Analysis of the Secondary Structure of ITS1 in Pectinidae : Implications for Phylogenetic Reconstruction and Structural Evolution
作者： Shi Wang , Zhenmin Bao , Ning Li , Lingling Zhang , Jingjie Hu
DOI: 10.1007/S10126-006-6113-6
关键词:
摘要: It is at present difficult to accurately position gaps in sequence alignment and determine substructural homology structure when reconstructing phylogenies based on highly divergent sequences. Therefore, we have developed a new strategy for inferring In this strategy, the whole secondary presented as string bracket notation used phylogenetic characters infer relationships. no longer necessary decompose into homologous components. study, reliable relationships of eight species Pectinidae were inferred from alignment, but not even with aid structural information. The results suggest that should be useful Moreover, evolution ITS1 was also investigated. could divided four domains. Compensatory changes found all Structural motifs these domains identified further. These motifs, especially those D2 D3, may important functions maturation rRNAs.
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Chaolun Allen Chen, Chang-Feng Dai, Carden C. Wallace, Chien-Hsun Chen, Yi-Ting Lein, Chau-Ching Chang, Nuwei Vivian Wei, Ho-E Lin, Secondary Structure and Phylogenetic Utility of the Ribosomal Internal Transcribed Spacer 2 (ITS2) in Scleractinian Corals Zoological Studies. ,vol. 43, pp. 759- 771 ,(2004)
Kaizhong Zhang, Lusheng Wang, Bin Ma, Computing Similarity between RNA Structures combinatorial pattern matching. ,vol. 1645, pp. 281- 293 ,(1999) , 10.1007/3-540-48452-3_21
Vineet Bafna, S. Muthukrishnan, R. Ravi, Computing similarity between RNA strings combinatorial pattern matching. pp. 1- 16 ,(1996) , 10.1007/3-540-60044-2_30
Zhuozhi Wang, Kaizhong Zhang, None, Alignment between Two RNA Structures mathematical foundations of computer science. pp. 690- 702 ,(2001) , 10.1007/3-540-44683-4_60
I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker, P. Schuster, Fast folding and comparison of RNA secondary structures Monatshefte Fur Chemie. ,vol. 125, pp. 167- 188 ,(1994) , 10.1007/BF00818163
Guo-Chiuan Hung, Neil B Chilton, Ian Beveridge, Robin B Gasser, Secondary structure model for the ITS-2 precursor rRNA of strongyloid nematodes of equids: implications for phylogenetic inference. International Journal for Parasitology. ,vol. 29, pp. 1949- 1964 ,(1999) , 10.1016/S0020-7519(99)00155-1
R Reddy, L I Rothblum, C S Subrahmanyam, M H Liu, D Henning, B Cassidy, H Busch, The nucleotide sequence of 8 S RNA bound to preribosomal RNA of Novikoff hepatoma. The 5'-end of 8 S RNA is 5.8 S RNA. Journal of Biological Chemistry. ,vol. 258, pp. 584- 589 ,(1983) , 10.1016/S0021-9258(18)33294-0
Gary J. Olsen, Phylogenetic analysis using ribosomal RNA. Methods in Enzymology. ,vol. 164, pp. 793- 812 ,(1988) , 10.1016/S0076-6879(88)64084-5
Kaizhong Zhang, Computing similarity between RNA secondary structures Proceedings. IEEE International Joint Symposia on Intelligence and Systems (Cat. No.98EX174). pp. 126- 132 ,(1998) , 10.1109/IJSIS.1998.685429
Carine A.F.M. van der Sande, Marcel Kwa, Rob W. van Nues, Harm van Heerikhuizen, Hendrik A. Raué, Rudi J. Planta, Functional analysis of internal transcribed spacer 2 of Saccharomyces cerevisiae ribosomal DNA. Journal of Molecular Biology. ,vol. 223, pp. 899- 910 ,(1992) , 10.1016/0022-2836(92)90251-E