DNA Research Advance Access published online on January 10, 2006
DNA Research, doi:10.1093/dnares/dsi015
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1 Center for Information Biology, National Institute of Genetics, The Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
* To whom correspondence should be addressed. A self-organizing map (SOM) was developed as a novel bioinformatics strategy for phylogenetic classification of sequence fragments obtained from pooled genome samples of uncultured microbes in environmental and clinical samples. This phylogenetic classification was possible without either orthologous sequence sets or sequence alignments. We first constructed SOMs for tetranucleotide frequencies in 210 000 5 kb sequence fragments obtained from 1502 prokaryotes for which at least 10 kb of genomic sequence has been deposited in public DNA databases. The sequences could be classified primarily according to phylogenetic groups without information regarding the species. We used the SOM method to classify sequence fragments derived from environmental samples of the Sargasso Sea and of an acidophilic biofilm growing in acid mine drainage. Phylogenetic diversity of the environmental sequences was effectively visualized on a single map. Sequences that were derived from a single genome but cloned independently could be reassociated in silico. G + C% has been used for a long period as a fundamental parameter for phylogenetic classification of microbes, but the G + C% is apparently too simple a parameter to differentiate a wide variety of known species. Oligonucleotide frequency can be used to distinguish the species because oligonucleotide frequencies vary significantly among their genomes.
Received July 11, 2005
Revised September 2, 2005
Full Papers
Novel Phylogenetic Studies of Genomic Sequence Fragments Derived from Uncultured Microbe Mixtures in Environmental and Clinical Samples
Takashi Abe 1 *,
Hideaki Sugawara 1,
Makoto Kinouchi 2,
Shigehiko Kanaya 3,
and
Toshimichi Ikemura 4
2 Department of Bio-System Engineering, Faculty of Engineering, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
3 Department of Bioinformatics and Genomes, Graduate School of Information Science, Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0101, Japan
4 The Graduate University for Advanced Studies (Sokendai), Hayama Center for Advanced Research, Hayama-cho, Kanagawa 240-0193, Japan
Takashi Abe, E-mail: takaabe{at}genes.nig.ac.jp
Abstract
Communicated by Katsumi Isono
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