口虾蛄转录组微卫星标记开发
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摘要
采用高通量测序技术获得的口虾蛄转录组测序数据,筛选具有多态性的SSR标记。结果共获得87 355条Unigene,67 657个微卫星位点,其中双碱基重复和三碱基重复的SSR较多,分别有30 235个和17 590个,占总数的44.69%和26%。获得230种重复类型,其中双碱基中的AC/GT重复和三碱基中的AGG/CCT重复是重复次数较多的重复类型。从中挑选碱基重复次数较多的微卫星引物共50对进行合成。用北海24个口虾蛄样品进行验证,获得条带清晰和多态性好的引物6对。6个微卫星位点在口虾蛄北海群体的遗传多样性分析中均表现出较高的多态性。平均有效等位基因数(k)为5.17,观测杂合度(Ho)为0.437 2,平均期望杂合度(He)为0.672 4,多态信息含量为(PIC)为0.602 3,这说明开发的6对SSR标记均适合群体遗传多样性研究。为口虾蛄进一步遗传多样性的研究奠定了基础。
This paper, we use high-throughput sequencing technology to obtain the sequencing data of the Oratosquilla oratoria transcriptome and filter and develop polymorphic SSR markers. A total of 87 355 unigene were obtained, include 67 657 microsatellite loci, which mostly SSRs were Di-nucleotide repeats and Tri-nucleotide repeats, with 30 235 and 17 590, respectively. A total of 230 types of repetition were obtained. In Dinucleotide SSR repeats, the most repeated type was AC/GT repetition In the Tri-nucleotide repeats of SSR, the repeated dominant type is AGG/CCT repetition. The 50 pairs of microsatellite primers with high number of base repetitions were selected to synthesize. A total of 6 pairs of SSR markers with clear bands and polymorphisms were identified by using 24 samples from Beihai. 6 microsatellite loci showed high polymorphism in the genetic diversity analysis of Beihai population.The average effective number of allele was 5.17, expected het-erozygosities and Average observed(He and Ho) were 0.437 2 and 0.672 4. Average polymorphism information content(PIC) is 0.602 3, result showed all of the 6 pairs of SSR markers were suitable for population genetic diversity. It lays a foundation for the further study of genetic diversity of O. oratoria.
This paper, we use high-throughput sequencing technology to obtain the sequencing data of the Oratosquilla oratoria transcriptome and filter and develop polymorphic SSR markers. A total of 87 355 unigene were obtained, include 67 657 microsatellite loci, which mostly SSRs were Di-nucleotide repeats and Tri-nucleotide repeats, with 30 235 and 17 590, respectively. A total of 230 types of repetition were obtained. In Dinucleotide SSR repeats, the most repeated type was AC/GT repetition In the Tri-nucleotide repeats of SSR, the repeated dominant type is AGG/CCT repetition. The 50 pairs of microsatellite primers with high number of base repetitions were selected to synthesize. A total of 6 pairs of SSR markers with clear bands and polymorphisms were identified by using 24 samples from Beihai. 6 microsatellite loci showed high polymorphism in the genetic diversity analysis of Beihai population.The average effective number of allele was 5.17, expected het-erozygosities and Average observed(He and Ho) were 0.437 2 and 0.672 4. Average polymorphism information content(PIC) is 0.602 3, result showed all of the 6 pairs of SSR markers were suitable for population genetic diversity. It lays a foundation for the further study of genetic diversity of O. oratoria.
引文
[1] MIESFELD R, KRYSTAL M, AMHEIM N. A member of a new repeated sequence family which is conserved throughout eucaryotic evolution is found between the humanδandβglobin genes[J]. Nucleic Acids Research, 1981, 9(22):5 931-5 947.
[2] BRINKMANN B, KLINTSCHAR M, NEUHUBER F, et al. Mutation Rate in Human Microsatellites:Influence of the Structure and Length of the Tandem Repeat[J]. American Journal of Human Genetics, 1998, 62(6):1 408-1 415.
[3]杨兵,林琳,李纯厚,等.基于高通量测序的二长棘鲷微卫星标记开发与评价[J].南方水产科学, 2015, 11(4):116-120.
[4]许益铵,柳敏海,油九菊,等.舟山附近海域3个大黄鱼养殖群体遗传多样性的微卫星分析[J].浙江海洋学院学报(自然科学版), 2014, 33(2):140-146.
[5]蔡磊,余露军,陈小曲,等.诸氏鲻虾虎鱼转录组序列中微卫星标记的初步筛选及特征分析[J].生物技术通报, 2015, 31(9):146-151.
[6]冯娜娜.拟穴青蟹基于转录组的分子标记筛选与遗传规律分析[D].上海:上海海洋大学, 2013.
[7]相瑜,任丽平,王日昕.三疣梭子蟹微卫星标记的筛选及特征分析[J].浙江海洋学院学报(自然科学版), 2013,(5):421-426.
[8]李威,赵姗,焦海峰,等.黄口荔枝螺转录组数据的微卫星标记开发与分析[J].海洋科学, 2015, 39(11):61-67.
[9]魏崇德.浙江动物志甲壳类[M].杭州:浙江科学技术出版社, 1991:74-94.
[10]刘瑞玉,王永良.南海虾蛄科及猛虾蛄科(甲壳动物口足目)二新种[J].海洋与湖沼, 1998, 29(6):588-596.
[11]王春琳,徐善良,梅文骧,等.口虾蛄的生物学基本特征[J].浙江水产学院学报, 1996, 15(1):60-62.
[12]谷德贤,刘茂利.渤海湾近海海域口虾蛄群体结构及资源量分析[C]//中国水产学会学术年会. 2010.
[13] ZHANG Daizhen, DING Ge, GE Baoming, et al. Development and characterization of microsatellite loci of Oratosquilla oratoria(Crustacea:Squillidae)[J]. Conservation Genetics Resources, 2012, 4(1):147-150.
[14] MARSHALL T C, SLATE J, KRUUK L, et al. Statistical confidence for likelihood-basedpaternity inference in natural populations[J]. Molecular Ecology, 1998, 7:639-655.
[15]董鑫.基于线粒体COI基因序列研究口虾蛄群体的遗传多样性及微卫星引物的开发[D].大连:大连海洋大学, 2014.
[16] NICOT N, CHIQUET V, GANDON B, et al. Study of simple sequence repeat(SSR)markers from wheat expressed sequence tags(ESTs)[J]. Theoretical&Applied Genetics, 2004, 109(4):800-805.
[17]宋春妮,李健,刘萍,等.日本蟳4个野生群体遗传多样性的微卫星分析[J].水产学报, 2011, 35(7):985-991.
[18]许晓军,张海琪,张超,等.中华鳖表达序列标签资源中的微卫星信息分析[J].经济动物学报, 2013, 17(1):15-18.
[2] BRINKMANN B, KLINTSCHAR M, NEUHUBER F, et al. Mutation Rate in Human Microsatellites:Influence of the Structure and Length of the Tandem Repeat[J]. American Journal of Human Genetics, 1998, 62(6):1 408-1 415.
[3]杨兵,林琳,李纯厚,等.基于高通量测序的二长棘鲷微卫星标记开发与评价[J].南方水产科学, 2015, 11(4):116-120.
[4]许益铵,柳敏海,油九菊,等.舟山附近海域3个大黄鱼养殖群体遗传多样性的微卫星分析[J].浙江海洋学院学报(自然科学版), 2014, 33(2):140-146.
[5]蔡磊,余露军,陈小曲,等.诸氏鲻虾虎鱼转录组序列中微卫星标记的初步筛选及特征分析[J].生物技术通报, 2015, 31(9):146-151.
[6]冯娜娜.拟穴青蟹基于转录组的分子标记筛选与遗传规律分析[D].上海:上海海洋大学, 2013.
[7]相瑜,任丽平,王日昕.三疣梭子蟹微卫星标记的筛选及特征分析[J].浙江海洋学院学报(自然科学版), 2013,(5):421-426.
[8]李威,赵姗,焦海峰,等.黄口荔枝螺转录组数据的微卫星标记开发与分析[J].海洋科学, 2015, 39(11):61-67.
[9]魏崇德.浙江动物志甲壳类[M].杭州:浙江科学技术出版社, 1991:74-94.
[10]刘瑞玉,王永良.南海虾蛄科及猛虾蛄科(甲壳动物口足目)二新种[J].海洋与湖沼, 1998, 29(6):588-596.
[11]王春琳,徐善良,梅文骧,等.口虾蛄的生物学基本特征[J].浙江水产学院学报, 1996, 15(1):60-62.
[12]谷德贤,刘茂利.渤海湾近海海域口虾蛄群体结构及资源量分析[C]//中国水产学会学术年会. 2010.
[13] ZHANG Daizhen, DING Ge, GE Baoming, et al. Development and characterization of microsatellite loci of Oratosquilla oratoria(Crustacea:Squillidae)[J]. Conservation Genetics Resources, 2012, 4(1):147-150.
[14] MARSHALL T C, SLATE J, KRUUK L, et al. Statistical confidence for likelihood-basedpaternity inference in natural populations[J]. Molecular Ecology, 1998, 7:639-655.
[15]董鑫.基于线粒体COI基因序列研究口虾蛄群体的遗传多样性及微卫星引物的开发[D].大连:大连海洋大学, 2014.
[16] NICOT N, CHIQUET V, GANDON B, et al. Study of simple sequence repeat(SSR)markers from wheat expressed sequence tags(ESTs)[J]. Theoretical&Applied Genetics, 2004, 109(4):800-805.
[17]宋春妮,李健,刘萍,等.日本蟳4个野生群体遗传多样性的微卫星分析[J].水产学报, 2011, 35(7):985-991.
[18]许晓军,张海琪,张超,等.中华鳖表达序列标签资源中的微卫星信息分析[J].经济动物学报, 2013, 17(1):15-18.
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