Phigaro: high throughput prophage sequence annotation

Starikova, Elizaveta V.; Tikhonova, Polina; Prianichnikov, Nikita; Rands, Chris M.; Zdobnov, Evgeny M.; Govorun, Vadim M.

doi:10.1101/598243

Cited by 24 publications

(29 citation statements)

References 10 publications

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“…Inverted terminal repeats are a hallmark of transposons 30 but have also been observed in complete viral genomes 31 and phages 32 . Lastly, complete proviruses are identified by a viral region flanked by host DNA on both sides and are commonly found in microbial (meta)genomes 10,11,23,24 . While these are well-established approaches, false positives have also been observed 33 and so, to mitigate this, CheckV reports a confidence level for putative complete genomes based on the estimated completeness from the AAI-or HMM-based approaches: high confidence (≥90% completeness), medium confidence (80-90% completeness) or low confidence (<80% completeness).…”

Section: Resultsmentioning

confidence: 99%

“…For comparison, we evaluated four other tools to identify hostprovirus boundaries, including VIBRANT 11 , VirSorter 10 , PhiSpy 23 and Phigaro 24 . Compared to these four tools, CheckV displayed consistently higher sensitivity but, in particular, when fragments were short or host contamination was low (Fig.…”

Section: Accurate Estimation Of Genome Completeness For Novel Virusesmentioning

confidence: 99%

“…With regard to host contamination on proviruses, existing approaches either remove viral contigs containing a high fraction of microbial genes 5 or predict host-virus boundaries 10,11,23,24 . The former approach allows for a small number of microbial genes while the latter may fail to identify a host region or misidentify the true boundary.…”

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confidence: 99%

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CheckV assesses the quality and completeness of metagenome-assembled viral genomes

et al. 2020

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Millions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying closed viral genomes, estimating the completeness of genome fragments and removing flanking host regions from integrated proviruses. CheckV estimates completeness by comparing sequences with a large database of complete viral genomes, including 76,262 identified from a systematic search of publicly available metagenomes, metatranscriptomes and metaviromes. After validation on mock datasets and comparison to existing methods, we applied CheckV to large and diverse collections of metagenome-assembled viral sequences, including IMG/VR and the Global Ocean Virome. This revealed 44,652 high-quality viral genomes (that is, >90% complete), although the vast majority of sequences were small fragments, which highlights the challenge of assembling viral genomes from short-read metagenomes. Additionally, we found that removal of host contamination substantially improved the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions.

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Section: Resultsmentioning

confidence: 99%

Section: Accurate Estimation Of Genome Completeness For Novel Virusesmentioning

confidence: 99%

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CheckV assesses the quality and completeness of metagenome-assembled viral genomes

et al. 2020

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“…Phylogroups were predicted using the ClermonTyping online tool 55 . Moreover, to characterize the strains mobilome, prophages were searched with Phigaro 56 and Phaster 57 ; CRISPRCasFinder 58 was used for the report of CRISPR/Cas cassettes and a custom database of IntI1, Intl2, Intl3, qacEdelta1 and sul1 genes was used for identification of integrons and Pipolins extraction and re-annotation. Pipolin-harboring E. coli genomes were retrieved from NCBI Genbank nucleotide collection using TBLASTN 63 (October 30, 2019) and the piPolB amino acid sequence from E. coli 3-373-03_S1_C2 (Uniprot P0DPS1) as a query.…”

Section: Discussionmentioning

confidence: 99%

High diversity and variability of pipolins among a wide range of pathogenic Escherichia coli strains

Flament-Simon

Toro

Chuprikova

et al. 2020

Sci Rep

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Self-synthesizing transposons are integrative mobile genetic elements (MGEs) that encode their own B-family DNA polymerase (PolB). Discovered a few years ago, they are proposed as key players in the evolution of several groups of DNA viruses and virus-host interaction machinery. Pipolins are the most recent addition to the group, are integrated in the genomes of bacteria from diverse phyla and also present as circular plasmids in mitochondria. Remarkably, pipolins-encoded PolBs are proficient DNA polymerases endowed with DNA priming capacity, hence the name, primer-independent PolB (piPolB). We have now surveyed the presence of pipolins in a collection of 2,238 human and animal pathogenic Escherichia coli strains and found that, although detected in only 25 positive isolates (1.1%), they are present in E. coli strains from a wide variety of pathotypes, serotypes, phylogenetic groups and sequence types. Overall, the pangenome of strains carrying pipolins is highly diverse, despite the fact that a considerable number of strains belong to only three clonal complexes (CC10, CC23 and CC32). Comparative analysis with a set of 67 additional pipolin-harboring genomes from GenBank database spanning strains from diverse origin, further confirmed these results. The genetic structure of pipolins shows great flexibility and variability, with the piPolB gene and the attachment sites being the only common features. Most pipolins contain one or more recombinases that would be involved in excision/integration of the element in the same conserved tRNA gene. This mobilization mechanism might explain the apparent incompatibility of pipolins with other integrative MGEs such as integrons. In addition, analysis of cophylogeny between pipolins and pipolin-harboring strains showed a lack of congruence between several pipolins and their host strains, in agreement with horizontal transfer between hosts. Overall, these results indicate that pipolins can serve as a vehicle for genetic transfer among circulating E. coli and possibly also among other pathogenic bacteria. Mobile genetic elements (MGE), comprising bacteriophages, transposons, plasmids, and insertion sequences, contribute to the great plasticity of the bacterial genome, resulting in an extremely large pangenomes that, in the case of Escherichia coli, can amount to more than 16,000 genes 1. Thus, MGEs dynamics is the main source of horizontal gene transfer, which leads to the spread of antimicrobial resistance (AR) among both E. coli and other commensals, thereby enlarging the spectrum of resistance (the resistome) among circulating strains 2. Pipolins constitute a recently reported new group of integrative MGEs widespread among diverse bacterial phyla and also identified in mitochondria as circular plasmids 3. The hallmark feature of the pipolins is a gene encoding for a replicative family B DNA polymerases (PolB) with an intrinsic de novo primer synthesis capacity,

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“…Phylogroups were predicted using the ClermonTyping online tool [55]. Moreover, to characterize the strains mobilome, prophages were searched with Phigaro [22] and Phaster [23]; CRISPRCasFinder [24] was used for the report of CRISPR/Cas cassettes and a custom database of IntI1, Intl2, Intl3, qacEdelta1 and sul1 genes was used for identification of integrons and subsequent integrity analysis with IntegronFinder [56].…”

Section: Antimicrobial Susceptibility Screening Of Lrec Pipolin-harbomentioning

confidence: 99%

High diversity and variability of pipolins among a wide range of pathogenicEscherichia colistrains

Flament-Simon¹,

Toro

Chuprikova

et al. 2020

Preprint

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31 32 Self-synthesizing transposons are integrative mobile genetic elements (MGEs) that 33 encode their own B-family DNA polymerase (PolB). Discovered a few years ago, they 34 are proposed as key players in the evolution of several groups of DNA viruses and 35 virus-host interaction machinery. Pipolins are the most recent addition to the group, are 36 integrated in the genomes of bacteria from diverse phyla and also present as circular 37 plasmids in mitochondria. Remarkably, pipolins-encoded PolBs are proficient DNA 38 polymerases endowed with DNA priming capacity, hence the name, primer-

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Phigaro: high throughput prophage sequence annotation

Cited by 24 publications

References 10 publications

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

High diversity and variability of pipolins among a wide range of pathogenic Escherichia coli strains

High diversity and variability of pipolins among a wide range of pathogenicEscherichia colistrains

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