title: Characterization of Uncultured Genome Fragment from Soil Metagenomic Library Exposed Rare Mismatch of Internal Tetranucleotide Frequency.
abstract: Exploring the genomic information of a specific uncultured soil bacterium is vital to understand its function in the ecosystem but is still a challenge due to the lack of culture techniques. To examine the genomes of uncultured bacteria, a metagenomic bacterial artificial chromosome library derived from a soil sample was screened for 16S rDNA-containing clones. Five clones (4C6, 5E7, 5G4, 5G12, and 5H7) containing uncultured soil bacteria genome fragment (with low 16S rDNA similarity to isolated bacteria) were selected for sequencing. Clone 5E7 and 5G4 showed only 82 and 83% of 16S rDNA identity to known sequences. Phylogenetic analysis of 16S rDNA indicated that 5E7 and 5G4 were potentially from new class of Chloroflexi. Only one-third of the 5G4 open reading frames have significant hits against HMMER. Internal tetranucleotide frequency analysis indicated that the unknown region of 5G4 was poorly correlated with other parts of the clone, indicating that this section might be obtained through lateral transfer. It was suggested that this region rich for unknown genes is under fast evolution.
authors.affiliation: Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Yunpeng
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University Nanjing, China.
authors.forename: Dongqing
authors.initials: D
authors.lastname: Yang
authors.affiliation: Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University Nanjing, China.
authors.forename: Nan
authors.initials: N
authors.lastname: Zhang
authors.affiliation: Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University Nanjing, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Chen
authors.affiliation: College of Life Sciences, Nanjing Agricultural University Nanjing, China.
authors.forename: Zhongli
authors.initials: Z
authors.lastname: Cui
authors.affiliation: Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University Nanjing, China.
authors.forename: Qirong
authors.initials: Q
authors.lastname: Shen
authors.affiliation: Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural SciencesBeijing, China; Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural UniversityNanjing, China.
authors.forename: Ruifu
authors.initials: R
authors.lastname: Zhang
keywords: 16S rDNA; bacterial artificial chromosome library; genome fragment; tetranucleotide correlation; uncultured soil bacterium