栉孔扇贝Chlamys farreri和特蛎Crassostrea的遗传多样性研究
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摘要
栉孔扇贝(Chlamys farreri)主要分布在我国北部沿海，极少数向南到东海，日本北海道以南及朝鲜西部沿海也有分布。在栉孔扇贝的养殖技术、生理生态等方面进行了广泛研究(王清印，2000，杨爱国，2002，周毅，2003)，取得了许多成果。在栉孔扇贝的遗传学分子生物学研究方面也作了许多工作(宋林生，2002；赵洋等，2002；李红蕾等，2002，潘洁等，2002)；在各种DNA多态分析技术中，DNA序列分析是遗传多样性和系统进化研究最有效的方法之一，但目前还没有栉孔扇贝DNA序列分析方面的研究。本研究利用DNA序列分析法进行了以下三个方面的研究：(1)研究了栉孔扇贝核基因片段ITS-1和ITS-2序列，探讨了栉孔扇贝该片段的特点，并对其进一步的应用进行了探讨；(2)对栉孔扇贝和海湾扇贝(Argopecten irradians)的线粒体16S rRNA基因片段的特点和同源性进行了比较；(3)利用线粒体16S rRNA基因片段对不同群体的栉孔扇贝的遗传多样性及群体的遗传结构进行了研究分析。希望丰富栉孔扇贝群体的遗传多样性研究内容，为今后的遗传育种和种质资源利用及管理提供理论基础。
首先利用两对通用引物ITS-1A／B和ITS-2A／B对采自青岛的栉孔扇贝进行PCR扩增。引物序列为：ITS-1A／1B：5’-GGTTCTGTAGGTGAACCTGC-3’／5’-CTGCGTTCTTCATCGACCC-3’；ITS-2A／2B：5’-GTCGATGAAGAACGCAG-3’／5’-GCTCTTCCCGCTT CACTCG-3’。PCR扩增得到了340bp(ITS-1，AF245687)和510bp(ITS-2，AF245688)的PCR产物。两种序列的碱基组成没有明显的差别，其A，T，G，C含量在ITS-1为32.06％，20.59％，22.35％和25.00％；在ITS-2为30.00％，21.37％，24.12％和24.51％，总的A+T含量略高于G+C的含量。本实验扩增所用引物表现出了良好的通用性，表明这两对引物的结合序列高度保守，结合前人研究的结果，可以推测该引物在贝类中通用性较强。
栉孔扇贝和牡蝎的遗传多样性研究
对栉孔扇贝和海湾扇贝的线粒体165 rRNA基因片段进行了PCR扩增，分别得到
634bp(AF526247)和542 bp(AF526239)长度的碱基序列，其A，T，G，C含量分别为
25.08%、29.65%、27.60%和17.67%(栉孔扇贝)，25.65%、29.52%、27.31%和17.53%
(海湾扇贝)。对位排序结果表明，两者的扩增片段其长度相差92bp，还有80个核
昔酸位点存在转换或颠换，同源性为68.1%，造成扩增片段长度差异的几个小区段的
缺失/插入出现在扩增片段中部约13Obp范围内。这表明，分别分布于太平洋西北部
沿海和大西洋北部沿海的两种扇贝在进化上分歧较早。
用线粒体165 rRNA基因片段研究了栉孔扇贝大连(DL)、烟台(YT)、荣成(RC)、
青岛(QD)、韩国(SK)和日本(JP)六个群体的遗传多样性，并探讨了栉孔扇贝各群体
的遗传结构。所有47个个体中得到了长度为592bp的165 rRNA基因片段序列，把所
有个体的165 rRNA基因片段序列用CIUSTALX(Thompson et al.1997)进行排序对
比，用ARLEQUIN(Sehneider et al.，2000)计算群体特异性、单倍型多样性(Nei and
Taj ima，1981)和核昔酸多样性(Nei，1987)。分析表明有31个核昔酸变异位点，共
23个单倍型。单倍型A和B为最常见单倍型，存在于所有群体，其频率分别为 29.8%
和17%，基于所有单倍型之间核昔酸歧异的网状图表明:大多数单倍型是互相密切
关联的，最常见的单倍型A居于辐射状网状图的中央。许多邻近的单倍型互相只有一
个核昔酸差异，有些单倍型则与A有两个核昔酸差异。EXACT TEXT单倍型频率分布
分析显示，在所有样品中单倍型频率分布没有明显差异(P=0 .925)，而且在所有两两
群体之间也无明显差异。分子变异分析表明:绝大多数(99.65%)的遗传变异是群体
内的变异。群体间无明显变异，只有少于2%的变异来源于不同地区的差异，而且这
部分变异不明显(P=0 .195)。在各群体的单倍型多样性、核昔酸多样性和其他群体多
样性指数中，SK群体的指数最大，其次为YT群体。YT群体为中国四个群体中各项值
最高的群体，DL为最小。群体间核昔酸分歧最大的各群体对之间的分歧值位于SK和
YT之间，最小的出现在DL和JP之间，而这两群体间的地理距离最大。结果表明，
栉孔扇贝165 rRNA基因片段显示出了相当程度的变异，虽然165 rRNA基因一般来
说是线粒体中基因组内变异较低的区域，但YT群体最丰富的变异支持这一事实;从
上述结果看，烟台群体的种质基本没有受到影响，没有表现出遗传退化现象。从韩国
群体的14个多态位点和8个单倍型来看，是六个群体中最丰富的变异，考虑从韩国引
栉孔扇贝和牡蛹的遗传多样性研究
进亲贝应是可行的。
在所有海洋无脊椎动物中，牡砺是最常见、研究最多、也是形态变异最大的一类。
由于它们均沿海岸分布，并且有很大的形态变异，因而，人们甚至是海洋动物学家有
时都很难把它们区分开。从目前的研究结果可以看出，DNA序列分析方法特别是线
粒体片段的序列分析是遗传学及分子系统进化研究非常有用的工具。本项研究中应用
该技术方法，对太平洋牡砺(。“sostreag电闷s)的线粒体1 65 rRNA、Col基因片段进
行PCR扩增及序列分析:对太平洋牡砺核基因片段rrs一1和ITS一2片段的遗传特点进
行了初步研究;并利用165 rRNA和COI基
Occurring along the coast of northern China, South Korea, North Korea and Japan, the Chinese scallop (Chlamys farreri) has been one of the major species of the shellfish industry in the northern coast China for several decades. In recent years, however, scallop culture has been haunted by a high mortality problem. It is believed that the problem was caused by a combination of overcrowding N high summer temperature and deteriorating water quality. Additionally, one more possible reason for the problem to some extent, is that the scallop stock may be deteriorating genetically. Based upon this reason, refreshing scallop stock by introducing new stocks from other populations outside the coast of north China was considered. Consequently, investigation and evaluation on its stock structure throughout its geographic range are required.
For benthic marine species with pelagic larvae, it has been proposed that they have population genetic structures reflecting the dispersal capacity of larvae. Most of them are supposed to have less or little genetic structure reflecting the dispersal capacity of larvae. Mitochondrial DNA sequences (including 16S rDNA) were used for many of these studies. In C. farreri, this hypothesis has almost never been tested. So, this also lead to our interest to examine population genetic structure using mitochondrial gene sequence data, with two more population samples (Korea and Japan) as well as four samples from China, within its geographic range of the species.
Ribosomal Internal Transcribed Spacer Regions ITS-1 and ITS-2 in Scallop C. farreri were amplified via PCR, Fragments of the 16S rRNA gene and COI gene were amplified using two pairs of universal primers:
The PCR products of ITS-1 and ITS-2 fragments from Scallop C.farrei were ligated into T-vector, cloned and sequenced. 340 bp (ITS-1, AF245687 ) and 510 bp (ITS-2, AF245688) nucleotide sequences were got respectively, and the contents of A, T, G and C were 32.06%, 20.59%, 22.35% and 25.00% in ITS-1, 30.00%, 21.37%, 24.12% and 24.51% in ITS-2. The primers of ITS-1 and ITS-2 proved to be very universal in a variety of mollusk species.
Mitochondria! 16S rRNA gene fragments from Scallop C. farrei and Argopecten irradians were amplified via PCR. 634bp and 542bp nucleotide sequences were retrieved respectively. The content of A, T, G and C were 25.08%, 29.65%, 27.60% and 17.67% in C. farreri, 25.65%, 29.52%, 27.31% and 17.53% in A. irradians. Alignment indicated that the homology of two fragments was 68.1%, the nucleotide difference number was 80, and several small deletion/insertion sections, which contributed to length difference of the two fragments in two species, occurred in the middle of fragments (around 130bp) .
A 592 base pairs fragment of the mitochondrial 16S ribosomal RNA gene in 47 Zhikong scallop (C. farreri) specimens was sequenced in order to examine its intra-specific genetic variation and geographic structure. These samples were collected from six populations (four from China, and one each from South Korea and Japan respectively) across its range. Thirty-one nucleotide positions were found variable and twenty-three haplotypes were detected in all samples, which showed that more 16S rDNA variation existed in C. farreri when compared with several oyster species. Analysis at the intra-population level showed that the South Korea samples had the richest sequence diversity. However, analysis of haplotype frequency distribution and analysis of molecular variance (AMOVA) indicated that little geographic structure was present among all samples, and an absolute majority (99.65%) of the genetic variation was distributed within populations, suggesting that the populations in this study may belong to a single panmictic unit. Relative smaller distribution range and various currents may account for sufficient gene flow among these populations for this benthic species.
With 14 polymorphic sites and 8 hyplotypes, SK population showed the richest variation in all 6 populations, this may support the idea of stock introduction from South Ko
首先利用两对通用引物ITS-1A／B和ITS-2A／B对采自青岛的栉孔扇贝进行PCR扩增。引物序列为：ITS-1A／1B：5’-GGTTCTGTAGGTGAACCTGC-3’／5’-CTGCGTTCTTCATCGACCC-3’；ITS-2A／2B：5’-GTCGATGAAGAACGCAG-3’／5’-GCTCTTCCCGCTT CACTCG-3’。PCR扩增得到了340bp(ITS-1，AF245687)和510bp(ITS-2，AF245688)的PCR产物。两种序列的碱基组成没有明显的差别，其A，T，G，C含量在ITS-1为32.06％，20.59％，22.35％和25.00％；在ITS-2为30.00％，21.37％，24.12％和24.51％，总的A+T含量略高于G+C的含量。本实验扩增所用引物表现出了良好的通用性，表明这两对引物的结合序列高度保守，结合前人研究的结果，可以推测该引物在贝类中通用性较强。
栉孔扇贝和牡蝎的遗传多样性研究
对栉孔扇贝和海湾扇贝的线粒体165 rRNA基因片段进行了PCR扩增，分别得到
634bp(AF526247)和542 bp(AF526239)长度的碱基序列，其A，T，G，C含量分别为
25.08%、29.65%、27.60%和17.67%(栉孔扇贝)，25.65%、29.52%、27.31%和17.53%
(海湾扇贝)。对位排序结果表明，两者的扩增片段其长度相差92bp，还有80个核
昔酸位点存在转换或颠换，同源性为68.1%，造成扩增片段长度差异的几个小区段的
缺失/插入出现在扩增片段中部约13Obp范围内。这表明，分别分布于太平洋西北部
沿海和大西洋北部沿海的两种扇贝在进化上分歧较早。
用线粒体165 rRNA基因片段研究了栉孔扇贝大连(DL)、烟台(YT)、荣成(RC)、
青岛(QD)、韩国(SK)和日本(JP)六个群体的遗传多样性，并探讨了栉孔扇贝各群体
的遗传结构。所有47个个体中得到了长度为592bp的165 rRNA基因片段序列，把所
有个体的165 rRNA基因片段序列用CIUSTALX(Thompson et al.1997)进行排序对
比，用ARLEQUIN(Sehneider et al.，2000)计算群体特异性、单倍型多样性(Nei and
Taj ima，1981)和核昔酸多样性(Nei，1987)。分析表明有31个核昔酸变异位点，共
23个单倍型。单倍型A和B为最常见单倍型，存在于所有群体，其频率分别为 29.8%
和17%，基于所有单倍型之间核昔酸歧异的网状图表明:大多数单倍型是互相密切
关联的，最常见的单倍型A居于辐射状网状图的中央。许多邻近的单倍型互相只有一
个核昔酸差异，有些单倍型则与A有两个核昔酸差异。EXACT TEXT单倍型频率分布
分析显示，在所有样品中单倍型频率分布没有明显差异(P=0 .925)，而且在所有两两
群体之间也无明显差异。分子变异分析表明:绝大多数(99.65%)的遗传变异是群体
内的变异。群体间无明显变异，只有少于2%的变异来源于不同地区的差异，而且这
部分变异不明显(P=0 .195)。在各群体的单倍型多样性、核昔酸多样性和其他群体多
样性指数中，SK群体的指数最大，其次为YT群体。YT群体为中国四个群体中各项值
最高的群体，DL为最小。群体间核昔酸分歧最大的各群体对之间的分歧值位于SK和
YT之间，最小的出现在DL和JP之间，而这两群体间的地理距离最大。结果表明，
栉孔扇贝165 rRNA基因片段显示出了相当程度的变异，虽然165 rRNA基因一般来
说是线粒体中基因组内变异较低的区域，但YT群体最丰富的变异支持这一事实;从
上述结果看，烟台群体的种质基本没有受到影响，没有表现出遗传退化现象。从韩国
群体的14个多态位点和8个单倍型来看，是六个群体中最丰富的变异，考虑从韩国引
栉孔扇贝和牡蛹的遗传多样性研究
进亲贝应是可行的。
在所有海洋无脊椎动物中，牡砺是最常见、研究最多、也是形态变异最大的一类。
由于它们均沿海岸分布，并且有很大的形态变异，因而，人们甚至是海洋动物学家有
时都很难把它们区分开。从目前的研究结果可以看出，DNA序列分析方法特别是线
粒体片段的序列分析是遗传学及分子系统进化研究非常有用的工具。本项研究中应用
该技术方法，对太平洋牡砺(。“sostreag电闷s)的线粒体1 65 rRNA、Col基因片段进
行PCR扩增及序列分析:对太平洋牡砺核基因片段rrs一1和ITS一2片段的遗传特点进
行了初步研究;并利用165 rRNA和COI基
Occurring along the coast of northern China, South Korea, North Korea and Japan, the Chinese scallop (Chlamys farreri) has been one of the major species of the shellfish industry in the northern coast China for several decades. In recent years, however, scallop culture has been haunted by a high mortality problem. It is believed that the problem was caused by a combination of overcrowding N high summer temperature and deteriorating water quality. Additionally, one more possible reason for the problem to some extent, is that the scallop stock may be deteriorating genetically. Based upon this reason, refreshing scallop stock by introducing new stocks from other populations outside the coast of north China was considered. Consequently, investigation and evaluation on its stock structure throughout its geographic range are required.
For benthic marine species with pelagic larvae, it has been proposed that they have population genetic structures reflecting the dispersal capacity of larvae. Most of them are supposed to have less or little genetic structure reflecting the dispersal capacity of larvae. Mitochondrial DNA sequences (including 16S rDNA) were used for many of these studies. In C. farreri, this hypothesis has almost never been tested. So, this also lead to our interest to examine population genetic structure using mitochondrial gene sequence data, with two more population samples (Korea and Japan) as well as four samples from China, within its geographic range of the species.
Ribosomal Internal Transcribed Spacer Regions ITS-1 and ITS-2 in Scallop C. farreri were amplified via PCR, Fragments of the 16S rRNA gene and COI gene were amplified using two pairs of universal primers:
The PCR products of ITS-1 and ITS-2 fragments from Scallop C.farrei were ligated into T-vector, cloned and sequenced. 340 bp (ITS-1, AF245687 ) and 510 bp (ITS-2, AF245688) nucleotide sequences were got respectively, and the contents of A, T, G and C were 32.06%, 20.59%, 22.35% and 25.00% in ITS-1, 30.00%, 21.37%, 24.12% and 24.51% in ITS-2. The primers of ITS-1 and ITS-2 proved to be very universal in a variety of mollusk species.
Mitochondria! 16S rRNA gene fragments from Scallop C. farrei and Argopecten irradians were amplified via PCR. 634bp and 542bp nucleotide sequences were retrieved respectively. The content of A, T, G and C were 25.08%, 29.65%, 27.60% and 17.67% in C. farreri, 25.65%, 29.52%, 27.31% and 17.53% in A. irradians. Alignment indicated that the homology of two fragments was 68.1%, the nucleotide difference number was 80, and several small deletion/insertion sections, which contributed to length difference of the two fragments in two species, occurred in the middle of fragments (around 130bp) .
A 592 base pairs fragment of the mitochondrial 16S ribosomal RNA gene in 47 Zhikong scallop (C. farreri) specimens was sequenced in order to examine its intra-specific genetic variation and geographic structure. These samples were collected from six populations (four from China, and one each from South Korea and Japan respectively) across its range. Thirty-one nucleotide positions were found variable and twenty-three haplotypes were detected in all samples, which showed that more 16S rDNA variation existed in C. farreri when compared with several oyster species. Analysis at the intra-population level showed that the South Korea samples had the richest sequence diversity. However, analysis of haplotype frequency distribution and analysis of molecular variance (AMOVA) indicated that little geographic structure was present among all samples, and an absolute majority (99.65%) of the genetic variation was distributed within populations, suggesting that the populations in this study may belong to a single panmictic unit. Relative smaller distribution range and various currents may account for sufficient gene flow among these populations for this benthic species.
With 14 polymorphic sites and 8 hyplotypes, SK population showed the richest variation in all 6 populations, this may support the idea of stock introduction from South Ko
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