SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments

Page, Andrew J.; Taylor, Ben; Delaney, Aidan; Soares, Jorge; Seemann, Torsten; Keane, Jacqueline A.; Harris, Simon R.

doi:10.1099/mgen.0.000056

Cited by 963 publications

(909 citation statements)

References 14 publications

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“…Reads from bneohCR1 and bneohCR2 genomes mapped to 98.6% of the B. suis 1330 genome. SNPs were called from the alignment by use of Samtools (http://samtools.sourceforge.net/), and 34,307 variable sites across all isolates were extracted by using SNP sites ( 13 ). The resulting alignment of SNPs was used for maximum-likelihood phylogenetic reconstruction by use of RAxML version 7.0.4 (https://github.com/stamatak/standard-RAxML).…”

Section: The Studymentioning

confidence: 99%

Brucella neotomaeInfection in Humans, Costa Rica

Suárez-Esquivel¹,

Ruíz-Villalobos²,

Jiménez-Rojas³

et al. 2017

Emerg. Infect. Dis.

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Section: The Studymentioning

confidence: 99%

Brucella neotomaeInfection in Humans, Costa Rica

Suárez-Esquivel¹,

Ruíz-Villalobos²,

Jiménez-Rojas³

et al. 2017

Emerg. Infect. Dis.

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“…SNP data were generated from a single multiple FASTA alignment of nucleotides for each species and each locus separately through SNP sites (v2.4.0; Page et al, ). We filtered this SNP set using vcftools (v0.1.13; Danecek et al, ) to select genotypes that were called in all samples and had no missing data.…”

Section: Methodsmentioning

confidence: 99%

Comparative phylogeography of trans‐Andean freshwater fishes based on genome‐wide nuclear and mitochondrial markers

2019

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The Neotropical region represents one of the greatest biodiversity hot spots on earth. Despite its unparalleled biodiversity, regional comparative phylogeographic studies are still scarce, with most focusing on model clades (e.g. birds) and typically examining a handful of loci. Here, we apply a genome‐wide comparative phylogeographic approach to test hypotheses of codiversification of freshwater fishes in the trans‐Andean region. Using target capture methods, we examined exon data for over 1,000 loci combined with complete mitochondrial genomes to study the phylogeographic history of five primary fish species (>150 individuals) collected from eight major river basins in Northwestern South America and Lower Central America. To assess their patterns of genetic structure, we inferred genealogical concordance taking into account all major aspects of phylogeography (within loci, across multiple genes, across species and among biogeographic provinces). Based on phylogeographic concordance factors, we tested four a priori biogeographic hypotheses, finding support for three of them and uncovering a novel, unexpected pattern of codiversification. The four emerging inter‐riverine patterns are as follows: (a) Tuira + Atrato, (b) Ranchería + Catatumbo, (c) Magdalena system and (d) Sinú + Atrato. These patterns are interpreted as shared responses to the complex uplifting and orogenic processes that modified or sundered watersheds, allowing codiversification and speciation over geological time. We also find evidence of cryptic speciation in one of the species examined and instances of mitochondrial introgression in others. These results help further our knowledge of the historical geographic factors shaping the outstanding biodiversity of the Neotropics.

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“…The consensus pseudo-sequences were generated from each BAM file and aligned with other sequences to generate whole-genome alignment of the study isolates. We adjusted for recombination and used Gubbins 29 to remove recombination sites from the whole-genome alignment and then generated an alignment of polymorphic (variable) sites only using SNP-Sites 30 . An ML phylogenetic tree was then reconstructed using this SNP alignment, again using RAxML with the same parameters used to construct the core-gene alignment tree.…”

Section: Methodsmentioning

confidence: 99%

Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting

Musicha¹,

Feasey

Cain

et al. 2017

Journal of Antimicrobial Chemotherapy

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Objectives: Efforts to treat Escherichia coli infections are increasingly being compromised by the rapid, global spread of antimicrobial resistance (AMR). Whilst AMR in E. coli has been extensively investigated in resource-rich settings, in sub-Saharan Africa molecular patterns of AMR are not well described. In this study, we have begun to explore the population structure and molecular determinants of AMR amongst E. coli isolates from Malawi. Methods: Ninety-four E. coli isolates from patients admitted to Queen’s Hospital, Malawi, were whole-genome sequenced. The isolates were selected on the basis of diversity of phenotypic resistance profiles and clinical source of isolation (blood, CSF and rectal swab). Sequence data were analysed using comparative genomics and phylogenetics. Results: Our results revealed the presence of five clades, which were strongly associated with E. coli phylogroups A, B1, B2, D and F. We identified 43 multilocus STs, of which ST131 (14.9%) and ST12 (9.6%) were the most common. We identified 25 AMR genes. The most common ESBL gene was blaCTX-M-15 and it was present in all five phylogroups and 11 STs, and most commonly detected in ST391 (4/4 isolates), ST648 (3/3 isolates) and ST131 [3/14 (21.4%) isolates]. Conclusions: This study has revealed a high diversity of lineages associated with AMR, including ESBL and fluoroquinolone resistance, in Malawi. The data highlight the value of longitudinal bacteraemia surveillance coupled with detailed molecular epidemiology in all settings, including low-income settings, in describing the global epidemiology of ESBL resistance.

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SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments

Cited by 963 publications

References 14 publications

Brucella neotomaeInfection in Humans, Costa Rica

Brucella neotomaeInfection in Humans, Costa Rica

Comparative phylogeography of trans‐Andean freshwater fishes based on genome‐wide nuclear and mitochondrial markers

Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting

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