Large-scale sequence comparisons with sourmash

Nt, Pierce; Irber, Luiz; Reiter, Taylor; Brooks, Phillip T.; Ct, Brown

doi:10.12688/f1000research.19675.1

Cited by 167 publications

(166 citation statements)

References 21 publications

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“…The UKMCC1015 strain has two plasmids: UKMCC1015_2 (7k bp) and UKMCC1015_3 (2k bp). We performed sequence comparison using sourmash (Pierce et al . 2019) against the PLSDB database (Galata et al .…”

Section: Resultsmentioning

confidence: 99%

Adaptation of a fluoroquinolone-sensitiveShigella sonneito norfloxacin exposure

Bao

Zoqratt

I-Ning

et al. 2020

Preprint

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Shigella spp. commonly causes gastroenteritis known as shigellosis, and severe cases require antibiotic treatments. However, the increased presence of antibiotics in the environment in recent years can lead to antibiotic resistance. Sub-lethal antibiotic concentrations can promote resistance, but its effect on sensitive bacteria prior to resistance development is unknown. In this study, the complete genome of Shigella sonnei UKMCC1015, a sensitive strain from Malaysia is presented. Subsequently, the transcriptomic response of this strain towards sub-MIC levels of norfloxacin, a commonly used fluoroquinolone is investigated. This study reveals that the expressions of the antimicrobial resistance genes and antibiotic targets (DNA gyrase and topoisomerase IV) are not affected. Interestingly, multiple ribosomal protein operons were downregulated while a small regulatory RNA (sRNA), GcvB was upregulated in response to constant exposure to sub-MIC norfloxacin.. To our knowledge, association between sub-lethal fluoroquinolone and expression of ribosomal protein operons as well as GcvB sRNA have never been reported. Collectively, these findings suggest that there are novel pathways possibly related to ppGpp levels that are involved in the adaptive response of S. sonnei towards fluoroquinolones.Impact StatementIn this study, the genome of a sensitive Shigella sonnei UKMCC1015 and the transcriptomic analysis of its response towards sub-lethal norfloxacin is presented. This study brings new information towards the multitudes of responses S. sonnei can have against a low concentration of antibiotics, including the involvement of the stringent response and a small non-coding RNA called GcvB. This study also highlights the idea that the response of a sensitive strain towards antibiotics are different compared to a resistant strain. Future studies elucidating the exact pathways involving the stringent response and GcvB can lead to the discovery of potential targets as antibiotics or as anti-resistance agents.Data SummaryThe complete genome of Shigella sonnei UKMCC1015 and its plasmids has been deposited at GenBank under accession numbers CP060117, CP060118 and CP060119. RNA-seq data are accessible through BioSample accession number SAMN16871737.

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Section: Resultsmentioning

confidence: 99%

Adaptation of a fluoroquinolone-sensitiveShigella sonneito norfloxacin exposure

Bao

Zoqratt

I-Ning

et al. 2020

Preprint

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“…Automated genome assembly was performed with the tool Automatic Assembly For The Fungi (AAFTF) which performs read trimming and filtering against PhiX and other contaminants using BBMap v38.16 followed by genome assembly with SPAdes v3.13.1 (Bankevich et al 2012;Bushnell 2014;Stajich 2018. Assemblies were further cleaned of vector sequences, screened for contaminant bacteria with sourmash using database Genbank Microbes 2018.03.29 (Brown and Irber 2016;Pierce et al 2019). Duplicated small contigs were removed using minimap2 v2.17 alignment of contigs smaller than the assembly N50 (Li 2018).…”

Section: Low-coverage Genome (Lcg) Sequence Analysismentioning

confidence: 99%

Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics

et al. 2020

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Early efforts to classify Mortierellaceae were based on macro-and micromorphology, but sequencing and phylogenetic studies with ribosomal DNA (rDNA) markers have demonstrated conflicting taxonomic groupings and polyphyletic genera. Although some taxonomic confusion in the family has been clarified, rDNA data alone is unable to resolve higher level phylogenetic relationships within Mortierellaceae. In this study, we applied two parallel approaches to resolve the Mortierellaceae phylogeny: low coverage genome (LCG) sequencing and high-throughput, multiplexed targeted amplicon sequencing to generate sequence data for multi-gene phylogenetics. We then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset. Resolving the Mortierellaceae phylogeny into monophyletic genera resulted in 13 genera, 7 of which are newly proposed. Low-coverage genome sequencing proved to be a relatively cost-effective means of generating a high-confidence phylogeny. The multi-gene phylogenetics approach enabled much greater sampling depth and breadth than the LCG approach, but has limitations too. We present this work to resolve some of the taxonomic confusion and provide a genus-level framework to empower future studies on Mortierellaceae diversity and evolution.

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“…The minhash techniques have been proven to be efficient for estimating similarity in many applications that involve large datasets [11]. They have also been used for many bioinformatics applications especially for analyzing large-scale sequencing datasets [14,18]. Our algorithm makes use of LSH-based bucketing from minhash signatures to cluster the isoform sequences.…”

Section: Resultsmentioning

confidence: 99%