Complete Genome Sequence of
            <i>Erythrobacter litoralis</i>
            HTCC2594

Oh, Hyun-Myung; Giovannoni, Stephen J.; Ferriera, Steve; Johnson, Justin; Cho, Jang-Cheon

doi:10.1128/jb.00026-09

Cited by 40 publications

(38 citation statements)

References 20 publications

(12 reference statements)

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“…In addition, genes for type IV secretion systems (T4SS) were identified, including seven genes encoding the secretion systems T4SS (virB2B3B4-virB6-virB9B10B11) but no virD4 gene. Interestingly, prophage sequences were also found in the genome coincident with the two PS operons, suggesting the possibility of lateral gene transfer in AAPB (11).…”

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confidence: 97%

Coexistence of Two Different Photosynthetic Operons in Citromicrobium bathyomarinum JL354 As Revealed by Whole-Genome Sequencing

2010

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Citromicrobium bathyomarinum is a bacteriochlorophyll a-containing aerobic anoxygenic phototrophic bacterium. Here, we report the draft genome sequence of C. bathyomarinum JL354, which was the first C. bathyomarinum strain isolated from a euphotic marine environment. The JL354 genome sequence reveals, for the first time, the coexistence of two different photosynthetic operons in a single strain.Knowledge of aerobic anoxygenic phototrophic bacteria (AAPB) is critical for understanding carbon cycling in the ocean (4, 7), and they have been studied extensively with regard to their abundance and diversity in different marine environments (4, 6, 7, 9, 13, 16, 18, 19). The known marine AAPB species are mainly affiliated with the Alphaproteobacteria (including the alpha-3 and alpha-4 subclusters) and Gammaproteobacteria (3,14). The genus Citromicrobium is one clade of the alpha-4 AAPB subcluster, and it contains only one species, Citromicrobium bathyomarinum. The type strain of C. bathyomarinum, strain JF-1, was isolated from deep-sea hydrothermal vent plume waters (17). Other strains of C. bathyomarinum were isolated at depths from 500 m to 2,379 m (12). All of these habitats are aphotic environments, and the known C. bathyomarinum strains may not play the same ecological role as those AAPB which are in the euphotic zone. Here, we report on the first epipelagic strain of C. bathyomarinum, strain JL354, which was isolated from the surface water of the South China Sea.The C. bathyomarinum JL354 16S rRNA gene shares 99.6% sequence similarity with that of the type strain JF-1. Wholegenome shotgun sequencing was performed on JL354 using 454 pyrosequencing technologies, which produced 207,125 reads and 85,861,877 bp sequences. A total of 201,805 highquality reads were used in assembling the genome to give 26.2-fold coverage of the genome. The complete sequence was analyzed using Glimmer 3.02 (2) for the protein-coding gene, tRNAscan-SE (10) for the tRNA, and RNAmmer (8) for the rRNA. The functions of predicted protein-coding genes were then annotated through comparisons with the databases of NCBI-NR (1), COG (15), and KEGG (5).The C. bathyomarinum JL354 draft genome sequence has a total of 3,273,334 bp (3,401 open reading frames) distributed in 68 contigs with an average GC content of 65.0%. One 16S-23S-5S operon and 45 tRNAs on the draft assembly were identified, as were complete sets of genes for the synthesis of amino acids, nucleotides, and prosthetic groups. In particular, this strain has two different photosynthetic (PS) operons; one is complete, and the other is incomplete. The complete one consists of the typical subclusters puhCBA-lhaA-bchMLHBNF and pufMLAB-bchZYXC-crtFDC, and the incomplete one only has pufLMC-puhCBA. The similarity of the two pufLM gene sequences is less than 70%, and the pufLM gene in the incomplete operon is affiliated with the Gammaproteobacteria group by phylogenetic analysis (3). This is the first report about two different PS operons coexisting in a single strain.A detailed inspection of th...

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confidence: 97%

Coexistence of Two Different Photosynthetic Operons in Citromicrobium bathyomarinum JL354 As Revealed by Whole-Genome Sequencing

2010

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“…As part of the Moore Foundation Microbial Genome Sequencing Project (http://www.moore.org/microgenome), the genomes were shotgun sequenced by the J. Craig Venter Institute, and the draft genomes of HTCC2148 and HTCC2080 containing 75 (ABXQ01000001 to ABXQ01000075) and 25 (AAVV01000001 to AAVV01000025) contigs, respectively, were annotated with the GenDB annotation application program (9) at the Center for Genome Research and Biocomputing at Oregon State University, similarly to that previously described (10,11). Autoannotation was completed by merging results from the Glimmer 2.0 modeling package (4) and contrasting to Basic Local Alignment Search Tool for Proteins (BLASTp).…”

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Genome Sequences of Strains HTCC2148 and HTCC2080, Belonging to the OM60/NOR5 Clade of the Gammaproteobacteria

et al. 2010

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“…The finished contigs were automatically annotated with a system based on the program GenDB (5) and manually annotated as described in previous reports (7,12). The annotation is available at http: //bioinfo.cgrb.oregonstate.edu/microbes/.…”

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Genome Sequence of the Oligotrophic Marine Gammaproteobacterium HTCC2143, Isolated from the Oregon Coast

Kang

Ferriera

et al. 2010

J Bacteriol

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Strain HTCC2143 was isolated from Oregon Coast surface waters using dilution-to-extinction culturing. Here we present the genome of strain HTCC2143 from the BD1-7 clade of the oligotrophic marine Gammaproteobacteria group. The genome of HTCC2143 contains genes for carotenoid biosynthesis and proteorhodopsin and for proteins that have potential biotechnological significance: epoxide hydrolases, Baeyer-Villiger monooxygenases, and polyketide synthases.

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Complete Genome Sequence of Erythrobacter litoralis HTCC2594

Cited by 40 publications

References 20 publications

Coexistence of Two Different Photosynthetic Operons in Citromicrobium bathyomarinum JL354 As Revealed by Whole-Genome Sequencing

Coexistence of Two Different Photosynthetic Operons in Citromicrobium bathyomarinum JL354 As Revealed by Whole-Genome Sequencing

Genome Sequences of Strains HTCC2148 and HTCC2080, Belonging to the OM60/NOR5 Clade of the Gammaproteobacteria

Genome Sequence of the Oligotrophic Marine Gammaproteobacterium HTCC2143, Isolated from the Oregon Coast

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