硬骨鱼类核糖体基因间隔区的序列特征分析

doi:10.11978/2016012

热带海洋学报 ›› 2016, Vol. 35 ›› Issue (6): 74-81.doi: 10.11978/2016012CSTR: 32234.14.2016012

硬骨鱼类核糖体基因间隔区的序列特征分析

司李真^{1, 2}, 时伟¹, 杨敏^{1, 2}, 龚理^{1, 2}, 孔晓瑜¹

1. 中国科学院南海海洋研究所, 热带海洋生物资源与生态重点实验室, 广东广州 510301;
2. 中国科学院大学, 北京 100049

收稿日期:2016-01-29 修回日期:2016-06-27 出版日期:2016-11-30 发布日期:2016-12-15
通讯作者: 孔晓瑜。E-mail: xykong@scsio.ac.cn
作者简介:作者简介：司李真(1990-), 女, 河南省荥阳市人, 硕士, 从事鱼类分类及系统进化研究。E-mail: LZsi314003@126.com
基金资助:
国家自然科学基金项目(31272273)

Feature analysis of the internal transcribed spacers in teleost ribosomal DNA

SI Lizhen^{1, 2}, SHI Wei¹, YANG Min^{1, 2}, GONG Li^{1, 2}, KONG Xiaoyu¹

1. Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China;
2. University of Chinese Academy of Sciences, Beijing 100049, China

Received:2016-01-29 Revised:2016-06-27 Online:2016-11-30 Published:2016-12-15
Contact: KONG Xiaoyu. E-mail: xykong@scsio.ac.cn
Supported by:
National Natural Science Foundation of China (31272273)

摘要/Abstract

摘要： 真核生物核糖体DNA (ribosomal DNA, 简称rDNA)是由几十个甚至上万个高度串联重复序列组成的多基因家族, 每个重复单元都包括编码区(18S、5.8S和28S)和非编码区(ITS1和ITS2)。间隔区ITS1和ITS2常被用于属级及以下阶元水平的系统关系研究。然而, 越来越多的研究发现, 这些串联重复序列并非完全一致, 有些甚至存在个体内差异, 这种基因组内ITS多态性的发现, 使我们对ITS用于物种系统发育重建的适用性产生了质疑。因此, 我们对GeneBank中硬骨鱼类的10目ITS序列的长度和保守位点比例进行了统计分析, 结果显示: ITS1长度范围为272~918bp, 保守位点比例在各分类单元之间具有明显的区别, 并且这种区别可以作为判断物种之间关系的特征。当序列之间保守位点比例为89.51%~100%时, 为种内关系; 在61.53%~81.36%范围时, 为种间关系; 在32.47%~58.87%范围时, 为属间关系; 而在1.62%~30.46%时, 达到科间水平。而一些物种的保守位点比例超出此范围时, 依据此标准判断就会产生偏差。ITS2的长度范围为128~694bp, 保守位点比例在各分类阶元之间互相重合, 在各分类阶元之间不存在明显的差异, 因此该特征不能用于区分各阶元之间的关系。

Abstract: Eukaryotic ribosomal DNA (rDNA) consists of dozens or even tens of thousands of tandem repeat Units. Each repeat unit includes three coding genes (18S, 5.8S and 28S) and two internal transcribed spacers (internal transcribed spacer 1 and internal transcribed spacer 2). The two internal transcribed spacers (ITS1 and ITS2) are often used for phylogenetic study of genus or lower level. However, an increasing number of studies have been shown that not all repeat units are identical; some of them have obviously intraspecific variations, as a result, which raise a question whether it is a useful tool for phylogenetic reconstruction. Accordingly, sequence length and conservation ratio of the internal transcribed spacers from GeneBank database including 10 orders of teleost were analyzed in order to explore the features of ITS1 and ITS2. The results showed that lengths of ITS1 were from 272 to 918 bp. The conservation ratio had distinct differences among each taxon, which could be used as a potential marker to identify the relationships among most species. When the conservation ratio ranged from 89.51% to 100%, it indicated an intraspecific relationship, from 61.53% to 81.36% as an interspecific relationship. When the number varied from 32.47% to 55.87%, the relationship was defined as an intergeneric one; and it was an interfamily relationship for the data between 1.62% and 30.46%. However, there were also several exceptions, which would lead to inaccuracy phylogenetic relationship. By contrast, the lengths of ITS2 varied from 128 to 694 bp, and the conservation ratio among each taxon almost had a continuous value, suggesting that it was not suitable for identifying taxonomic category.

Key words: Sciences, Guangzhou 510301, China, 2. University of Chinese Academy of Sciences, Beijing 100049, China

司李真, 时伟, 杨敏, 龚理, 孔晓瑜. 硬骨鱼类核糖体基因间隔区的序列特征分析[J]. 热带海洋学报, 2016, 35(6): 74-81.

SI Lizhen, SHI Wei, YANG Min, GONG Li, KONG Xiaoyu. Feature analysis of the internal transcribed spacers in teleost ribosomal DNA[J]. Journal of Tropical Oceanography, 2016, 35(6): 74-81.

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硬骨鱼类核糖体基因间隔区的序列特征分析

Feature analysis of the internal transcribed spacers in teleost ribosomal DNA

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