The CGView Server: a comparative genomics tool for circular genomes

Grant, Jason R.; Stothard, Paul

doi:10.1093/nar/gkn179

Cited by 1,222 publications

(867 citation statements)

References 12 publications

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“…In the absence of a characteristic cluster of dnaA boxes, we used the CGview Server [46] to analyze the GC skew of the genome. The CGView Server calculates GC skew as (G-C)/(G+C) using sliding windows of 1000 bp and a step size of 10 bp.…”

Section: Methodsmentioning

confidence: 99%

Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist

Williams

Wernegreen

2010

BMC Genomics

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BackgroundBlochmannia are obligately intracellular bacterial mutualists of ants of the tribe Camponotini. Blochmannia perform key nutritional functions for the host, including synthesis of several essential amino acids. We used Illumina technology to sequence the genome of Blochmannia associated with Camponotus vafer.ResultsAlthough Blochmannia vafer retains many nutritional functions, it is missing glutamine synthetase (glnA), a component of the nitrogen recycling pathway encoded by the previously sequenced B. floridanus and B. pennsylvanicus. With the exception of Ureaplasma, B. vafer is the only sequenced bacterium to date that encodes urease but lacks the ability to assimilate ammonia into glutamine or glutamate. Loss of glnA occurred in a deletion hotspot near the putative replication origin. Overall, compared to the likely gene set of their common ancestor, 31 genes are missing or eroded in B. vafer, compared to 28 in B. floridanus and four in B. pennsylvanicus. Three genes (queA, visC and yggS) show convergent loss or erosion, suggesting relaxed selection for their functions. Eight B. vafer genes contain frameshifts in homopolymeric tracts that may be corrected by transcriptional slippage. Two of these encode DNA replication proteins: dnaX, which we infer is also frameshifted in B. floridanus, and dnaG.ConclusionsComparing the B. vafer genome with B. pennsylvanicus and B. floridanus refines the core genes shared within the mutualist group, thereby clarifying functions required across ant host species. This third genome also allows us to track gene loss and erosion in a phylogenetic context to more fully understand processes of genome reduction.

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Section: Methodsmentioning

confidence: 99%

Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist

Williams

Wernegreen

2010

BMC Genomics

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“…Rho-independent terminators were identified using Softberry's FINDTERM, with the default energy threshold set to À 16 kCal (Weigele et al, 2007). The genomic map was constructed using GCview (Grant and Stothard, 2008). The genome of S-EIV1 was compared with fosmid MEDDCM-OCT-S04-C348 (Ghai et al, 2010) by using a tBLASTx analysis (cutoff e-value40.0001).…”

Section: Structural Proteinsmentioning

confidence: 99%

Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages

et al. 2015

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Cyanobacteria are often the dominant phototrophs in polar freshwater communities; yet, the phages that infect them remain unknown. Here, we present a genomic and morphological characterization of cyanophage S-EIV1 that was isolated from freshwaters on Ellesmere Island (Nunavut, High Arctic Canada), and which infects the polar Synechococcus sp., strain PCCC-A2c. S-EIV1 represents a newly discovered evolutionary lineage of bacteriophages whose representatives are widespread in aquatic systems. Among the 130 predicted open reading frames (ORFs) there is no recognizable similarity to genes that encode structural proteins other than the large terminase subunit and a distant viral morphogenesis protein, indicating that the genes encoding the structural proteins of S-EIV1 are distinct from other viruses. As well, only 19 predicted coding sequences on the 79 178 bp circularly permuted genome have homology with genes encoding proteins of known function. Although S-EIV1 is divergent from other sequenced phage isolates, it shares synteny with phage genes captured on a fosmid from the deep-chlorophyll maximum in the Mediterranean Sea, as well as with an incision element in the genome of Anabaena variabilis (ATCC 29413). Sequence recruitment of metagenomic data indicates that S-EIV1-like viruses are cosmopolitan and abundant in a wide range of aquatic systems, suggesting they have an important ecological role.

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“…Regions containing adhesins are marked with red boxes, and single adhesin genes are maked with a red arrow. The atlas was constructed using the CGView Server (70), and a large-scale version can be found in SI Appendix, Fig. S2.…”

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confidence: 99%

At the crossroads of vaginal health and disease, the genome sequence of Lactobacillus iners AB-1

Macklaim

Gloor²,

Anukam

et al. 2010

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

196

191

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Lactobacilli have long been regarded as important constituents of the healthy human vagina. Lactobacillus iners is the most frequently detected bacterial species in the vagina, but little is known about its characteristics. We report a description of the whole-genome sequence of L. iners AB-1 along with comparative analysis of published genomes of closely related strains of lactobacilli. The genome is the smallest Lactobacillus reported to date, with a 1.3-Mbp single chromosome. The genome seems to have undergone one or more rapid evolution events that resulted in large-scale gene loss and horizontal acquisition of a number of genes for survival in the vagina. L. iners may exhibit specialized adaptation mechanisms to the vaginal environment, such as an iron–sulfur cluster assembly system, and several unique σ factors to regulate gene transcription in this fluctuating environment. A potentially highly expressed homolog of a cholesterol-binding lysin may also contribute to host cell adhesion or act as a defense mechanism against other microbes. Notably, there is a lack of apparent adhesion proteins, but several cell-anchor proteins were identified and may be important for interaction with the host mucosal tissues. L. iners is widely present in healthy females as well as those suffering from bacterial vaginosis or who have undergone antimicrobial therapy, suggesting that it is an important indigenous species of the vagina.

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The CGView Server: a comparative genomics tool for circular genomes

Cited by 1,222 publications

References 12 publications

Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist

Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist

Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages

At the crossroads of vaginal health and disease, the genome sequence of Lactobacillus iners AB-1

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