Ribosomal RNA phylogenetics: the third dimension
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With integration of secondary structures, ribosomal genes have once again become very popular for phylogenetic analyses. This additional source of information to the nucleotide sequence provides a massive boost for taxonomic inferences. Herein, we propose that in the near future a further benefit for phylogenetics with such genes will be very likely by inclusion of the third dimension. For the first time, we determined the tertiary structure of the ribosomal internal transcribed spacer 2 for Chlamydomonas rheinhardtii by application of two different in silico prediction algorithms. We compared these methods with focus on phylogenetic usability. Further, we determined the tertiary structures for closely related green algae to provide a small phylogenetic example. The results suggest that the tertiary structure inherits evolutionary information observable neither within the sequence nor in the secondary structure.
Key wordsmolecular systematics internal transcribed spacer 2 ITS2 non-coding RNA secondary structure tertiary structure
internal transcribed spacer 2
Protein Data Bank
root mean square deviation
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- Henrick K., Feng Z., Bluhm W.F., Dimitropoulos D., Doreleijers J.F., Dutta S., Flippen-Anderson J.L., Ionides J., Kamada C., Krissinel E., Lawson C.L., Markley J.L., Nakamura H., Newman R., Shimizu Y., Swaminathan J., Velankar S., Ory J., Ulrich E.L., Vranken W., Westbrook J., Yamashita R., Yang H., Young J., Yousufuddin M. & Berman H.M. 2008. Remediation of the protein data bank archive. Nucleic Acids Res.36(Database Issue): D426–D433.PubMedGoogle Scholar