基于SLAF-seq技术的沙带鱼(Lepturacanthus savala)微卫星标记开发以及在近缘种中的通用性
|
摘要
沙带鱼是带鱼科中一种重要的海洋经济鱼类,广泛分布于印度-西太平洋海域。近年来,过度捕捞和渔业生态环境变化使沙带鱼的自然资源和种群结构受到了严重影响。因此,为了制定出科学合理的资源保护和管理措施,急需开发出大量多态的沙带鱼微卫星位点以促进其种群遗传学研究。本研究采用SLAF-seq技术,首次在沙带鱼基因组DNA中筛选出28个多态性微卫星位点。每个位点的等位基因数为2~18,平均值9.11;观测杂合度和期望杂合度分别为0.077~0.871(平均值0.634)和0.151~0.942(平均值0.711);各位点多态信息含量为0.137~0.919,平均值0.670。经过Bonferroni校正后,有3个位点显著偏离哈迪-温伯格平衡(HWE),并显示出较高的近交系数和无效等位基因频率,其余25个位点均符合HWE。这些多态性微卫星DNA标记可为沙带鱼的种群遗传资源研究提供有效的分子标记和技术支撑。此外,跨物种扩增结果表明,有19个微卫星标记在4种带鱼属鱼类中具有较好的通用性,这些标记可为阐明带鱼科属间或种间的系统进化关系提供新的研究手段和视角。
Savalai hairtail(Lepturacanthus savala) is a commercially important marine fish belonging to the family Trichiuridae,with a wide distribution in the Indian-western Pacific coastal waters.In recent years,overfishing and the changes in the ecological environment of fisheries have brought a severe impact on the natural resources and population structure of L.savala.Thus,in order to carry out reasonable resource conservations and managements of L.savala,the developing of a large number of polymorphic microsatellite loci for promoting its population genetics research is urgently needed.In this study,based on SLAF-seq technology,28 polymorphic microsatellite loci were isolated for the first time in the genomic DNA of L.savala.The number of alleles per locus ranged from2 to 18,with an average of 9.11.The observed and expected heterozygosity varied from 0.077 to 0.871(average at0.634) and from 0.151 to 0.942(average at 0.711),respectively.The polymorphism information content of each locus was from 0.137 to 0.919,and the average was 0.670.After Bonferroni correction,three loci were significantly deviated from the Hardy-Weinberg equilibrium(HWE) and showed high inbreeding coefficient and null allele frequencies,with the remaining 25 locus meeting the HWE.These polymorphic microsatellite DNA markers could provide effective molecular markers and technical support for studying the population genetic resources of L.savala.Furthermore,cross-species amplifications showed that 19 microsatellite markers were transferable in four species of the genus Trichiurus.The cross-amplified markers would provide new method and insight for illustrating the phylogenetic relationship between species and genus of the family Trichiuridae.
Savalai hairtail(Lepturacanthus savala) is a commercially important marine fish belonging to the family Trichiuridae,with a wide distribution in the Indian-western Pacific coastal waters.In recent years,overfishing and the changes in the ecological environment of fisheries have brought a severe impact on the natural resources and population structure of L.savala.Thus,in order to carry out reasonable resource conservations and managements of L.savala,the developing of a large number of polymorphic microsatellite loci for promoting its population genetics research is urgently needed.In this study,based on SLAF-seq technology,28 polymorphic microsatellite loci were isolated for the first time in the genomic DNA of L.savala.The number of alleles per locus ranged from2 to 18,with an average of 9.11.The observed and expected heterozygosity varied from 0.077 to 0.871(average at0.634) and from 0.151 to 0.942(average at 0.711),respectively.The polymorphism information content of each locus was from 0.137 to 0.919,and the average was 0.670.After Bonferroni correction,three loci were significantly deviated from the Hardy-Weinberg equilibrium(HWE) and showed high inbreeding coefficient and null allele frequencies,with the remaining 25 locus meeting the HWE.These polymorphic microsatellite DNA markers could provide effective molecular markers and technical support for studying the population genetic resources of L.savala.Furthermore,cross-species amplifications showed that 19 microsatellite markers were transferable in four species of the genus Trichiurus.The cross-amplified markers would provide new method and insight for illustrating the phylogenetic relationship between species and genus of the family Trichiuridae.
引文
Abdelkrim J.,Robertson B.C.,Stanton J.A.,and Gemmell N.,2009,Fast,cost-effective development of species-specific microsatellite markers by genomic sequencing,Biotechniques,46(3):185-192
An H.S.,Lee J.H.,Noh J.K.,Kim H.C.,Park C.J.,Min B.H.,and Myeong J.I.,2010,Ten new microsatellite markers in cutlassfish Trichiurus lepturus derived from an enriched genomic library,Animal Cells and Systems,14(3):169-174
Bi J.Z.,Shao C.W.,Miao G.D.,Ma H.Y.,and Chen S.L.,2009,Isolation and characterization of 12 microsatellite loci from cutlassfish(Trichiurus haumela),Conservation Genetics,10(4):1171-1173
Botstein D.,White R.L.,Skolnick M.,and Davis R.W.,1980,Construction of a genetic linkage map in man using restriction fragment length polymorphisms,American Journal of Human Genetics,32(3):314-331
Carreras-Carbonell J.,Macpherson E.,and Pascual M.,2008,U-tility of pairwise mt DNA genetic distances for predicting cross-species microsatellite amplification and polymorphism success in fishes,Conservation Genetics,9(1):181-190
Castoe T.A.,Streicher J.W.,Meik J.M.,Ingrasci M.J.,Poole A.W.,De Koning A.P.J.,Campbell J.A.,Parkinson C.L.,Smith E.N.,and Pollock D.D.,2012,Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related species,Molecular Ecology Resources,12(6):1105-1113
Chakravarty M.S.,Pavani B.,and Ganesh P.R.C.,2013,Gonado-somatic index and fecundity studies in two species of ribbon fishes,Trichiurus lepturus(Linnaeus,1758)and Lepturacanthus savala(Cuvier,1829)off Visakhapatnam,east coast of India,Indian Journal of Fisheries,60(2):163-165
Dewoody J.A.,and Avise J.C.,2000,Microsatellite variation in marine,freshwater and anadromous fishes compared with other animals,Journal of Fish Biology,56(3):461-473
Gemayel R.,Cho J.,Boeynaems S.,and Verstrepen K.J.,2012,Beyond junk-variable tandem repeats as facilitators of rapid evolution of regulatory and coding sequences,Genes,3(3):461-480
Grover A.,and Sharma P.C.,2016,Development and use of molecular markers:past and present,Critical Reviews in Biotechnology,36(2):290-302
Guo Y.S.,Liu X.M.,Wang Z.D.,Lu H.S.,and Liu C.W.,2014,Isolation and characterization of microsatellite DNA loci from Naihai cutlassfish(Trichiurus nanhaiensis),Journal of genetics,91(3):1-4
He P.,1998,Abundance,polymorphism and applications of microsatellite in eukaryote,Yichuan(Hereditas),20(4):42-47(何平,1998,真核生物中的微卫星及其应用,遗传,20(4):42-47)
Kalinowski S.T.,Taper M.L.,and Marshall T.C.,2007,Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment,Molecular Ecology,16(5):1099-1106
Li B.,Tian L.,Zhang J.,Huang L.,Han F.,Yan S.,Wang L.,Zheng H.,and Sun J.,2014,Construction of a high-density genetic map based on large-scale markers developed by specific length amplified fragment sequencing(SLAF-seq)and its application to QTL analysis for isoflavone content in Glycine max,BMC Genomics,15:1086
Li C.S.,1987,Trichiuroidei,In:Cheng Q.T.,and Zheng B.S.,(eds.),Systematic synopsis of Chinese fishes,Science Press,Beijing,China,pp.414-416(李春生,1987,带鱼亚目,见:成庆泰,郑葆珊,(编著),中国鱼类系统检索,科学出版社,中国,北京,pp.414-416)
Liu S.F.,Zu D.M.,Liu Q.,Dai F.Q.,Ma Q.,and Zhuang Z.M.,2015,Isolation and characterization of polymorphic microsatellite markers for Eupleurogrammus muticus,Conservation Genetics Resources,7(2):487-488
Nakamura I.,and Parin N.V.,1993,FAO species catalog.Snake mackerel and cutlass fishes of the world(Families Gempylidae and Trichiuridae).An annotated and illustrated catalog of the snake mackerel,snoeks,escolars,gem fishes,sack fishes,domine,oil fish,cutlassfishes,scabbar fishes,hairtail and frostfishes know to date,Fao Fish Synop.,82(82):1-14
Nazeer R.A.,and Deeptha R.,2013,Antioxidant activity and amino acid profiling of protein hydrolysates from the skin of Sphyraena barracuda and Lepturacanthus savala,International Journal of Food Properties,16(3):500-511
Nei M.,Maruyama T.,and Chakraborty R.,1975,The bottleneck effect and genetic variability in populations,Evolution,29(1):1-10
Niu S.,Liu Y.,Qin C.,Wang X.,and Wu R.,2017,The complete mitochondrial genome and phylogenetic analysis of Lateolabrax maculatus(Perciformes,Moronidae),Mitochondrial DNA Part A,28(2):173-175
Memon K.H.,Liu Q.,Kalhoro M.A.,Chang M.S.,Baochao L.,Memon A.M.,Hyder S.,and Tabassum S.,2016,Growth and Mortality Parameters of Hairtail Lepturacanthus savala from Pakistan Waters,Pakistan Journal of Zoology,48(3):829-829
Pemberton J.M.,Slate J.,Bancroft D.R.,and Barrett J.A.,1995,Nonamplifying alleles at microsatellite loci:a caution for parentage and population studies,Molecular Ecology,4(2):249
Primmer C.R.,Moller A.P.,and Ellegren H.,1996,A wide-range survey of cross-species microsatellite amplification in birds,Molecular Ecology,5:365-378
Primmer C.R.,Painter J.N.,Koskinen M.T.,Palo J.U.,and MerilJ.,2005,Factors affecting avian cross-species microsatellite amplification,Journal of Avian Biology,36(4):348-360
Rizvi F.A.,Deshmukh V.D.,and Chakraborty S.K.,2010,Stock assessment of Lepturacanthus savala(Cuvier,1829)along north-west sector of Mumbai coast in Arabian Sea,Indian Journal of Fisheries,57(2):1-6
Rousset F.,2008,genepop'007:a complete re-implementation of the genepop software for Windows and Linux,Molecular E-cology Resources,8(1):103-106
Saha S.,and Subhedar N.,2011,Calcitonin-like immunoreactivity in the subcommissural organ-Reissner's fiber complex of some freshwater and marine teleosts,Journal of Chemical Neuroanatomy,41(2):122-128
Sambrook J.,and Russell D.W.,eds.,Huang P.T.,et al.,trans.,2002,Molecular cloning:A laboratory manual,Third edition,Science Press,Beijing,China,pp.463-471(萨姆布鲁克J.,拉塞尔D.W.,编著,黄培堂等,主译,2002,分子克隆实验指南,第三版,科学出版社,北京,pp.463-471)
Schuelke M.,2000,An economic method for the fluorescent labeling of PCR fragments,Naturebiotechnology,18(2):233-234
Sun X.,Liu D.,Zhang X.,Li W.,Liu H.,Hong W.,Jiang C.,Guan N.,Ma C.,Zeng H.,Xu C.,Song J.,Huang L.,Wang C.,Shi J.,Wang R.,Zheng X.,Lu C.,Wang X.,and Zheng H.,2013,SLAF-seq:an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing,Plo S One,8(3):e58700
Tzeng C.H.,and Chiu T.S.,2012,DNA barcode-based identification of commercially caught cutlassfishes(Family:Trichiuridae)with a phylogenetic assessment,Fisheries Research,s127-128(9):176-181
Umino T.,Ueno K.,Mihara T.,Koike M.,Watanabe M.,Syazni A.,Ishitani M.,and Ohara K.,2013,Isolation of eleven polymorphic microsatellite loci for the endangered Sillago parvisquamis and cross-species amplification with Sillago japonica,Conservation Genetics Resources,5(3):771-773
Van Oosterhout C.,Hutchinson W.F.,Wills D.P.M.,and Shipley P.,2004,MICRO-CHECKER:software for identifying and correcting genotyping errors in microsatellite data,Molecular Ecology Notes,4(3):535-538
Varshney R.K.,Graner A.,Sorrells M.E.,2005,Genic microsatellite markers in plants:features and applications,Trends in Biotechnology,23(1):48-55
Carneiro V.M.L.,Luciane S.,Lima D.A.,Freitas M.C.D.,2016,Microsatellite markers:what they mean and why they are so useful,Genetics and Molecular Biology,39(3):312-328
Wang H.Y.,Dong C.A.,and Lin H.C.,2017,DNA barcoding of fisheries catch to reveal composition and distribution of cutlassfishes along the Taiwan coast,Fisheries Research,187:103-109
Wu R.X.,Zhang H.R.,Niu S.F.,Zhai Y.,and Liu X.F.,2016,Development of polymorphic microsatellites for Sillago sihama based on next-generation sequencing and transferability to Sillago japonica,Genetics and molecular research,15(4):gmr15049046
Yang W.,Feng F.,and Yue G.,2007,Isolation and characterization of microsatellites from a marine foodfish species ribbonfish Trichiurus haumela,Molecular Ecology Notes,7(5):781-783
Yu H.T.,Lee Y.J.,Huang S.W.,and Chiu T.S.,2002,Genetic analysis of the populations of Japanese anchovy(Engraulidae:Engraulis japonicus)using microsatellite DNA,Marine Biotechnology,4(5):471-479
Zhang H.R.,Niu S.F.,Wu R.X.,Zhai Y.,and Tian L.T.,2016,Development and characterization of 26 polymorphic microsatellite markers in Lateolabrax maculatus and crossspecies amplification for the phylogenetically related taxa,Biochemical Systematics and Ecology,66:326-330
Zhao L.,Shao C.W.,Liao X.L.,and Chen S.L.,2009,Isolation and characterization of polymorphic microsatellite loci from a dinucleotide-enriched genomic library of seven-band grouper(Epinephelus septemfasciatus)and cross-species amplification,Conservation genetics,10(4):955-957
An H.S.,Lee J.H.,Noh J.K.,Kim H.C.,Park C.J.,Min B.H.,and Myeong J.I.,2010,Ten new microsatellite markers in cutlassfish Trichiurus lepturus derived from an enriched genomic library,Animal Cells and Systems,14(3):169-174
Bi J.Z.,Shao C.W.,Miao G.D.,Ma H.Y.,and Chen S.L.,2009,Isolation and characterization of 12 microsatellite loci from cutlassfish(Trichiurus haumela),Conservation Genetics,10(4):1171-1173
Botstein D.,White R.L.,Skolnick M.,and Davis R.W.,1980,Construction of a genetic linkage map in man using restriction fragment length polymorphisms,American Journal of Human Genetics,32(3):314-331
Carreras-Carbonell J.,Macpherson E.,and Pascual M.,2008,U-tility of pairwise mt DNA genetic distances for predicting cross-species microsatellite amplification and polymorphism success in fishes,Conservation Genetics,9(1):181-190
Castoe T.A.,Streicher J.W.,Meik J.M.,Ingrasci M.J.,Poole A.W.,De Koning A.P.J.,Campbell J.A.,Parkinson C.L.,Smith E.N.,and Pollock D.D.,2012,Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related species,Molecular Ecology Resources,12(6):1105-1113
Chakravarty M.S.,Pavani B.,and Ganesh P.R.C.,2013,Gonado-somatic index and fecundity studies in two species of ribbon fishes,Trichiurus lepturus(Linnaeus,1758)and Lepturacanthus savala(Cuvier,1829)off Visakhapatnam,east coast of India,Indian Journal of Fisheries,60(2):163-165
Dewoody J.A.,and Avise J.C.,2000,Microsatellite variation in marine,freshwater and anadromous fishes compared with other animals,Journal of Fish Biology,56(3):461-473
Gemayel R.,Cho J.,Boeynaems S.,and Verstrepen K.J.,2012,Beyond junk-variable tandem repeats as facilitators of rapid evolution of regulatory and coding sequences,Genes,3(3):461-480
Grover A.,and Sharma P.C.,2016,Development and use of molecular markers:past and present,Critical Reviews in Biotechnology,36(2):290-302
Guo Y.S.,Liu X.M.,Wang Z.D.,Lu H.S.,and Liu C.W.,2014,Isolation and characterization of microsatellite DNA loci from Naihai cutlassfish(Trichiurus nanhaiensis),Journal of genetics,91(3):1-4
He P.,1998,Abundance,polymorphism and applications of microsatellite in eukaryote,Yichuan(Hereditas),20(4):42-47(何平,1998,真核生物中的微卫星及其应用,遗传,20(4):42-47)
Kalinowski S.T.,Taper M.L.,and Marshall T.C.,2007,Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment,Molecular Ecology,16(5):1099-1106
Li B.,Tian L.,Zhang J.,Huang L.,Han F.,Yan S.,Wang L.,Zheng H.,and Sun J.,2014,Construction of a high-density genetic map based on large-scale markers developed by specific length amplified fragment sequencing(SLAF-seq)and its application to QTL analysis for isoflavone content in Glycine max,BMC Genomics,15:1086
Li C.S.,1987,Trichiuroidei,In:Cheng Q.T.,and Zheng B.S.,(eds.),Systematic synopsis of Chinese fishes,Science Press,Beijing,China,pp.414-416(李春生,1987,带鱼亚目,见:成庆泰,郑葆珊,(编著),中国鱼类系统检索,科学出版社,中国,北京,pp.414-416)
Liu S.F.,Zu D.M.,Liu Q.,Dai F.Q.,Ma Q.,and Zhuang Z.M.,2015,Isolation and characterization of polymorphic microsatellite markers for Eupleurogrammus muticus,Conservation Genetics Resources,7(2):487-488
Nakamura I.,and Parin N.V.,1993,FAO species catalog.Snake mackerel and cutlass fishes of the world(Families Gempylidae and Trichiuridae).An annotated and illustrated catalog of the snake mackerel,snoeks,escolars,gem fishes,sack fishes,domine,oil fish,cutlassfishes,scabbar fishes,hairtail and frostfishes know to date,Fao Fish Synop.,82(82):1-14
Nazeer R.A.,and Deeptha R.,2013,Antioxidant activity and amino acid profiling of protein hydrolysates from the skin of Sphyraena barracuda and Lepturacanthus savala,International Journal of Food Properties,16(3):500-511
Nei M.,Maruyama T.,and Chakraborty R.,1975,The bottleneck effect and genetic variability in populations,Evolution,29(1):1-10
Niu S.,Liu Y.,Qin C.,Wang X.,and Wu R.,2017,The complete mitochondrial genome and phylogenetic analysis of Lateolabrax maculatus(Perciformes,Moronidae),Mitochondrial DNA Part A,28(2):173-175
Memon K.H.,Liu Q.,Kalhoro M.A.,Chang M.S.,Baochao L.,Memon A.M.,Hyder S.,and Tabassum S.,2016,Growth and Mortality Parameters of Hairtail Lepturacanthus savala from Pakistan Waters,Pakistan Journal of Zoology,48(3):829-829
Pemberton J.M.,Slate J.,Bancroft D.R.,and Barrett J.A.,1995,Nonamplifying alleles at microsatellite loci:a caution for parentage and population studies,Molecular Ecology,4(2):249
Primmer C.R.,Moller A.P.,and Ellegren H.,1996,A wide-range survey of cross-species microsatellite amplification in birds,Molecular Ecology,5:365-378
Primmer C.R.,Painter J.N.,Koskinen M.T.,Palo J.U.,and MerilJ.,2005,Factors affecting avian cross-species microsatellite amplification,Journal of Avian Biology,36(4):348-360
Rizvi F.A.,Deshmukh V.D.,and Chakraborty S.K.,2010,Stock assessment of Lepturacanthus savala(Cuvier,1829)along north-west sector of Mumbai coast in Arabian Sea,Indian Journal of Fisheries,57(2):1-6
Rousset F.,2008,genepop'007:a complete re-implementation of the genepop software for Windows and Linux,Molecular E-cology Resources,8(1):103-106
Saha S.,and Subhedar N.,2011,Calcitonin-like immunoreactivity in the subcommissural organ-Reissner's fiber complex of some freshwater and marine teleosts,Journal of Chemical Neuroanatomy,41(2):122-128
Sambrook J.,and Russell D.W.,eds.,Huang P.T.,et al.,trans.,2002,Molecular cloning:A laboratory manual,Third edition,Science Press,Beijing,China,pp.463-471(萨姆布鲁克J.,拉塞尔D.W.,编著,黄培堂等,主译,2002,分子克隆实验指南,第三版,科学出版社,北京,pp.463-471)
Schuelke M.,2000,An economic method for the fluorescent labeling of PCR fragments,Naturebiotechnology,18(2):233-234
Sun X.,Liu D.,Zhang X.,Li W.,Liu H.,Hong W.,Jiang C.,Guan N.,Ma C.,Zeng H.,Xu C.,Song J.,Huang L.,Wang C.,Shi J.,Wang R.,Zheng X.,Lu C.,Wang X.,and Zheng H.,2013,SLAF-seq:an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing,Plo S One,8(3):e58700
Tzeng C.H.,and Chiu T.S.,2012,DNA barcode-based identification of commercially caught cutlassfishes(Family:Trichiuridae)with a phylogenetic assessment,Fisheries Research,s127-128(9):176-181
Umino T.,Ueno K.,Mihara T.,Koike M.,Watanabe M.,Syazni A.,Ishitani M.,and Ohara K.,2013,Isolation of eleven polymorphic microsatellite loci for the endangered Sillago parvisquamis and cross-species amplification with Sillago japonica,Conservation Genetics Resources,5(3):771-773
Van Oosterhout C.,Hutchinson W.F.,Wills D.P.M.,and Shipley P.,2004,MICRO-CHECKER:software for identifying and correcting genotyping errors in microsatellite data,Molecular Ecology Notes,4(3):535-538
Varshney R.K.,Graner A.,Sorrells M.E.,2005,Genic microsatellite markers in plants:features and applications,Trends in Biotechnology,23(1):48-55
Carneiro V.M.L.,Luciane S.,Lima D.A.,Freitas M.C.D.,2016,Microsatellite markers:what they mean and why they are so useful,Genetics and Molecular Biology,39(3):312-328
Wang H.Y.,Dong C.A.,and Lin H.C.,2017,DNA barcoding of fisheries catch to reveal composition and distribution of cutlassfishes along the Taiwan coast,Fisheries Research,187:103-109
Wu R.X.,Zhang H.R.,Niu S.F.,Zhai Y.,and Liu X.F.,2016,Development of polymorphic microsatellites for Sillago sihama based on next-generation sequencing and transferability to Sillago japonica,Genetics and molecular research,15(4):gmr15049046
Yang W.,Feng F.,and Yue G.,2007,Isolation and characterization of microsatellites from a marine foodfish species ribbonfish Trichiurus haumela,Molecular Ecology Notes,7(5):781-783
Yu H.T.,Lee Y.J.,Huang S.W.,and Chiu T.S.,2002,Genetic analysis of the populations of Japanese anchovy(Engraulidae:Engraulis japonicus)using microsatellite DNA,Marine Biotechnology,4(5):471-479
Zhang H.R.,Niu S.F.,Wu R.X.,Zhai Y.,and Tian L.T.,2016,Development and characterization of 26 polymorphic microsatellite markers in Lateolabrax maculatus and crossspecies amplification for the phylogenetically related taxa,Biochemical Systematics and Ecology,66:326-330
Zhao L.,Shao C.W.,Liao X.L.,and Chen S.L.,2009,Isolation and characterization of polymorphic microsatellite loci from a dinucleotide-enriched genomic library of seven-band grouper(Epinephelus septemfasciatus)and cross-species amplification,Conservation genetics,10(4):955-957