| Literature DB >> 28066395 |
Yunpeng Liu1, Dongqing Yang2, Nan Zhang2, Lin Chen2, Zhongli Cui3, Qirong Shen2, Ruifu Zhang4.
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.Entities:
Keywords: 16S rDNA; bacterial artificial chromosome library; genome fragment; tetranucleotide correlation; uncultured soil bacterium
Year: 2016 PMID: 28066395 PMCID: PMC5177636 DOI: 10.3389/fmicb.2016.02081
Source DB: PubMed Journal: Front Microbiol ISSN: 1664-302X Impact factor: 5.640
General information of five BAC inserts.
| 4C6 | 5E7 | 5G4 | 5G12 | 5H7 | |
|---|---|---|---|---|---|
| BAC insert length (bp) | 23,678 | 46,092 | 30,180 | 43,604 | 56,420 |
| G + C content (%) | 51.6 | 49.6 | 48.2 | 49.2 | 49.0 |
| No. of predicted ORF | 18 | 44 | 36 | 42 | 59 |
| No. of hypothetical protein | 8 | 6 | 19 | 14 | 14 |
| Proteins assigned to COGs | 7 | 32 | 12 | 29 | 39 |
| Average ORF length (bp) | 1,017 | 981 | 617 | 912 | 788 |
| Coding regions (%) | 54.4 | 75.6 | 44.4 | 58 | 65 |
| rrn operon | 16S | 16S-23S-5.8S | 16S-23S | 16S-23S-5.8S | 16S-23S-5.8S |
| Nearest relation (accession no.) | HQ118747.1 | EF516466.1 | FJ479355.1 | KC555030.1 | FJ820395.1 |
| Uncultured | Uncultured | Uncultured | Uncultured | Uncultured | |
| Identities to cultivable samplea | 97% (94%) | 82% (82%) | 83% (83%) | 93% (88%) | 98% (97%) |