Recycler: an algorithm for detecting plasmids from <i>de novo</i> assembly graphs

Rozov, Roye; Kav, Aya Brown; Bogumil, David; Shterzer, Naama; Halperin, Eran; Mizrahi, Itzhak; Shamir, Ron

doi:10.1093/bioinformatics/btw651

Cited by 126 publications

(90 citation statements)

References 29 publications

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“…Detection and reconstruction of plasmids in the different L. mudanjiangensis strains 443 was performed using Recycler v0.7 [46], with the original fastq files and SPAdes 444 assembly graphs as input. The assembled plasmids were annotated with Prokka and 445 further characterized by scanning against the EggNOG database, as described in above.…”

Section: Plasmid Identification 442mentioning

confidence: 99%

“…the L. plantarum group, using a comparative genomics approach. Therefore, the 45 genome of the type strain of L. mudanjiangensis was sequenced together with three 46 strains isolated from fermented carrot juice. These and other publicly available genome 47 sequences were used to screen for L. mudanjiangensis species-specific properties, which 48 included an analysis for the presence of genes related to pili formation and conjugation.…”

mentioning

confidence: 99%

“…In contrast, the system was completely absent in clade5a, L. Many conjugation systems are coded on plasmids [27]. Therefore, all four L. 224 mudanjiangensis genomes were screened for plasmid presence using Recycler [46].…”

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confidence: 99%

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Comparative genome analysis ofLactobacillus mudanjiangensis, an understudied member of theLactobacillus plantarumgroup

Wuyts

Allonsius

Wittouck

et al. 2019

Preprint

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The genus Lactobacillus is known to be extremely diverse and consists of different phylogenetic groups that show a diversity roughly equal to the expected diversity of a typical bacterial genus. One of the most prominent phylogenetic groups within this genus is the Lactobacillus plantarum group which contains the understudied Lactobacillus mudanjiangensis species. Before this study, only one L. mudanjiangensis strain, DSM 28402 T , was described but without whole-genome analysis. In this study, three strains classified as L. mudanjiangensis, were isolated from three different carrot juice fermentations and their whole-genome sequence was determined, together with the genome sequence of the type strain. The genomes of all four strains were compared with publicly available L. plantarum group genome sequences. This analysis showed that L. mudanjiangensis harbored the second largest genome size and gene count of the whole L. plantarum group. In addition, all members of this species showed the presence of a gene coding for a putative cellulose-degrading enzyme. Finally, three of the four L. mudanjiangensis strains studied showed the presence of pili on scanning electron microscopy (SEM) images, which were linked to conjugative gene regions, coded on plasmids in at least two of the strains studied. Author summaryLactobacillus mudanjiangensis is an understudied species within the Lactobacillus plantarum group. Since its first description, no other studies have reported its isolation. Here, we present the first four genome sequences of this species, which include the genome sequence of the type strain and three new L. mudanjiangensis strains isolated from fermented carrot juice. The genomes of all four strains were compared with publicly available L. plantarum group genome sequences. We found that this species February 5, 2019 1/20 harbored the second largest genome size and gene count of the whole L. plantarum group. Furthermore, we present the first scanning electron microscopy (SEM) images of L. mudanjiangensis, which showed the formation of pili in three strains that we linked to genes related to conjugation. Finally, we found the presence of a unique putative cellulose-degrading enzyme, opening the door for different industrial applications of these Lactobacillus strains. Introduction 1The genus Lactobacillus is known to be extremely diverse [1]. Furthermore, it has been 2 shown that different phylogenetic groups within this genus display a diversity roughly 3 equal to the expected diversity of a typical bacterial genus [2][3][4][5][6]. Each of these 4 phylogenetic groups can be recognized as an entity with unique properties and a distinct 5 natural history, ecology, function and physiology [5]. Therefore, the study of these 6 phylogenetic groups separately, as if they would be one genus, can be an interesting 7 approach that might reveal new, previously overlooked, phylogenetic relationships and 8 functional properties. 9 One of the more abundantly studied species within the genus Lactobacillus, is 10 Lactobacillus...

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Section: Plasmid Identification 442mentioning

confidence: 99%

mentioning

confidence: 99%

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Comparative genome analysis ofLactobacillus mudanjiangensis, an understudied member of theLactobacillus plantarumgroup

Wuyts

Allonsius

Wittouck

et al. 2019

Preprint

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“…Repeated sequences, often shared between plasmid and chromosomal DNA, hinder the assembly of the bacterial genome from short-read sequence data, often resulting in contigs of which the origin, either plasmid or chromosomal, cannot be resolved. In recent years, several tools to study plasmids using WGS data were developed and include PLACNET, PlasmidFinder, cBar, HyAsP, MOB-suite, PlasmidTron, Recycler, and PlasmidSPAdes ( [4][5][6][7][8][9][10][11]. Only Recycler and PlasmidSPAdes are fully automated computer programs that aim to de novo reconstruct whole plasmid sequences from short-read sequence data ( 7,8 ).…”

Section: Introductionmentioning

confidence: 99%

“…In recent years, several tools to study plasmids using WGS data were developed and include PLACNET, PlasmidFinder, cBar, HyAsP, MOB-suite, PlasmidTron, Recycler, and PlasmidSPAdes ( [4][5][6][7][8][9][10][11]. Only Recycler and PlasmidSPAdes are fully automated computer programs that aim to de novo reconstruct whole plasmid sequences from short-read sequence data ( 7,8 ). Recent studies benchmarked the PlasmidSPAdes and Recycler algorithm for genomes of Gram-negative bacteria ( 12,13 ).…”

Section: Introductionmentioning

confidence: 99%

Detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicons in Enterobacteriaceae using PlasmidSPAdes assembly of short-read sequence data

Stohr

Bergh

Wedema

et al. 2019

Preprint

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INTRODUCTION: Knowledge of the epidemiology of plasmids is essential for understanding the evolution and spread of antimicrobial resistance. PlasmidSPAdes attempts to reconstruct plasmids using short-read sequence data. Accurate detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicon genes is a prerequisite for the use of plasmid assembly tools to investigate the role of plasmids in the spread and evolution of ESBL production in Enterobacteriaceae. This study evaluated the performance of PlasmidSPAdes plasmid assembly for Enterobacteriaceae in terms of detection of ESBL-encoding genes, plasmid replicons and chromosomal genes, and assessed the effect of k-mer size.METHODS: Short-read sequence data of 59 ESBL-producing Enterobacteriaceae were assembled with PlasmidSPAdes using different k-mer sizes (21, 33, 55, 77, 99 and 127). For every k-mer size, the presence of ESBL genes, plasmid replicons and a selection of chromosomal genes in the plasmid assembly was determined.RESULTS: Out of 241 plasmid replicons and 66 ESBL genes detected by whole-genome assemblies, 213 plasmid replicons (88%; 95% Confidence Interval (CI): 83.9-91.9) and 43 ESBL genes (65%; 95%CI: 53.1-75.6) were detected in the plasmid assemblies obtained by PlasmidSPAdes. For most ESBL genes (83.3%) and plasmid replicons (72.0%), detection results did not differ between the k-mer sizes used in the plasmid assembly. No optimal k-mer size could be defined for the number of ESBL genes and plasmid replicons detected. For most isolates, the number of chromosomal genes detected in the plasmid assemblies decreased with increasing k-mer size.CONCLUSION: Based on our findings, PlasmidSPAdes is not a suitable plasmid assembly tool for short-read sequence data of ESBL-encoding plasmids of Enterobacteriaceae.

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The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements

Browne¹,

Kot²,

Jørgensen³

et al. 2019

Methods in Molecular Biology

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Recycler: an algorithm for detecting plasmids from de novo assembly graphs

Cited by 126 publications

References 29 publications

Comparative genome analysis ofLactobacillus mudanjiangensis, an understudied member of theLactobacillus plantarumgroup

Comparative genome analysis ofLactobacillus mudanjiangensis, an understudied member of theLactobacillus plantarumgroup

Detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicons in Enterobacteriaceae using PlasmidSPAdes assembly of short-read sequence data

The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements

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