Clayton R A, Sutton G, Hinkle P S, Bult C, Fields C
Institute for Genomic Research, Gaithersburg, Maryland 20878, USA.
Int J Syst Bacteriol. 1995 Jul;45(3):595-9. doi: 10.1099/00207713-45-3-595.
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.
小亚基核糖体RNA（SSU rRNA）测序是检测、鉴定和分类原核生物的有力工具，目前微生物学界SSU rRNA测序呈爆发式增长。我们报告了GenBank中存档的原核生物SSU rRNA序列存在意外高水平的种内变异（菌株内和菌株间）。在有两条已发表的SSU rRNA序列的原核生物物种中，共有82%的物种具有比0.1%随机测序错误所预测的更多可变位点，并且这些序列对中有48%具有比1.0%随机测序错误所预测的更多可变位点。序列变异性的其他来源必定是造成这种种内变异的部分原因。鉴于这些结果，利用原核生物SSU rRNA序列进行的系统发育研究和生物多样性估计不能在单分离株的单个操纵子的rRNA序列能充分代表其分类单元这一假设下进行。强烈建议对多个操纵子和多个分离株的SSU rRNA分子进行测序，以获得有意义的系统发育假设，同时也要密切关注准确的菌株鉴定。
