Mash Screen: High-throughput sequence containment estimation for genome discovery

Ondov, Brian D.; Starrett, Gabriel J.; Sappington, Anna; Kostic, Aleksandra M.; Koren, Sergey; Buck, Christopher B.; Phillippy, Adam M.

doi:10.1101/557314

Cited by 54 publications

(67 citation statements)

References 28 publications

(28 reference statements)

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“…Because the PLASMIDOME data set did not contain information about the reference plasmids, we generated some references for this data set by mapping the assembled PLASMIDOME contigs against the plasmid database (with Mash screen [Ondov et al 2019], QUAST [Gurevich et al 2013], and BLAST). This analysis revealed 10 reference plasmids with a total length of ≈100 kb.…”

Section: Analyzing the Plasmidome Data Setmentioning

confidence: 99%

Plasmid detection and assembly in genomic and metagenomic data sets

et al. 2019

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Although plasmids are important for bacterial survival and adaptation, plasmid detection and assembly from genomic, let alone metagenomic, samples remain challenging. The recently developed plasmidSPAdes assembler addressed some of these challenges in the case of isolate genomes but stopped short of detecting plasmids in metagenomic assemblies, an untapped source of yet to be discovered plasmids. We present the metaplasmidSPAdes tool for plasmid assembly in metagenomic data sets that reduced the false positive rate of plasmid detection compared with the state-of-the-art approaches. We assembled plasmids in diverse data sets and have shown that thousands of plasmids remained below the radar in already completed genomic and metagenomic studies. Our analysis revealed the extreme variability of plasmids and has led to the discovery of many novel plasmids (including many plasmids carrying antibiotic-resistance genes) without significant similarities to currently known ones.

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Section: Analyzing the Plasmidome Data Setmentioning

confidence: 99%

Plasmid detection and assembly in genomic and metagenomic data sets

et al. 2019

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“…From these, we selected n=726 plasmids which contained an IncF replicon after classification with MOB-typer (see below). We searched all plasmids against PLSDB (version 2020-03-04) [33] which contains 20,668 complete published plasmids, using mash screen [34] and keeping the top hit. All plasmids had a match.…”

Section: Discussionmentioning

confidence: 99%

Genomic network analysis of an environmental and livestock IncF plasmid population

Matlock

Chau

AbuOun

et al. 2020

Preprint

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IncF plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacteriaceae. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of IncF plasmids from environmental (influent, effluent, and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable IncF plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The recent association of IncF plasmids with AMR likely reflects their suitability for rapid niche adaptation.

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“…To date, a total of 102 polyomaviruses have been reported around the world, 13 of which are human polyomaviruses (HPyVs), including BKPyV and JCPyV identi ed in the early 1970s, and 11 types of HPyV detected since 2007, including KIPyV, WUPyV, and MCPyV [2]. Additionally, Quebec polyomavirus (QPyV) discovered recently from human fecal samples through MinHash algorithm has not yet be included by ICTV [22]. HPyVs can cause diseases of the nervous system, hematopoietic system, urogenital tract, and skin [6], with two main characteristics.…”

Section: Discussionmentioning

confidence: 99%

Isolation and Characterization of WUPyV in Polarized Human Airway Epithelial Cells

Wang

Wei

Huang

et al. 2020

Preprint

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Abstract Background: Washington University polyomavirus (WUPyV) is a novel human polyomavirus detected in childwith acute respiratory infection in 2007. However, the relationship between WUPyV and respiratory diseases has yet to be established for lacking of a suitable in vitro culture system. Methods: To isolate WUPyV with human airway epithelial (HAE) cells, the positive samples were incubated in HAE, and then the nucleic acid, VP1 protein and virions were detected using real-time PCR, immunofluorescence and electron microscopy respectively. Results: The result showed that WUPyV could replicate effectively in HAE cells and virions with typical polyomavirus characteristics could be observed. Additionally, the entire genome sequence of the isolated strain (BJ0771) was obtained and phylogenetic analysis indicated that BJ0771 belongs to gene cluster Ⅰ. Conclusions: Our findings demonstrated clinical WUPyV strain was successfully isolated for the first time in the world and this will help unravel the etiology and pathogenic mechanisms of WUPyV in respiratory infection diseases.

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Mash Screen: High-throughput sequence containment estimation for genome discovery

Cited by 54 publications

References 28 publications

Plasmid detection and assembly in genomic and metagenomic data sets

Plasmid detection and assembly in genomic and metagenomic data sets

Genomic network analysis of an environmental and livestock IncF plasmid population

Isolation and Characterization of WUPyV in Polarized Human Airway Epithelial Cells

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