ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes

Varani, Alessandro de Mello; Siguier, Patricia; Gourbeyre, Edith; Charneau, Vincent; Chandler, Michaël

doi:10.1186/gb-2011-12-3-r30

Cited by 296 publications

(291 citation statements)

References 19 publications

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“…The contig sequences were submitted to the online tool and analysed using the default setting. The web-based tool ISsaga (issaga.biotoul.fr/ ISsaga/issaga_index.php) was used to predict putative insertion sequences (Varani et al, 2011). Both the nucleic acid contigs and the amino acid fasta file were uploaded and analysed using the default settings.…”

Section: Methodsmentioning

confidence: 99%

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Comparison of Lactobacillus crispatus isolates from Lactobacillus-dominated vaginal microbiomes with isolates from microbiomes containing bacterial vaginosis-associated bacteria

et al. 2016

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Vaginal lactobacilli can inhibit colonization by and growth of other bacteria, thereby preventing development of bacterial vaginosis (BV). Amongst the lactobacilli, Lactobacillus crispatus appears to be particularly effective at inhibiting growth of BV-associated bacteria. Nonetheless, some women who are colonized with this species can still develop clinical BV. Therefore, we sought to determine whether strains of L. crispatus that colonize women with lactobacillidominated vaginal microbiomes are distinct from strains that colonize women who develop BV. The genomes of L. crispatus isolates from four women with lactobacilli-dominated vaginal microbiomes (,1 % 16S rRNA reads above threshold from genera other than Lactobacillus) and four women with microbiomes containing BV-associated bacteria (.12 % 16S rRNA reads from bacterial taxa associated with BV) were sequenced and compared. Lactic acid production by the different strains was quantified. Phage induction in the strains was also analysed. There was considerable genetic diversity between strains, and several genes were exclusive to either the strains from Lactobacillus-dominated microbiomes or those containing BV-associated bacteria. Overall, strains from microbiomes dominated by lactobacilli did not differ from strains from microbiomes containing BV-associated bacteria with respect to lactic acid production. All of the strains contained multiple phage, but there was no clear distinction between the presence or absence of BV-associated bacteria with respect to phage-induced lysis. Genes found to be exclusive to the Lactobacillus-dominated versus BV-associated bacteria-containing microbiomes could play a role in the maintenance of vaginal health and the development of BV, respectively.

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Section: Methodsmentioning

confidence: 99%

“…Insertion sequences in the strains were identified using ISsaga (Varani et al, 2011). Each strain was found to contain multiple insertion sequences from different insertion sequence families (Table S3).…”

Section: Mobile Elementsmentioning

confidence: 99%

Comparison of Lactobacillus crispatus isolates from Lactobacillus-dominated vaginal microbiomes with isolates from microbiomes containing bacterial vaginosis-associated bacteria

et al. 2016

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“…The sequence was analyzed using Prodigal to call protein-coding genes, tRNAscan-SE (Lowe and Eddy 1997) to locate tRNA genes, MUMmer (Kurtz et al 2004) to detect repeats, ISSaga (Varani et al 2011) to identify IS elements, BLAST (Altschul et al 1990) and InterProScan (Zdobnov and Apweiler 2001) to assign putative functions to protein-coding genes, and ORTHOMCL to define orthologs shared with other Wolbachia strains. Metabolic pathways were examined using the SEED (Overbeek et al 2005) and Kyoto Encyclopaedia of Genes and Genomes (Kanehisa and Goto 2000) databases.…”

Section: Genome Sequencementioning

confidence: 99%

Analysis of gene expression from theWolbachiagenome of a filarial nematode supports both metabolic and defensive roles within the symbiosis

et al. 2012

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The a-proteobacterium Wolbachia is probably the most prevalent, vertically transmitted symbiont on Earth. In contrast with its wide distribution in arthropods, Wolbachia is restricted to one family of animal-parasitic nematodes, the Onchocercidae. This includes filarial pathogens such as Onchocerca volvulus, the cause of human onchocerciasis, or river blindness. The symbiosis between filariae and Wolbachia is obligate, although the basis of this dependency is not fully understood. Previous studies suggested that Wolbachia may provision metabolites (e.g., haem, riboflavin, and nucleotides) and/or contribute to immune defense. Importantly, Wolbachia is restricted to somatic tissues in adult male worms, whereas females also harbor bacteria in the germline. We sought to characterize the nature of the symbiosis between Wolbachia and O. ochengi, a bovine parasite representing the closest relative of O. volvulus. First, we sequenced the complete genome of Wolbachia strain wOo, which revealed an inability to synthesize riboflavin de novo. Using RNA-seq, we also generated endobacterial transcriptomes from male soma and female germline. In the soma, transcripts for membrane transport and respiration were up-regulated, while the gonad exhibited enrichment for DNA replication and translation. The most abundant Wolbachia proteins, as determined by geLC-MS, included ligands for mammalian Toll-like receptors. Enzymes involved in nucleotide synthesis were dominant among metabolism-related proteins, whereas the haem biosynthetic pathway was poorly represented. We conclude that Wolbachia may have a mitochondrion-like function in the soma, generating ATP for its host. Moreover, the abundance of immunogenic proteins in wOo suggests a role in diverting the immune system toward an ineffective antibacterial response.

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“…The coding sequences (CDS) were predicted by using Glimmer version 3.02 (5), and homologous comparison to the NCBI nonredundant public database for function annotations was performed by BLAST. The rRNA and tRNA were identified using RNAmmer (8) and tRNAscan-SE 1.21 (14), respectively, and the insertion sequence (IS) elements were annotated with ISsaga (16).…”

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confidence: 99%

Draft Genome Sequences of Two Legionella dumoffii Strains, TEX-KL and NY-23

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et al. 2012

Journal of Bacteriology

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ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes

Cited by 296 publications

References 19 publications

Comparison of Lactobacillus crispatus isolates from Lactobacillus-dominated vaginal microbiomes with isolates from microbiomes containing bacterial vaginosis-associated bacteria

Comparison of Lactobacillus crispatus isolates from Lactobacillus-dominated vaginal microbiomes with isolates from microbiomes containing bacterial vaginosis-associated bacteria

Analysis of gene expression from theWolbachiagenome of a filarial nematode supports both metabolic and defensive roles within the symbiosis

Draft Genome Sequences of Two Legionella dumoffii Strains, TEX-KL and NY-23

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