Abstract
Citromicrobium is a member of the alpha-4 subcluster in the Alphaproteobacteria and is identified as a typical aerobic anoxygenic phototrophic bacterium (AAPB). Here we report the draft genome sequence of a non-AAPB strain, Citromicrobium sp. JLT1363. The genome sequence reveals a multimechanism of horizontal gene transfer, as well.
The genus Citromicrobium was first named by Yurkov et al. in 1999, and it is one clade of the alpha-4 subcluster in the Alphaproteobacteria (14). Currently, this genus contains only one species, Citromicrobium bathyomarinum. The type strain C. bathyomarinum JF-1 was isolated from deep-sea hydrothermal vent plume waters. C. bathyomarinum JF-1 and other Citromicrobium spp. were identified as aerobic anoxygenic phototrophic bacteria (AAPB) (6, 11, 14). We isolated a Citromicrobium sp. strain, JLT1363 (98.0% sequence similarity of 16S rRNA gene with that of JF-1), not showing phototrophic growth, from the surface water of the South China Sea. Here we report the whole-genome sequence of Citromicrobium sp. JLT1363.
Whole-genome shotgun sequencing was performed on JLT1363 using 454 pyrosequencing technologies, which produced 362,544 reads and 154,451,585 bp sequences. We used 355,141 high-quality reads to assemble the genome and obtained a 49.5-fold coverage of the genome. The complete sequence was analyzed using the Glimmer 3.02 software program (4) for the protein-coding genes, tRNAscan-SE (9) for the tRNA, and RNAmmer (8) for the rRNA. The functions of predicted protein-coding genes were then annotated through comparisons with the NCBI-NR (1), COG (12), and KEGG (7) databases.
The Citromicrobium sp. JLT1363 draft genome sequence has a total of 3,117,324 bp (3,198 open reading frames [ORFs]) distributed in 26 contigs with an average GC content of 64.9%. One 16S-23S-5S operon and 46 tRNAs on the draft assembly were identified, as were complete sets of genes for the synthesis of amino acids and nucleotides. A detailed inspection of the genome sequence revealed the presence of complete sets of genes encoding flagellum formation and the complete tricarboxylic acid cycle.
In particular, the Citromicrobium sp. JLT1363 genome showed various mechanisms for horizontal gene transfer. An integrative conjugative element (ICE) (about 100 kb) was observed in the Citromicrobium sp. JLT1363 genome (2, 5). Two regions carrying exogenous DNA were discovered in the ICE. We further found a nearly complete gene transfer agent (GTA) (about 15 kb) gene cluster. In addition, seven genes (virB2B3B4-virB6-virB9B10B11) of the type IV secretion system (T4SS) (about 7 kb) existed in the genome.
In the JLT1363 genome, we found exactly the same genes as those located upstream and downstream of the photosynthetic gene cluster (PGC) of JL354 (6). Their order and direction are the same as well. This suggests a loss of PGC in Citromicrobium sp. JLT1363 (10). So far, JLT1363 is the only isolate in the Citromicrobium genus without phototrophic capability.
The exchange of genetic information by horizontal gene transfer plays important roles in the evolution of bacteria (3, 13). A multimechanism of horizontal gene transfer and the loss of PGC in Citromicrobium sp. JLT1363 may give us some clues for further studies on the evolution of the photosynthesis gene of AAPB.
Nucleotide sequence accession number.
The data from this whole-genome shotgun project have been deposited at DDBJ/EMBL/GenBank under accession number AEUE01000000.
ACKNOWLEDGMENTS
This work was supported by the 973 Program (2011 CB808800), the NSFC project (91028001), the SOA project (201105021), and the NSFC project (40821063, 41076063).
All authors contributed equally.
Footnotes
Published ahead of print on 11 February 2011.
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