TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences

Members of the gammaproteobacterial clade NOR5/OM60 regularly form an abundant part, up to 11%, of the bacterioplankton community in coastal systems during the summer months. Here, we report the nearly complete genome sequence of one cultured representative, Congregibacter litoralis strain KT71, isolated from North Sea surface water. Unexpectedly, a complete photosynthesis superoperon, including genes for accessory pigments, was discov- from a surface water sample taken near the North Sea island Helgoland, by direct plating on complex low-nutrient media. Phylogenetic analysis showed that KT71 was the first cultured representative of a cosmopolitan gammaproteobacterial lineage, which we in the following refer to as the NOR5/OM60 clade (Fig. 1). The first indication for this clade dates back to 1997, when Rappe et al. retrieved two 16S rRNA clones, OM60 and OM241, from the continental shelf off Cape Hatteras, NC (2). In the following years, many sequences have been retrieved that were related to the clone OM60 (e.g.,. By the end of 2005, Ͼ180 partial and full length 16S rRNA sequences available within the public databases were related to KT71 and OM60.KT71 is a Gram-negative, pleomorphic, strictly aerobic, and motile bacterium. It is of an average size of 2 ϫ 0.5 m, has a generation time of 4.5 h, and often grows in flocs. Based on this conspicuous trait and the site of isolation, the name Congregibacter litoralis has been proposed. A full taxonomic description of strain KT71 is currently ongoing (B.M.F., S.S., and R.A., unpublished work). Several more strains belonging to the NOR5/ OM60 clade were isolated off the coast of Oregon, in sterilized seawater, using a high-throughput dilution-to-extinction technique (9, 10). Meanwhile, representatives of the NOR5/OM60 clade were also isolated from Arctic sea ice (11) and coastal sediments (12,13).FISH with rRNA-targeted oligonucleotide probes for NOR5/ OM60 confirmed this clade as an abundant component of the bacterioplankton community in the North Sea around the island Helgoland (1). By the end of July 1998, up to 8% of the total bacterioplankton community comprised members of the NOR5/ OM60 clade (1). A second peak of NOR5/OM60 cells was visible in mid-June (6%). However, NOR5/OM60 was not detected by FISH during the winter months, October to March, suggesting a marked seasonality. The fraction of DNA-synthesizing NOR5/ OM60 cells seems to be quite variable. Active DNA synthesis could be detected in August but not in May 2002, even though NOR5/OM60 was present in high numbers in both samples (6% and 11% of total bacterioplankton cell, respectively) (14).In 2004, KT71 was selected for whole-genome sequencing as part of the Gordon and Betty Moore Foundation (GBMF) Marine Microbiology Initiative. Here, we present data derived from the analysis of the genome of strain KT71 and from ecophysiological experiments addressing some of the predictions derived from genome annotation. Results and Discussion Structure and Phylogenetic Analysis of the Photosynthesis (PS)Operon. The...

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“…Genome-wide fluctuations in tetranucleotide composition (SI Fig. 5) were calculated and plotted with the program TETRA (16).…”

Section: Methodsmentioning

confidence: 99%

“…Both a smooth tetranucleotide signature (SI Fig. 5) (16) and the absence of transposons in the vicinity make it highly unlikely that the PS operon has been obtained by a recent lateral gene transfer. The operon consists of the typical subclusters crtEF-bchCXYZ-puf and bchFNBHLM ( Fig.…”

Section: Structure and Phylogenetic Analysis Of The Photosynthesis (Ps)mentioning

confidence: 99%

Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis

Fuchs

Spring

Teeling

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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123

119

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“…Scaffolds and contigs were initially assigned to fer1(env) based solely on assembly and subsequent analyses including % GϩC, read depth, and profiling of nucleotide frequencies using TETRA (42). Subsequently, community genome contigs and scaffolds assigned to fer1(env) were verified by comparison with the F. acidarmanus fer1 genome by using BLAST (43) and MUMmer 3.0 software package's NUCmer (44).…”

Section: Population Structure In the Context Of Environmental And Geomentioning

confidence: 99%

Genome dynamics in a natural archaeal population

Allen¹,

Tyson²,

Whitaker³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

118

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Evolutionary processes that give rise to, and limit, diversification within strain populations can be deduced from the form and distribution of genomic heterogeneity. The extent of genomic change that distinguishes the acidophilic archaeon Ferroplasma acidarmanus fer1 from an environmental population of the same species from the same site, fer1(env), was determined by comparing the 1.94-megabase (Mb) genome sequence of the isolate with that reconstructed from 8 Mb of environmental sequence data. The fer1(env) composite sequence sampled Ϸ92% of the isolate genome. Environmental sequence data were also analyzed to reveal genomic heterogeneity within the coexisting, coevolving fer1(env) population. Analyses revealed that transposase movement and the insertion and loss of blocks of novel genes of probable phage origin occur rapidly enough to give rise to heterogeneity in gene content within the local population. Because the environmental DNA was derived from many closely related individuals, it was possible to quantify gene sequence variability within the population. All but a few gene variants show evidence of strong purifying selection. Based on the small number of distinct sequence types and their distribution, we infer that the population is undergoing frequent genetic recombination, resulting in a mosaic genome pool that is shaped by selection. The larger genetic potential of the population relative to individuals within it and the combinatorial process that results in many closely related genome types may provide the basis for adaptation to environmental fluctuations.

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“…The Galaxy framework supports basic metagenomic analyses (Kosakovsky Pond et al 2009). An alternative to using a homology-based approach is to employ a machine-learning method that uses simple signatures of the reads, as implemented in TETRA (Teeling et al 2004), PhyloPythia (McHardy et al 2007, and GSOM/S-GSOM (Chan et al 2008). More recent tools include Phymm (Brady and Salzberg 2009) and NBC (Rosen et al 2010).…”

mentioning

confidence: 99%

Integrative analysis of environmental sequences using MEGAN4

Huson¹,

Mitra²,

Ruscheweyh³

et al. 2011

Genome Res.

1,263

1,067

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A major challenge in the analysis of environmental sequences is data integration. The question is how to analyze different types of data in a unified approach, addressing both the taxonomic and functional aspects. To facilitate such analyses, we have substantially extended MEGAN, a widely used taxonomic analysis program. The new program, MEGAN4, provides an integrated approach to the taxonomic and functional analysis of metagenomic, metatranscriptomic, metaproteomic, and rRNA data. While taxonomic analysis is performed based on the NCBI taxonomy, functional analysis is performed using the SEED classification of subsystems and functional roles or the KEGG classification of pathways and enzymes. A number of examples illustrate how such analyses can be performed, and show that one can also import and compare classification results obtained using others' tools. MEGAN4 is freely available for academic purposes, and installers for all three major operating systems can be downloaded from www-ab.informatik.uni-tuebingen.de/software/megan.

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TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences

Cited by 310 publications

References 22 publications

Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis

Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis

Genome dynamics in a natural archaeal population

Integrative analysis of environmental sequences using MEGAN4

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