plasmidSPAdes: assembling plasmids from whole genome sequencing data

Antipov, Dmitry; Hartwick, Nolan; Shen, Max W.; Raiko, Mikhail; Lapidus, Alla; Pevzner, Pavel A.

doi:10.1093/bioinformatics/btw493

Cited by 462 publications

(350 citation statements)

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“…To find this cryptic plasmid the contigs from the de novo assembly were mapped against the reference PacBio sequence of JF4335 using Bowtie2 v2.2.4 with default settings. Additionally, the raw reads of all 20 strains were assembled with plasmidSPAdes (Antipov et al, 2016). …”

Section: Methodsmentioning

confidence: 99%

Clostridium chauvoei, an Evolutionary Dead-End Pathogen

et al. 2017

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Full genome sequences of 20 strains of Clostridium chauvoei, the etiological agent of blackleg of cattle and sheep, isolated from four different continents over a period of 64 years (1951–2015) were determined and analyzed. The study reveals that the genome of the species C. chauvoei is highly homogeneous compared to the closely related species C. perfringens, a widespread pathogen that affects human and many animal species. Analysis of the CRISPR locus is sufficient to differentiate most C. chauvoei strains and is the most heterogenous region in the genome, containing in total 187 different spacer elements that are distributed as 30 – 77 copies in the various strains. Some genetic differences are found in the 3 allelic variants of fliC1, fliC2 and fliC3 genes that encode structural flagellin proteins, and certain strains do only contain one or two alleles. However, the major virulence genes including the highly toxic C.chauvoei toxin A, the sialidase and the two hyaluronidases are fully conserved as are the metabolic and structural genes of C. chauvoei. These data indicate that C. chauvoei is a strict ruminant-associated pathogen that has reached a dead end in its evolution.

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Section: Methodsmentioning

confidence: 99%

Clostridium chauvoei, an Evolutionary Dead-End Pathogen

et al. 2017

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“…For a previously uncharacterized bacterium, multiple contigs could lead to the impression of having a near-finished genome assembly instead of megaplasmid sequences in the absence of manual inspection. We expect new tools such as plasmidSPAdes (Antipov et al, 2016) will be useful in assembling and assessing plasmid DNA content from whole genome sequencing data. Automated HGAP assembly of LQRI obtained a near-finished assembly containing two contigs.…”

Section: Resultsmentioning

confidence: 99%

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

et al. 2017

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This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.

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“…The final assembly yielded 21 contigs (≥500 bp), for a total genome length of 5,651,625 bp, a G+C content of 65.05%, and an N 50 value of 327,924 bp. One plasmid (8,482 bp) similar to the plasmid of the strain CGA009 (12) was confirmed by plasmidSPAdes (27). Gene annotations were carried out with the Prokaryotic Genome Annotation Pipeline (PGAP) (28) and RAST version 2.0 (29).…”

Section: Genome Announcementmentioning

confidence: 86%