| 不同DNA条形码基因在帘蛤目贝类分类鉴定中的比较分析 |
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| 引用本文： | 吴彪,赵庆,刘寒苗,刘志鸿,孙秀俊,孙超,周丽青,杨爱国.不同DNA条形码基因在帘蛤目贝类分类鉴定中的比较分析[J].中国水产科学,2018,25(4):880-890. |
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| 作者姓名： | 吴彪 赵庆 刘寒苗 刘志鸿 孙秀俊 孙超 周丽青 杨爱国 |
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| 作者单位： | 中国水产科学研究院黄海水产研究所农业农村部海洋渔业可持续发展重点实验室;海洋渔业科学与食物产出过程功能实验室青岛海洋科学与技术国家实验室;水产科学国家级实验教学示范中心上海海洋大学;烟台市水产研究所 |
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| 基金项目： | 科技部科技基础性工作专项（2013FY110700）;国家水产种质资源共享服务平台（2017DKA30470）. |
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| 摘 要： | DNA条形码基因已经广泛应用在海洋贝类的分类鉴定、系统发育进化、种群遗传分析等领域的研究。为进一步研究评估不同DNA条形码基因在海洋贝类鉴定中的作用,本研究利用从Gen Bank数据库随机下载的帘蛤目COI、16S r RNA、18S r RNA和28S r RNA基因序列,通过传统距离法和单系聚类法结合分析,比较了上述DNA条形码基因在鉴定物种及系统发育进化中的鉴定效率,并以本实验室已获得的部分贝类DNA序列进行了验证。结果表明,根据"10倍法则"和"2%"阈值标准,本研究中COI能够鉴定57.1%物种,16S r RNA能够鉴定60.9%,18S r RNA鉴定16.7%,而28S r RNA无法有效鉴定;多数种COI和16S r RNA基因序列的种间遗传距离和种内遗传距离存在"条形码间隙",而18S r RNA和28S r RNA序列的种间和种内的遗传距离存在显著重叠,没有明显"条形码间隙";聚类分析结果表明,基于COI基因序列,87.9%的个体与同种聚为单系,以16S r RNA序列,65.6%的个体与同种聚为单系,未聚成单系的个体则形成姐妹系,未出现不同种聚为单系现象,能够呈现与形态分类基本一致的系统发生关系;但18S r RNA和28S r RNA呈现的聚类关系相对混乱。相对而言,在鉴定帘蛤目物种时,COI和16S r RNA都能够作为条形码基因,且COI有效性更高,18S r RNA和28S r RNA基因由于种内变异较大,不适于作为条码基因。研究结果为科学选用DNA条形码基因进行帘蛤目贝类的鉴定提供了参考资料。
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| 关 键 词： | DNA条形码 帘蛤目 比较分析 有效性 |
| 修稿时间： | 2018/8/20 0:00:00 |
Comparative analysis of different DNA barcoding methods for Veneroida classification and identification |
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| WU Biao,ZHAO Qing,LIU Hanmiao,LIU Zhihong,SUN Xiujun,SUN Chao,ZHOU Liqing,YANG Aiguo.Comparative analysis of different DNA barcoding methods for Veneroida classification and identification[J].Journal of Fishery Sciences of China,2018,25(4):880-890. |
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| Authors: | WU Biao ZHAO Qing LIU Hanmiao LIU Zhihong SUN Xiujun SUN Chao ZHOU Liqing YANG Aiguo |
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| Institution: | 1. Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs;Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China;2. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266273, China;3. National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China;4. Yantai Fisheries Research Institute, Yantai 264000, China |
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| Abstract: | DNA barcoding has been widely used in the fields of taxonomy, identification, phylogenetic evolution, and population genetic analysis of marine shellfish. To further evaluate the identification validity of different DNA barcoding genes in marine shellfish, sequences of COI, 16S rRNA, 18S rRNA, and 28S rRNA from Veneroida were randomly downloaded from the GenBank database, analyzed by the distance-and tree-based methods, and taxonomic relation established by the tree-based method, and compared the results with some sequences from our laboratory. According to the "10×rule" and "2%" standard criterion, 57.1% of species could be distinguished using the COI gene, whereas 16S rRNA identified 60.9%, 18S rRNA identified 16.7%, and 28S rRNA did not identify any species. We also found that there were significant barcode gaps between the genetic distances of pairwise-and within-species in most genera based on COI and 16S rRNA genes; however, there were significant overlaps, instead of barcode gaps, based on 18S rRNA and 28S rRNA. The cluster analysis showed that 87.9% of individuals clustered to a monophyletic group, with other within-species individuals clustered on the COI; and 65.6% 16S rRNA individuals clustered in monophyletic groups. Furthermore individuals without monophyletic groups clustered into sister groups, which revealed that the evolutionary relationships showed by the NJ tree constructed via COI and 16S rRNA mainly agreed with that from the morphological classification, especially that of the COI gene. In contrast, the NJ tree constructed via 18S rRNA and 28S rRNA genes showed disordered clustering relationships, including some individuals from different species cluster to monophyletic groups. In the present study, the results clearly suggested that both COI and 16S rRNA can be used as DNA barcodes in identifying species in Veneroida, particular COI, but 18S rRNA and 28S rRNA are not suitable because of the large intraspecific variation. This study provides new data for DNA barcode selection in Veneroida. |
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| Keywords: | DNA barcode Veneroida comparative analysis validity |
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