Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency

BMC Bioinformatics

Research Article

Francis C Weng¹  Daryi Wang¹  Ming-Tsung Hsu²  Tse-Yi Wang³  Huai-Kuang Tsai³  Chien-Hao Su⁴ 

[1] Biodiversity Research Center, Academia Sinica, 115, Taipei, Taiwan;Institute of Information Science, Academia Sinica, 115, Taipei, Taiwan;Institute of Information Science, Academia Sinica, 115, Taipei, Taiwan;Research Center for Information Technology Innovation, Academia Sinica, 115, Taipei, Taiwan;Institute of Information Science, Academia Sinica, 115, Taipei, Taiwan;Research Center for Information Technology Innovation, Academia Sinica, 115, Taipei, Taiwan;Department of Computer Science and Information Engineering, National Taiwan University, 106, Taipei, Taiwan;

关键词: Basic Local Alignment Search Tool;    Genomic Fragment;    Taxonomic Assignment;    Metagenomic Data;    Taxonomic Class;   

DOI  :  10.1186/1471-2105-11-565

 received in 2009-12-24, accepted in 2010-11-18,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundInvestigation of metagenomes provides greater insight into uncultured microbial communities. The improvement in sequencing technology, which yields a large amount of sequence data, has led to major breakthroughs in the field. However, at present, taxonomic binning tools for metagenomes discard 30-40% of Sanger sequencing data due to the stringency of BLAST cut-offs. In an attempt to provide a comprehensive overview of metagenomic data, we re-analyzed the discarded metagenomes by using less stringent cut-offs. Additionally, we introduced a new criterion, namely, the evolutionary conservation of adjacency between neighboring genes. To evaluate the feasibility of our approach, we re-analyzed discarded contigs and singletons from several environments with different levels of complexity. We also compared the consistency between our taxonomic binning and those reported in the original studies.ResultsAmong the discarded data, we found that 23.7 ± 3.9% of singletons and 14.1 ± 1.0% of contigs were assigned to taxa. The recovery rates for singletons were higher than those for contigs. The Pearson correlation coefficient revealed a high degree of similarity (0.94 ± 0.03 at the phylum rank and 0.80 ± 0.11 at the family rank) between the proposed taxonomic binning approach and those reported in original studies. In addition, an evaluation using simulated data demonstrated the reliability of the proposed approach.ConclusionsOur findings suggest that taking account of conserved neighboring gene adjacency improves taxonomic assignment when analyzing metagenomes using Sanger sequencing. In other words, utilizing the conserved gene order as a criterion will reduce the amount of data discarded when analyzing metagenomes.

【 授权许可】

Unknown   
© Weng et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.