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The Institute for Genomic Research, Gaithersburg, Maryland 20878
* Corresponding author. Mailing address: The Institute for Genomic Research, 932 Clopper Road, Gaithersburg, MD 20878. Phone: (301) 216-9589. Fax: (301) 869-9423. Electronic mail address: rclayton{at}tigr.org.
ABSTRACT
Small-subunit rRNA (SSU rRNA) sequencing is a powerful tool to detect, identify, and classify prokaryotic organisms, and there is currently an explosion of SSU rRNA sequencing in the microbiology community. We report unexpectedly high levels of intraspecific variation (within and between strains) of prokaryote SSU rRNA sequences deposited in GenBank. A total of 82% of the prokaryote species with two published SSU rRNA sequences had more variable positions than a 0.1% random sequencing error would predict, and 48% of these sequence pairs had more variable positions than predicted by a 1.0% random sequencing error. Other sources of sequence variability must account for some of this intraspecific variation. Given these results, phylogenetic studies and biodiversity estimates obtained by using prokaryotic SSU rRNA sequences cannot proceed under the assumption that rRNA sequences of single operons from single isolates adequately represent their taxa. Sequencing SSU rRNA molecules from multiple operons and multiple isolates is highly recommended to obtain meaningful phylogenetic hypotheses, as is careful attention to accurate strain identification.
Present address: The National Center for Genome Resources, Santa Fe, NM 87505. This article has been cited by other articles:
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U. Reischl, K. Feldmann, L. Naumann, B. J. M. Gaugler, B. Ninet, B. Hirschel, and S. Emler 16S rRNA Sequence Diversity in Mycobacterium celatum Strains Caused by Presence of Two Different Copies of 16S rRNA Gene J. Clin. Microbiol., June 1, 1998; 36(6): 1761 - 1764. [Abstract] [Full Text]
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