New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras

• Published in: Applied and Environmental Microbiology Vol. 72; no. 9; pp. 5734 - 5741
• Main Authors: Ashelford, Kevin E, Chuzhanova, Nadia A, Fry, John C, Jones, Antonia J, Weightman, Andrew J
• Format: Journal Article
• Language: English
• Published: Washington, DC American Society for Microbiology 01.09.2006
• Subjects: Archaea; Archaea - classification; Archaea - genetics; Bacteria; Bacteria - classification; Bacteria - genetics; Base Sequence; Biological and medical sciences; Chimera; Chimera - genetics; chimerism; classification; clones; Cloning; Cloning, Molecular; computer software; computers; DNA libraries; DNA, Archaeal; DNA, Archaeal - genetics; DNA, Bacterial; DNA, Bacterial - genetics; DNA, Ribosomal; DNA, Ribosomal - genetics; Environmental Microbiology; Fundamental and applied biological sciences. Psychology; Gene Library; Genes; genetics; Internet; Java; languages; Marine Biology; Microbiology; Molecular Sequence Data; nucleotide sequences; Object repository; Operating systems; phylogeny; researchers; ribosomal RNA; RNA, Archaeal; RNA, Archaeal - genetics; RNA, Bacterial; RNA, Bacterial - genetics; RNA, Ribosomal, 16S; RNA, Ribosomal, 16S - genetics; screening; Software; 16S-RNA; Screening; Software; Gene library; Ribosomal DNA
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/AEM.00556-06

A new computer program, called Mallard, is presented for screening entire 16S rRNA gene libraries of up to 1,000 sequences for chimeras and other artifacts. Written in the Java computer language and capable of running on all major operating systems, the program provides a novel graphical approach for visualizing phylogenetic relationships among 16S rRNA gene sequences. To illustrate its use, we analyzed most of the large libraries of cloned bacterial 16S rRNA gene sequences submitted to the public repository during 2005. Defining a large library as one containing 100 or more sequences of 1,200 bases or greater, we screened 25 of the 28 libraries and found that all but three contained substantial anomalies. Overall, 543 anomalous sequences were found. The average anomaly content per clone library was 9.0%, 4% higher than that previously estimated for the public repository overall. In addition, 90.8% of anomalies had characteristic chimeric patterns, a rise of 25.4% over that found previously. One library alone was found to contain 54 chimeras, representing 45.8% of its content. These figures far exceed previous estimates of artifacts within public repositories and further highlight the urgent need for all researchers to adequately screen their libraries prior to submission. Mallard is freely available from our website at http://www.cardiff.ac.uk/biosi/research/biosoft/.