SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry; Gurevich, Alexey; Dvorkin, Mikhail; Kulikov, Alexander S.; Lesin, Valery M.; Nikolenko, Sergey I.; Pham, Son; Prjibelski, Andrey D.; Pyshkin, Alexey V.; Sirotkin, Alexander; Vyahhi, Nikolay; Tesler, Glenn; Alekseyev, Max A.; Pevzner, Pavel A.

doi:10.1089/cmb.2012.0021

Cited by 21,128 publications

(16,489 citation statements)

References 41 publications

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“…We compared short-read NLR assemblies with long-read assemblies, and confirmed the fragmented reconstruction of the NLR-complement from short-read sequencing data; 41% CLC Assembly Cell (CLC, www.clcbio.com) or 43% SPAdes assembler 16 (Figure 1a-c). We found 327 sequences assembled from long-read data for which no high confidence short-read assembly is present.…”

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confidence: 66%

Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing

et al. 2016

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mentioning

confidence: 66%

Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing

et al. 2016

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“…We also attempted filtering the reads by alignment to w Ri and assembling with SPAdes 3.0 (Bankevich et al. 2012). The assembly of w Spc is available from GenBank under accession number NTHL00000000 (project number PRJNA401169, Biosample SAMN07599555).…”

Section: Methodsmentioning

confidence: 99%

Genome comparisons indicate recent transfer ofwRi‐likeWolbachiabetween sister speciesDrosophila suzukiiandD. subpulchrella

Conner

Blaxter

Anfora

et al. 2017

Ecology and Evolution

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Wolbachia endosymbionts may be acquired by horizontal transfer, by introgression through hybridization between closely related species, or by cladogenic retention during speciation. All three modes of acquisition have been demonstrated, but their relative frequency is largely unknown. Drosophila suzukii and its sister species D. subpulchrella harbor Wolbachia, denoted wSuz and wSpc, very closely related to wRi, identified in California populations of D. simulans. However, these variants differ in their induced phenotypes: wRi causes significant cytoplasmic incompatibility (CI) in D. simulans, but CI has not been detected in D. suzukii or D. subpulchrella. Our draft genomes of wSuz and wSpc contain full‐length copies of 703 of the 734 single‐copy genes found in wRi. Over these coding sequences, wSuz and wSpc differ by only 0.004% (i.e., 28 of 704,883 bp); they are sisters relative to wRi, from which each differs by 0.014%–0.015%. Using published data from D. melanogaster, Nasonia wasps and Nomada bees to calibrate relative rates of Wolbachia versus host nuclear divergence, we conclude that wSuz and wSpc are too similar—by at least a factor of 100—to be plausible candidates for cladogenic transmission. These three wRi‐like Wolbachia, which differ in CI phenotype in their native hosts, have different numbers of orthologs of genes postulated to contribute to CI; and the CI loci differ at several nucleotides that may account for the CI difference. We discuss the general problem of distinguishing alternative modes of Wolbachia acquisition, focusing on the difficulties posed by limited knowledge of variation in absolute and relative rates of molecular evolution for host nuclear genomes, mitochondria, and Wolbachia.

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“…The short read sequences were mapped using SMALT (http://www.sanger.ac.uk/resources/software/smalt/) to the reference emm 1 genome MGAS5005 (Genbank accession number NC_007297.2) and single nucleotide polymorphisms (SNPs) were identified. De novo sequences were generated using SPAdes [15]. Mapping and SNPs over regulatory regions and the hasA promoter were manually checked using Artemis [16].…”

Section: Methodsmentioning

confidence: 99%

Impact of contusion injury on intramuscular emm1 group a streptococcus infection and lymphatic spread

Siggins

Scudamore

et al. 2018

Virulence

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Invasive group A Streptococcus (iGAS) is frequently associated with emm1 isolates, with an attendant mortality of around 20%. Cases occasionally arise in previously healthy individuals with a history of upper respiratory tract infection, soft tissue contusion, and no obvious portal of entry. Using a new murine model of contusion, we determined the impact of contusion on iGAS bacterial burden and phenotype.Calibrated mild blunt contusion did not provide a focus for initiation or seeding of GAS that was detectable following systemic GAS bacteremia, but instead enhanced GAS migration to the local draining lymph node following GAS inoculation at the same time and site of contusion. Increased migration to lymph node was associated with emergence of mucoid bacteria, although was not specific to mucoid bacteria. In one study, mucoid colonies demonstrated a significant increase in capsular hyaluronan that was not linked to a covRS or rocA mutation, but to a deletion in the promoter of the capsule synthesis locus, hasABC, resulting in a strain with increased fitness for lymph node migration.In summary, in the mild contusion model used, we could not detect seeding of muscle by GAS. Contusion promoted bacterial transit to the local lymph node. The consequences of contusion-associated bacterial lymphatic migration may vary depending on the pathogen and virulence traits selected.

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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Cited by 21,128 publications

References 41 publications

Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing

Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing

Genome comparisons indicate recent transfer ofwRi‐likeWolbachiabetween sister speciesDrosophila suzukiiandD. subpulchrella

Impact of contusion injury on intramuscular emm1 group a streptococcus infection and lymphatic spread

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