几种双壳贝类ITS区序列分析与遗传多样性研究
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摘要
采用聚合酶链式反应(PCR)对采自日本半岛、俄罗斯海参葳地区以及中国威海等三个自然群体的魁蚶样本的核糖体RNA两个转录间区域(ITS-1和ITS-2)进行了扩增，电泳检测在500bp左右都得到了清晰的扩增产物条带。PCR产物纯化后与T载体连接，进行了克隆、测序。分别得到了长度为421bp和495bp(不含引物)的碱基序列，其中A，C，G，T含量分别为21.85％，25.87％，27.23％，25.04％；26.66％，22.18％，24.04％，27.13％。ITS2片段序列中的AT含量明显高于ITS1。魁蚶7个个体ITS2片段序列经Gendoc软件排序后检测到两个多态位点，3种单倍型；魁蚶7个个体间的遗传距离为0-0.2％。魁蚶16个个体的ITS1片段去除引物排序后检测到了9个多态性核苷酸位点，共7种单倍型；其中发生转换突变的核苷酸位点数为4个，颠换突变位点2个。在三个群体中，通过计算不同个体间的遗传距离构建NJ和MP系统树，16个个体没有明显的聚类现象。ITS1和ITS2片段的在魁蚶中的成功扩增，再次证实两对引物在贝类中通用性良好，而且对小样本量中个体间两个片段的遗传特征的分析比较，为该区域在魁蚶群体遗传多样性研究中的应用提供了基础并展现了良好的应用前景。
通过PCR扩增得到了太平洋牡蛎、近江牡蛎、大连湾牡蛎、褶牡蛎、美洲牡蛎(外群)五种牡蛎的ITS1和ITS2及部分核糖体RNA基因片段，通过序列测定及碱基相应长度处理得到了403-524bp长度的ITS1片段和585-651bp的ITS2片段。五种牡蛎的33个个体得到的ITS1片段的32种单倍型，检测到193个多态位点(包括插入／缺失多态位点)，其中95个(49.2％)为美洲牡蛎与其他四种牡蛎之间特有的变异位点；我国四种牡蛎比较多态位点有98个。五种牡蛎的21个个体得到的ITS2片段的21种单倍型，共检测到331个多态位点(包括插入／缺失多态位点)，其中210个(63.4％)为美洲牡蛎与其他四种牡蛎之间特有的变异位点；我国四种牡蛎所有的多态位点有121个。用MEGA2软件计算出ITS1和ITS2片段不同单倍型间的遗传距离构建NJ和MP系统树，两个片段得到的结果一致：太平洋牡蛎和大连湾牡蛎牢固聚为一支，褶牡蛎和近江牡蛎牢固聚为另一支。分析表明大连湾牡蛎和太平洋牡蛎应为同一种类；褶牡蛎可能是生活与较
几种双壳贝类ITs区序列分析与遗传多样性研究
高盐度生境的近江牡蜗，这一点有待于进一步的工作证实。
PCR扩增来自黄渤海(青岛和大连)、东海(宁波)和东南沿海(厦门)四种小型
牡砺的ITSI和ITSZ片段，序列测定及碱基相应长度处理得到493一510的ITSI片段和
585一65lbp的ITSZ片段。四组小型牡蜘38个个体的ITSI序列中检测到36种单倍型，
81个多态位点;24个个体的ITSZ序列中检测到24种单倍型，120个多态位点。通过计
算ITSI和ITSZ序列不同单倍型间的遗传距离构建NJ和MP系统树，两个片段得到的结
果基本一致。宁波组群的牡蝠单独成一支，其它三个组群的牡蝠聚为一支，结果显示，
我国沿海这四种均被称作“褶牡蜘”的小型牡蜗，并非全部都是褶牡蜗，应属于不同种
类。从四个地理位置的小型牡蜘、太平洋牡蜘、大连湾牡砺、近江牡蜘的ITSI和工TSZ
序列的单倍型中随机选取2一3个单倍型，计算单倍型间的遗传距离，并以美洲牡蜘为外
群构建NJ和MP系统树。结果显示宁波的小型牡蜗与近江牡蜘亲缘关系较近;而青岛、
大连、厦门三地的小型牡砺则与大连湾牡砺或太平洋牡蝠亲缘关系较近。综合本文研究
结果和实验室已有的线粒体基因片段的研究结果得出:青岛和大连的小型牡砺可能是大
连湾或太平洋牡蜘早期个体;因两方面研究结果不同，对厦门组群的分类地位尚有待于
研究。
Robosomal RNA gene internal Inscribed spacers ITS1 and ITS2 fragments of bloody clam (Scapharca broughtonif) coming from Japanese, Russion and Wei Hai city of China were amplified via Polymerase Chain Reaction. The PCR products were ligated into T-vector, cloned and sequenced. 421bp and 495bp nucleotide sequences were got respectively, and the contents of A, C, G, T is 21.85%, 25.87%, 27.23%, 25.04% in ITS1; 26.66%, 22.18%, 24.04%, 27.13% in ITS2. The content of A+T in ITS2 is higher than that in ITS1 obviously. 2 polymorphic sites and 3 haplotypes were found in ITS2 sequences from 7 bloody clams. Genetic distance between 7 clams is 0-0.2%. 9 polymorphic sites and 7 haplotypes were found in ITS1 sequences from 16 bloody clams, and 4 transition sites and 2 transvertion sites were involved. NJ and MP molecular phylogenetic trees were constructed which showed that there is no obvious clustering phenomenon between all the 16 specimens coming from different geographic populations. The primers of ITS-1 and ITS-2 p
roved to be very universal in a variety of mollusk species. The potential uses of the two sequences for genetic variation studies and phylogenetic research in Bloody Clam species were discussed.
It has been presumed that there are four common Crassostrea oyster species along the coast of China: Pacific oyster (Crassostrea gigas), Zhe oyster (C.plicacula), Suminoe oyster(C. rivularis) and Dalianwan oyster (C. talienwhanensis). Classification and species identification of these oysters have been difficult because of morphological plasticity. In this article, phylogenetic analysis was performed to clarify taxonomic status of these species using ribosomal Internal Transcribed Spacer regions ITS-1 and ITS-2. Nucleotide sequences of 403-524bp ITS1 and 585-65 Ibp ITS2 after excluding the primer combined sequences and partial sequences at the two end of the fragments.32 haplotypes and 193 polymorphic sites were found in ITS1 sequences of 33 specimens coming from 5 Crassostrea oyster species (including C. virginica as outgroup) , in which 98 polymorphic sites were found in 4 Chinese oyster species. 21 haplotypes and 331 polymorphic sites were found in ITS2 sequences of 21 specimens coming from 5 Crassostrea
oyster species (including C. virginica as outgroup), in which 121 polymorphic sites were found in 4 Chinese oyster species. The divergence between C. gigas and C. talienwhanensis was very low, as was that between C. plicatula and C. rivularis . Phylogenetic analysis showed that haplotypes of C gigas and C. talienwhanensis clustered in one clade and those of C. plicatula and C. ariakensis in another one. Our molecular data suggests that C. gigas and C. talienwhanensis may be the same species. However, the lack of divergence between C. plicatula and C, rivularis samples may indicate that the C. plicatula specimens we sampled
could actually be a morph of C. rivularis living in higher salinity habitats. More work is needed for confirmation.
It has been presumed that there are several common Crassostrea oyster species and they are difficult to classify and identify clearly because of their morphological plasticity. There exists a lot of dispute especially on classification of C.plicacula. In this paper, phylogenetic analysis was performed to identify these small oyster species from different sites along the coast of China (QingDao, DaLian, NingBo, XiaMen) using ITS1 and ITS2 fragments. 493-510 bp ITS1 sequence and 585bp-651bp ITS2 sequence were amplified and sequenced. 36 haplotypes and 81 polymorphic sites were found in ITS1 sequences; 24 haplotypes and 120 polymorphic sites were found in ITS2 sequences. Phylogenetic analysis showed that haplotypes of QD (QingDao), DL(DaLian), XM(XiaMen) clustered in one clade and those of NB (NingBo) in another one, which showed the small oysters called "Zhe oyster" coming from different geographic sites may be different species. 2 or 3 haplotypes were chosen to do phylogenetic analysis based on the two fragme
nts ITS1 and ITS2 between the small oysters mentioned above, C. gigas,
通过PCR扩增得到了太平洋牡蛎、近江牡蛎、大连湾牡蛎、褶牡蛎、美洲牡蛎(外群)五种牡蛎的ITS1和ITS2及部分核糖体RNA基因片段，通过序列测定及碱基相应长度处理得到了403-524bp长度的ITS1片段和585-651bp的ITS2片段。五种牡蛎的33个个体得到的ITS1片段的32种单倍型，检测到193个多态位点(包括插入／缺失多态位点)，其中95个(49.2％)为美洲牡蛎与其他四种牡蛎之间特有的变异位点；我国四种牡蛎比较多态位点有98个。五种牡蛎的21个个体得到的ITS2片段的21种单倍型，共检测到331个多态位点(包括插入／缺失多态位点)，其中210个(63.4％)为美洲牡蛎与其他四种牡蛎之间特有的变异位点；我国四种牡蛎所有的多态位点有121个。用MEGA2软件计算出ITS1和ITS2片段不同单倍型间的遗传距离构建NJ和MP系统树，两个片段得到的结果一致：太平洋牡蛎和大连湾牡蛎牢固聚为一支，褶牡蛎和近江牡蛎牢固聚为另一支。分析表明大连湾牡蛎和太平洋牡蛎应为同一种类；褶牡蛎可能是生活与较
几种双壳贝类ITs区序列分析与遗传多样性研究
高盐度生境的近江牡蜗，这一点有待于进一步的工作证实。
PCR扩增来自黄渤海(青岛和大连)、东海(宁波)和东南沿海(厦门)四种小型
牡砺的ITSI和ITSZ片段，序列测定及碱基相应长度处理得到493一510的ITSI片段和
585一65lbp的ITSZ片段。四组小型牡蜘38个个体的ITSI序列中检测到36种单倍型，
81个多态位点;24个个体的ITSZ序列中检测到24种单倍型，120个多态位点。通过计
算ITSI和ITSZ序列不同单倍型间的遗传距离构建NJ和MP系统树，两个片段得到的结
果基本一致。宁波组群的牡蝠单独成一支，其它三个组群的牡蝠聚为一支，结果显示，
我国沿海这四种均被称作“褶牡蜘”的小型牡蜗，并非全部都是褶牡蜗，应属于不同种
类。从四个地理位置的小型牡蜘、太平洋牡蜘、大连湾牡砺、近江牡蜘的ITSI和工TSZ
序列的单倍型中随机选取2一3个单倍型，计算单倍型间的遗传距离，并以美洲牡蜘为外
群构建NJ和MP系统树。结果显示宁波的小型牡蜗与近江牡蜘亲缘关系较近;而青岛、
大连、厦门三地的小型牡砺则与大连湾牡砺或太平洋牡蝠亲缘关系较近。综合本文研究
结果和实验室已有的线粒体基因片段的研究结果得出:青岛和大连的小型牡砺可能是大
连湾或太平洋牡蜘早期个体;因两方面研究结果不同，对厦门组群的分类地位尚有待于
研究。
Robosomal RNA gene internal Inscribed spacers ITS1 and ITS2 fragments of bloody clam (Scapharca broughtonif) coming from Japanese, Russion and Wei Hai city of China were amplified via Polymerase Chain Reaction. The PCR products were ligated into T-vector, cloned and sequenced. 421bp and 495bp nucleotide sequences were got respectively, and the contents of A, C, G, T is 21.85%, 25.87%, 27.23%, 25.04% in ITS1; 26.66%, 22.18%, 24.04%, 27.13% in ITS2. The content of A+T in ITS2 is higher than that in ITS1 obviously. 2 polymorphic sites and 3 haplotypes were found in ITS2 sequences from 7 bloody clams. Genetic distance between 7 clams is 0-0.2%. 9 polymorphic sites and 7 haplotypes were found in ITS1 sequences from 16 bloody clams, and 4 transition sites and 2 transvertion sites were involved. NJ and MP molecular phylogenetic trees were constructed which showed that there is no obvious clustering phenomenon between all the 16 specimens coming from different geographic populations. The primers of ITS-1 and ITS-2 p
roved to be very universal in a variety of mollusk species. The potential uses of the two sequences for genetic variation studies and phylogenetic research in Bloody Clam species were discussed.
It has been presumed that there are four common Crassostrea oyster species along the coast of China: Pacific oyster (Crassostrea gigas), Zhe oyster (C.plicacula), Suminoe oyster(C. rivularis) and Dalianwan oyster (C. talienwhanensis). Classification and species identification of these oysters have been difficult because of morphological plasticity. In this article, phylogenetic analysis was performed to clarify taxonomic status of these species using ribosomal Internal Transcribed Spacer regions ITS-1 and ITS-2. Nucleotide sequences of 403-524bp ITS1 and 585-65 Ibp ITS2 after excluding the primer combined sequences and partial sequences at the two end of the fragments.32 haplotypes and 193 polymorphic sites were found in ITS1 sequences of 33 specimens coming from 5 Crassostrea oyster species (including C. virginica as outgroup) , in which 98 polymorphic sites were found in 4 Chinese oyster species. 21 haplotypes and 331 polymorphic sites were found in ITS2 sequences of 21 specimens coming from 5 Crassostrea
oyster species (including C. virginica as outgroup), in which 121 polymorphic sites were found in 4 Chinese oyster species. The divergence between C. gigas and C. talienwhanensis was very low, as was that between C. plicatula and C. rivularis . Phylogenetic analysis showed that haplotypes of C gigas and C. talienwhanensis clustered in one clade and those of C. plicatula and C. ariakensis in another one. Our molecular data suggests that C. gigas and C. talienwhanensis may be the same species. However, the lack of divergence between C. plicatula and C, rivularis samples may indicate that the C. plicatula specimens we sampled
could actually be a morph of C. rivularis living in higher salinity habitats. More work is needed for confirmation.
It has been presumed that there are several common Crassostrea oyster species and they are difficult to classify and identify clearly because of their morphological plasticity. There exists a lot of dispute especially on classification of C.plicacula. In this paper, phylogenetic analysis was performed to identify these small oyster species from different sites along the coast of China (QingDao, DaLian, NingBo, XiaMen) using ITS1 and ITS2 fragments. 493-510 bp ITS1 sequence and 585bp-651bp ITS2 sequence were amplified and sequenced. 36 haplotypes and 81 polymorphic sites were found in ITS1 sequences; 24 haplotypes and 120 polymorphic sites were found in ITS2 sequences. Phylogenetic analysis showed that haplotypes of QD (QingDao), DL(DaLian), XM(XiaMen) clustered in one clade and those of NB (NingBo) in another one, which showed the small oysters called "Zhe oyster" coming from different geographic sites may be different species. 2 or 3 haplotypes were chosen to do phylogenetic analysis based on the two fragme
nts ITS1 and ITS2 between the small oysters mentioned above, C. gigas,
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