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Studying the evolutionary relationships and phylogenetic trees of 21 groups of tRNA sequences based on complex networks

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Abstract

To find out the evolutionary relationships among different tRNA sequences of 21 amino acids, 22 networks are constructed. One is constructed from whole tRNAs, and the other 21 networks are constructed from the tRNAs which carry the same amino acids. A new method is proposed such that the alignment scores of any two amino acids groups are determined by the average degree and the average clustering coefficient of their networks. The anticodon feature of isolated tRNA and the phylogenetic trees of 21 group networks are discussed. We find that some isolated tRNA sequences in 21 networks still connect with other tRNAs outside their group, which reflects the fact that those tRNAs might evolve by intercrossing among these 21 groups. We also find that most anticodons among the same cluster are only one base different in the same sites when S ≥ 70, and they stay in the same rank in the ladder of evolutionary relationships. Those observations seem to agree on that some tRNAs might mutate from the same ancestor sequences based on point mutation mechanisms.

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Acknowledgements

This paper was supported by Guangxi Natural Science Foundation (No. 0728003), National Natural Science Foundation of China (Nos. 10662002, 10865001), the Graduate Student Innovation Program of Guangxi Zhuang Autonomous Region (Grant No. T32070), and the 973 Program (2010CB328204).

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Authors and Affiliations

  1. Physical Science & Technology College, Guangxi University, Nanning, Guangxi, 530004, China

    Fangping Wei & Bowen Chen

  2. Key Laboratory of Information Photonics and Optical Communications, Ministry of Education, Beijing University of Posts and Telecommunications, Beijing, 100876, China

    Bowen Chen

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  1. Fangping Wei
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  2. Bowen Chen
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Correspondence to Fangping Wei.

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Wei, F., Chen, B. Studying the evolutionary relationships and phylogenetic trees of 21 groups of tRNA sequences based on complex networks. J Biol Phys 38, 241–250 (2012). https://doi.org/10.1007/s10867-011-9236-6

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  • DOI: https://doi.org/10.1007/s10867-011-9236-6

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