquacultural and economic potential.However,the species faces c...Coilia nasus,a migratory fish species found in the middle and lower reaches of the Yangtze River and along offshore areas of China,possesses considerable aquacultural and economic potential.However,the species faces challenges due to significant variation in the gonadal development rate among females,resulting in inconsistent ovarian maturation times at the population level,an extended reproductive period,and limitations on fish growth rate due to ovarian prematurity.In the present study,we combined genome-wide association study(GWAS)and comparative transcriptome analysis to investigate the potential single nucleotide polymorphisms(SNPs)and candidate genes associated with population-asynchronous ovarian development in C.nasus.Genotyping of the female population based on whole-genome resequencing yielded 2120695 high-quality SNPs,39 of which were suggestively associated with ovarian development.Of note,a significant SNP peak on LG21 containing 30 suggestively associated SNPs was identified,with cpne5a determined as the causal gene of the peak.Therefore,single-marker and haplotype association analyses were performed on cpne5a,revealing four genetic markers(P<0.05)and seven haplotypes(r2>0.9)significantly associated with the phenotype.Comparative transcriptome analysis of precociously and normally maturing individuals screened out 29 and 426 overlapping differentially expressed genes in the brain and ovary,respectively,between individuals of different body sizes.Integrating the GWAS and transcriptome analysis results,this study identified genes and pathways related to hypothalamic-pituitary-gonadal axis hormone secretion,extracellular matrix,angiogenesis,and gap junctions involved in population-asynchronous ovarian development.The insights gained from this study provide a basis for a deeper understanding of the molecular mechanisms underlying ovarian development in fish and may facilitate the genetic breeding of C.nasus strains exhibiting population-synchronous ovarian development in the future.展开更多
The migratory history of the engraulid fish Coilia nasus in the Rokkaku and Chikugo River estuaries of the Ariake Sea, Japan was assessed using otolith strontium（Sr） X-ray intensity maps and strontium：calcium（Sr...The migratory history of the engraulid fish Coilia nasus in the Rokkaku and Chikugo River estuaries of the Ariake Sea, Japan was assessed using otolith strontium（Sr） X-ray intensity maps and strontium：calcium（Sr：Ca） ratio life history transects by an electron probe microanalyzer（EPMA）. The results showed that seven of the ten specimens from the Rokkaku River Estuary（LJC） and all 15 specimens collected in the Chikugo River Estuary（ZHC） had low Sr：Ca ratios（≤3） at the central otolith area, indicating their riverine origin and initial freshwater residence. After the first regime shift adjacent to natal regions, the Sr level mapping displayed a wide variety of color patterns, and the Sr：Ca ratios obtained by the line transect analysis could be divided into one to six significantly different phases indicative of gradual life history transition. The other three specimens from the Rokkaku River Estuary had high Sr：Ca ratios（3–6.7） at the central otolith area but showed alternating changes between low and high values outside the natal region, suggesting that estuarine-origin individuals occurred in the Rokkaku River Estuary. The two-dimensional maps of the Sr level and average of the otolith Sr：Ca ratios along the life-history transects could be used as effective tools for reconstruction of past habitat use of the tapertail anchovy in estuaries of the Ariake Sea, Japan.展开更多
The estuarine tapertail anchovy(Coilia nasus)is a high-value commercial fish.Estimating the spawning site or hatchery origin and habitat is essential for its conservation.This study aimed to determine the habitat use ...The estuarine tapertail anchovy(Coilia nasus)is a high-value commercial fish.Estimating the spawning site or hatchery origin and habitat is essential for its conservation.This study aimed to determine the habitat use and life history characteristics of C.nasus from the Changjiang River Estuary.We investigated the environmental signatures of strontium(Sr)and calcium(Ca)in the otoliths of the collected specimens using electron probe microanalysis;additionally,we examined their gonadal maturity stage.Our results indicate that the 31 adult C.nasus specimens used in this study could be classified into two types based on their otolith Sr:Ca concentration ratios and their gonadal maturity stage.The long freshwater early life history type(Type LF)had wider central region in the otolith with low Sr:Ca concentration ratios ranging from 1.24±0.62 to 1.92±0.78 and a bluish pattern of low Sr content level.These fish are of riverine origin and had a relatively long early life history in freshwater and low gonadal maturation when captured.The short freshwater early life history type(Type SF)had a shorter central region in the otolith with low Sr:Ca concentration ratios ranging from 1.35±0.5 to 2.82±0.97 and a correspondingly bluish pattern.These fish also had a relatively short-term early life history in freshwater and high gonadal maturation when captured.The results of the otolith microchemical analysis indicated that Type LF and Type SF originated in spawning/hatching sites far from and close to the estuary,respectively.The mature gonads of Type SF fish indicated that they may breed in areas close to the estuary,whereas the immature gonads of Type LF fish indicated that they may breed in areas far from the estuary.This study is the first to reveal that the Changjiang River Estuary contains stocks of anadromous C.nasus originating in different spawning sites during the same season.The estuarine habitat plays a critical role in the connectivity between freshwater recruitment and the marine resources available to adult spawners of this commercially valued species.From a conservation perspective,this study provides important information for identifying anadromous C.nasus stocks originating in different spawning sites in the Changjiang River Basin.展开更多
Spatial-temporal distribution of marine fishes is strongly influenced by environmental factors.To obtain a more continuous distribution of these variables usually measured by stationary sampling designs,spatial interp...Spatial-temporal distribution of marine fishes is strongly influenced by environmental factors.To obtain a more continuous distribution of these variables usually measured by stationary sampling designs,spatial interpolation methods(SIMs)is usually used.However,different SIMs may obtain varied estimation values with significant differences,thus affecting the prediction of fish spatial distribution.In this study,different SIMs were used to obtain continuous environmental variables(water depth,water temperature,salinity,dissolved oxygen(DO),p H,chlorophyll a and chemical oxygen demand(COD))in the Changjiang River Estuary(CRE),including inverse distance weighted(IDW)interpolation,ordinary Kriging(OK)(semivariogram model:exponential(OKE),Gaussian(OKG)and spherical(OKS))and radial basis function(RBF)(regularized spline function(RS)and tension spline function(TS)).The accuracy and effect of SIMs were cross-validated,and two-stage generalized additive model(GAM)was used to predict the distribution of Coilia nasus from 2012 to 2014 in CRE.DO and COD were removed before model prediction due to their autocorrelation coefficient based on variance inflation factors analysis.Results showed that the estimated values of environmental variables obtained by the different SIMs differed(i.e.,mean values,range etc.).Cross-validation revealed that the most suitable SIMs of water depth and chlorophyll a was IDW,water temperature and salinity was RS,and p H was OKG.Further,different interpolation results affected the predicted spatial distribution of Coilia nasus in the CRE.The mean values of the predicted abundance were similar,but the differences between and among the maximum value were large.Studies showed that different SIMs can affect estimated values of the environmental variables in the CRE(especially salinity).These variations further suggest that the most applicable SIMs to each variable will also differ.Thus,it is necessary to take these potential impacts into consideration when studying the relationship between the spatial distribution of fishes and environmental changes in the CRE.展开更多
Coilia nasus is an important economic migratory fish in China, and it is known as ＂Three Delicious Fish of the Yangtze River＂ with puffer fishes and reeves shad. However, because of water pollution, blocked migratio...Coilia nasus is an important economic migratory fish in China, and it is known as ＂Three Delicious Fish of the Yangtze River＂ with puffer fishes and reeves shad. However, because of water pollution, blocked migration and overfishing, wild resources of C. nasus have suffered severe damage. This article gives an overview on genetic diversity of C. nasus from morphology, protein and DNA levels, to supply a theoretical foundation for protection of C. nasus resources.展开更多
Coilia nasus is an endangered fish species in the Yangtze River,and there is urgent need to know the genes related to its reproduction and fertility.The DAZ family including boule,daz and dazl,plays an important role ...Coilia nasus is an endangered fish species in the Yangtze River,and there is urgent need to know the genes related to its reproduction and fertility.The DAZ family including boule,daz and dazl,plays an important role in germ cells development.In this study,the cDNA sequence of boule(Cnbol)and dazl(Cndazl)genes were cloned and their expression patterns were characterized in Coilia nasus.RT-PCR showed that the expression of Cnbol and Cndazl mRNAs was restricted in adult gonads.The section in situ hybridization indicated that the temporospatial expression patterns of Cnbol and Cndazl were significantly different.In the testis,Cnbol was mainly detected in spermatocytes and spermatids,while Cndazl was prominently expressed in s permatogonia.In the ovary,Cnbol and Cndazl were highly expressed in the early stages of oocytes.Interestingly,Cndazl was also concentrated in perinuclear speckle and then localized to the Balbiani body in late stages of oocytes.In addition,Cnbol and Cndazl 3′UTR can specifically label medaka Primordial Germ Cells(PGCs).According to our results,Cnbol and Cndazl are marker genes of germ cells and may play a vital role in the development and differentiation of germ cells in Coilia nasus.展开更多
This study was designed to generate the full-length transcriptome of Coilia nasus using single-molecule long read isoform sequencing(SMRT-seq)technology.RNAs of brains,ovaries,and testes of C.nasus conditioned in both...This study was designed to generate the full-length transcriptome of Coilia nasus using single-molecule long read isoform sequencing(SMRT-seq)technology.RNAs of brains,ovaries,and testes of C.nasus conditioned in both seawater and freshwater except for gut which was only from the fish conditioned in freshwater,were isolated.All the RNAs were pooled together equally for SMRT sequencing.One SMRT cell produced 64.18 Gb clean data,including 765,184 circular consensus(CCS)reads and 616,126 full-length non-chimeric(FLNC)reads.Finally,93,793 non-redundant transcripts were obtained after clustered and polished.Structural analysis of the 93,793 non-redundant transcripts predicted 8242 alternative splicing events,a total of 229,825 SSR and 72,037 complete CDS.A total of 8437 lncRNA were identified.84,617 transcripts were annotated in NR,Swissprot,GO,COG,KOG,eggnog,Pfam and KEGG database totally.This is the first full-length transcriptome of Coilia nasus,including transcripts appeared in the case of seawater,which will facilitate exploration of genetic data and life story of Coilia nasus.展开更多
基金supported by the National Key R&D Program of China(2022YFD2400904)Key R&D Projects in Hubei Province(2022BBA008)+1 种基金Zhenjiang Jinshan TalentsWuhan Yangtze River Characteristic Fish Breeding and Domestication Project。
文摘Coilia nasus,a migratory fish species found in the middle and lower reaches of the Yangtze River and along offshore areas of China,possesses considerable aquacultural and economic potential.However,the species faces challenges due to significant variation in the gonadal development rate among females,resulting in inconsistent ovarian maturation times at the population level,an extended reproductive period,and limitations on fish growth rate due to ovarian prematurity.In the present study,we combined genome-wide association study(GWAS)and comparative transcriptome analysis to investigate the potential single nucleotide polymorphisms(SNPs)and candidate genes associated with population-asynchronous ovarian development in C.nasus.Genotyping of the female population based on whole-genome resequencing yielded 2120695 high-quality SNPs,39 of which were suggestively associated with ovarian development.Of note,a significant SNP peak on LG21 containing 30 suggestively associated SNPs was identified,with cpne5a determined as the causal gene of the peak.Therefore,single-marker and haplotype association analyses were performed on cpne5a,revealing four genetic markers(P<0.05)and seven haplotypes(r2>0.9)significantly associated with the phenotype.Comparative transcriptome analysis of precociously and normally maturing individuals screened out 29 and 426 overlapping differentially expressed genes in the brain and ovary,respectively,between individuals of different body sizes.Integrating the GWAS and transcriptome analysis results,this study identified genes and pathways related to hypothalamic-pituitary-gonadal axis hormone secretion,extracellular matrix,angiogenesis,and gap junctions involved in population-asynchronous ovarian development.The insights gained from this study provide a basis for a deeper understanding of the molecular mechanisms underlying ovarian development in fish and may facilitate the genetic breeding of C.nasus strains exhibiting population-synchronous ovarian development in the future.
基金The National Natural Science Foundation of China under contract No.31372533China Central Governmental Research Institutional Basic Special Research Project from Public Welfare Fund under contract No.2016PT01the“948”Program of the Ministry of Agriculture under contract No.2014-S6
文摘The migratory history of the engraulid fish Coilia nasus in the Rokkaku and Chikugo River estuaries of the Ariake Sea, Japan was assessed using otolith strontium（Sr） X-ray intensity maps and strontium：calcium（Sr：Ca） ratio life history transects by an electron probe microanalyzer（EPMA）. The results showed that seven of the ten specimens from the Rokkaku River Estuary（LJC） and all 15 specimens collected in the Chikugo River Estuary（ZHC） had low Sr：Ca ratios（≤3） at the central otolith area, indicating their riverine origin and initial freshwater residence. After the first regime shift adjacent to natal regions, the Sr level mapping displayed a wide variety of color patterns, and the Sr：Ca ratios obtained by the line transect analysis could be divided into one to six significantly different phases indicative of gradual life history transition. The other three specimens from the Rokkaku River Estuary had high Sr：Ca ratios（3–6.7） at the central otolith area but showed alternating changes between low and high values outside the natal region, suggesting that estuarine-origin individuals occurred in the Rokkaku River Estuary. The two-dimensional maps of the Sr level and average of the otolith Sr：Ca ratios along the life-history transects could be used as effective tools for reconstruction of past habitat use of the tapertail anchovy in estuaries of the Ariake Sea, Japan.
基金The National Natural Science Foundation of China under contract No.31602159the Agricultural Finance Special Project under contract No.CJDC-2017-22the Scientific Research Foundation of Wuxi City for Returned Oversea Chinese Scholars under contract No.CZ2019231400.
文摘The estuarine tapertail anchovy(Coilia nasus)is a high-value commercial fish.Estimating the spawning site or hatchery origin and habitat is essential for its conservation.This study aimed to determine the habitat use and life history characteristics of C.nasus from the Changjiang River Estuary.We investigated the environmental signatures of strontium(Sr)and calcium(Ca)in the otoliths of the collected specimens using electron probe microanalysis;additionally,we examined their gonadal maturity stage.Our results indicate that the 31 adult C.nasus specimens used in this study could be classified into two types based on their otolith Sr:Ca concentration ratios and their gonadal maturity stage.The long freshwater early life history type(Type LF)had wider central region in the otolith with low Sr:Ca concentration ratios ranging from 1.24±0.62 to 1.92±0.78 and a bluish pattern of low Sr content level.These fish are of riverine origin and had a relatively long early life history in freshwater and low gonadal maturation when captured.The short freshwater early life history type(Type SF)had a shorter central region in the otolith with low Sr:Ca concentration ratios ranging from 1.35±0.5 to 2.82±0.97 and a correspondingly bluish pattern.These fish also had a relatively short-term early life history in freshwater and high gonadal maturation when captured.The results of the otolith microchemical analysis indicated that Type LF and Type SF originated in spawning/hatching sites far from and close to the estuary,respectively.The mature gonads of Type SF fish indicated that they may breed in areas close to the estuary,whereas the immature gonads of Type LF fish indicated that they may breed in areas far from the estuary.This study is the first to reveal that the Changjiang River Estuary contains stocks of anadromous C.nasus originating in different spawning sites during the same season.The estuarine habitat plays a critical role in the connectivity between freshwater recruitment and the marine resources available to adult spawners of this commercially valued species.From a conservation perspective,this study provides important information for identifying anadromous C.nasus stocks originating in different spawning sites in the Changjiang River Basin.
基金The Shanghai Municipal Science and Technology Commission Local Capacity Construction Project under contract No.18050502000the Monitoring and Evaluation of National Sea Ranch Demonstration Area Project in Changjiang River Estuary under contract No.171015the National Natural Science Foundation of China under contract No.41906074。
文摘Spatial-temporal distribution of marine fishes is strongly influenced by environmental factors.To obtain a more continuous distribution of these variables usually measured by stationary sampling designs,spatial interpolation methods(SIMs)is usually used.However,different SIMs may obtain varied estimation values with significant differences,thus affecting the prediction of fish spatial distribution.In this study,different SIMs were used to obtain continuous environmental variables(water depth,water temperature,salinity,dissolved oxygen(DO),p H,chlorophyll a and chemical oxygen demand(COD))in the Changjiang River Estuary(CRE),including inverse distance weighted(IDW)interpolation,ordinary Kriging(OK)(semivariogram model:exponential(OKE),Gaussian(OKG)and spherical(OKS))and radial basis function(RBF)(regularized spline function(RS)and tension spline function(TS)).The accuracy and effect of SIMs were cross-validated,and two-stage generalized additive model(GAM)was used to predict the distribution of Coilia nasus from 2012 to 2014 in CRE.DO and COD were removed before model prediction due to their autocorrelation coefficient based on variance inflation factors analysis.Results showed that the estimated values of environmental variables obtained by the different SIMs differed(i.e.,mean values,range etc.).Cross-validation revealed that the most suitable SIMs of water depth and chlorophyll a was IDW,water temperature and salinity was RS,and p H was OKG.Further,different interpolation results affected the predicted spatial distribution of Coilia nasus in the CRE.The mean values of the predicted abundance were similar,but the differences between and among the maximum value were large.Studies showed that different SIMs can affect estimated values of the environmental variables in the CRE(especially salinity).These variations further suggest that the most applicable SIMs to each variable will also differ.Thus,it is necessary to take these potential impacts into consideration when studying the relationship between the spatial distribution of fishes and environmental changes in the CRE.
文摘Coilia nasus is an important economic migratory fish in China, and it is known as ＂Three Delicious Fish of the Yangtze River＂ with puffer fishes and reeves shad. However, because of water pollution, blocked migration and overfishing, wild resources of C. nasus have suffered severe damage. This article gives an overview on genetic diversity of C. nasus from morphology, protein and DNA levels, to supply a theoretical foundation for protection of C. nasus resources.
基金supported by the National Key R&D Program of China(2018YFD0901205)National Natural Science Foundation of China(31672700).
文摘Coilia nasus is an endangered fish species in the Yangtze River,and there is urgent need to know the genes related to its reproduction and fertility.The DAZ family including boule,daz and dazl,plays an important role in germ cells development.In this study,the cDNA sequence of boule(Cnbol)and dazl(Cndazl)genes were cloned and their expression patterns were characterized in Coilia nasus.RT-PCR showed that the expression of Cnbol and Cndazl mRNAs was restricted in adult gonads.The section in situ hybridization indicated that the temporospatial expression patterns of Cnbol and Cndazl were significantly different.In the testis,Cnbol was mainly detected in spermatocytes and spermatids,while Cndazl was prominently expressed in s permatogonia.In the ovary,Cnbol and Cndazl were highly expressed in the early stages of oocytes.Interestingly,Cndazl was also concentrated in perinuclear speckle and then localized to the Balbiani body in late stages of oocytes.In addition,Cnbol and Cndazl 3′UTR can specifically label medaka Primordial Germ Cells(PGCs).According to our results,Cnbol and Cndazl are marker genes of germ cells and may play a vital role in the development and differentiation of germ cells in Coilia nasus.
基金This work was supported by the Project of Centre for Research on Environmental Ecology and Fish Nutrition(CREEFN)of the Ministry of Agriculture and Rural Affairs,Shanghai Ocean University(A1-3201-19-300204)the Project of Science and Technology Commission Shanghai Municipality(17391900300).
文摘This study was designed to generate the full-length transcriptome of Coilia nasus using single-molecule long read isoform sequencing(SMRT-seq)technology.RNAs of brains,ovaries,and testes of C.nasus conditioned in both seawater and freshwater except for gut which was only from the fish conditioned in freshwater,were isolated.All the RNAs were pooled together equally for SMRT sequencing.One SMRT cell produced 64.18 Gb clean data,including 765,184 circular consensus(CCS)reads and 616,126 full-length non-chimeric(FLNC)reads.Finally,93,793 non-redundant transcripts were obtained after clustered and polished.Structural analysis of the 93,793 non-redundant transcripts predicted 8242 alternative splicing events,a total of 229,825 SSR and 72,037 complete CDS.A total of 8437 lncRNA were identified.84,617 transcripts were annotated in NR,Swissprot,GO,COG,KOG,eggnog,Pfam and KEGG database totally.This is the first full-length transcriptome of Coilia nasus,including transcripts appeared in the case of seawater,which will facilitate exploration of genetic data and life story of Coilia nasus.
