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Journal of Tropical Oceanography >

2016 , Vol. 35 >Issue 6: 74 - 81

DOI: https://doi.org/10.11978/2016012

Marine Biology

Feature analysis of the internal transcribed spacers in teleost ribosomal DNA

  • SI Lizhen ,
  • SHI Wei ,
  • YANG Min ,
  • GONG Li ,
  • KONG Xiaoyu
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  • 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 date: 2016-01-29

  Revised date: 2016-06-27

  Online published: 2016-12-15

Supported by

National Natural Science Foundation of China (31272273)

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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

Cite this article

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 . DOI: 10.11978/2016012

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