Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows

Lemoine, Frédéric; Gascuel, Olivier

doi:10.1093/nargab/lqab075

Cited by 90 publications

(58 citation statements)

References 31 publications

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“…The multiple sequence alignment was trimmed using trimAl version 1.3 [ 55 ] to remove any positions where greater than 25% of the sequences had gaps. Identical sequences were then removed from the alignment so that only one copy was kept using the dedup function of Goalign version 0.3.5 [ 67 ]. In total, 182 out of 509 sequences were removed during the deduplication process.…”

Section: Methodsmentioning

confidence: 99%

Taxonomic distribution and evolutionary analysis of the equol biosynthesis gene cluster

Dufault‐Thompson

Hall

2022

BMC Genomics

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Background Equol, an isoflavonoid metabolite with possible health benefits in humans, is known to be produced by some human gut bacteria. While the genes encoding the equol production pathway have been characterized in a few bacterial strains, a systematic analysis of the equol production pathway is currently lacking. Results This study presents an analysis of the taxonomic distribution and evolutionary history of the gene cluster encoding the equol production pathway. A survey for equol gene clusters within the Genome Taxonomy Database bacterial genomes and human gut metagenomes resulted in the identification of a highly conserved gene cluster found in nine bacterial species from the Eggerthellaceae family. The identified gene clusters from human gut metagenomes revealed potential variations in the equol gene cluster organization and gene content within the equol-producing Eggerthellaceae clades. Subsequent analysis showed that in addition to the four genes directly involved in equol production, multiple other genes were consistently found in the equol gene clusters. These genes were predicted to encode a putative electron transport complex and hydrogenase maturase system, suggesting potential roles for them in the equol production pathway. Analysis of the gene clusters and a phylogenetic reconstruction of a putative NAD kinase gene provided evidence of the recent transfer of the equol gene cluster from a basal Eggerthellaceae species to Slackia_A equolifaciens, Enteroscipio sp000270285, and Lactococcus garvieae 20–92. Conclusions This analysis demonstrates that the highly conserved equol gene cluster is taxonomically restricted to the Eggerthellaceae family of bacteria and provides evidence of the role of horizontal gene transfer in the evolutionary history of these genes. These results provide a foundation for future studies of equol production in the human gut and future efforts related to bioengineering and the use of equol-producing bacteria as probiotics.

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Section: Methodsmentioning

confidence: 99%

Taxonomic distribution and evolutionary analysis of the equol biosynthesis gene cluster

Dufault‐Thompson

Hall

2022

BMC Genomics

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“…Phylogenies were produced from the entire set of sequences in each wave, using a custom workflow for building fast SARS-CoV-2 trees available at github.com/MDU-PHL/kovid-trees-nf. Briefly, sequences were cleaned to remove sites with > 5% missing calls and de-duplicated with GOALIGN [20]. An approximate maximum-likelihood tree was built using FastTree [21] and the branch lengths optimised with RAxML-NG [22].…”

Section: Methodsmentioning

confidence: 99%

Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19

Stockdale

Susvitasari

Tupper

et al. 2022

Preprint

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Estimating key aspects of transmission is crucial in infectious disease control. Serial intervals - the time between symptom onset in an infector and infectee - are fundamental, and help to define rates of transmission, estimates of reproductive numbers, and vaccination levels needed to prevent transmission. However, estimating the serial interval requires knowledge of individuals' contacts and exposures (who infected whom), which is typically obtained through resource-intensive contact tracing efforts. We develop an alternate framework that uses virus sequences to inform who infected whom and thereby estimate serial intervals. The advantages are many-fold: virus sequences are often routinely collected to support epidemiological investigations and to monitor viral evolution. The genomic approach offers high resolution and cluster-specific estimates of the serial interval that are comparable with those obtained from contact tracing data. Our approach does not require contact tracing data, and can be used in large populations and over a range of time periods. We apply our techniques to SARS-CoV-2 sequence data from the first two waves of COVID-19 in Victoria, Australia. We find that serial interval estimates vary between clusters, supporting the need to monitor this key parameter and use updated estimates in onward applications. Compared to an early published serial interval estimate, using cluster-specific serial intervals can cause estimates of the effective reproduction number Rt to vary by a factor of up to 2-3. We also find that serial intervals estimated in settings such as schools and meat processing/packing plants tend to be shorter than those estimated in healthcare facilities.

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“…To generate a global alignment of all sequences, reads and shredded assemblies were mapped to reference genome USA300 FPR3757 (assembly accession: GCF_000013465.1) (using Snippy, v4.6.0 (https://github.com/tseemann/snippy). The core genome alignment was obtained using Snippy; sites with > 10% gaps were removed using Goalign (102) and constant sites were removed using SNP-sites (103), for a final length of 186,825 bp. A maximum-likelihood phylogenetic tree of 2,590 sequences (those kept in the analysis after excluding genetically unrelated strains, see below) was inferred using IQ-TREE, v2.0.3 (104).…”

Section: Methodsmentioning

confidence: 99%

Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections

Giulieri

Guérillot

Duchêne

et al. 2022

Preprint

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During severe infections, Staphylococcus aureus moves from its colonising sites to blood and tissues, and is exposed to new selective pressures, thus potentially driving adaptive evolution. Previous studies have shown the key role of the agr locus in S. aureus pathoadaptation, however a more comprehensive characterisation of genetic signatures of bacterial adaptation may enable prediction of clinical outcomes and reveal new targets for treatment and prevention of these infections. Here, we measured adaptation using within-host evolution analysis of 2,590 S. aureus genomes from 396 independent episodes of infection. By capturing a comprehensive repertoire of single-nucleotide and structural genome variations, we found evidence of a distinctive evolutionary pattern within the infecting populations compared to colonising bacteria. These invasive strains had up to 20-fold enrichments for genome degradation signatures and displayed significantly convergent mutations in a distinctive set of genes, linked to antibiotic response and pathogenesis. In addition to agr-mediated adaptation we identified non-canonical, genome-wide significant loci including sucA-sucB and stp1. The prevalence of adaptive changes increased with infection extent, emphasising the clinical significance of these signatures. These findings provide a high-resolution picture of the molecular changes when S. aureus transitions from colonisation to severe infection and may inform correlation of infection outcomes with adaptation signatures.

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Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows

Cited by 90 publications

References 31 publications

Taxonomic distribution and evolutionary analysis of the equol biosynthesis gene cluster

Taxonomic distribution and evolutionary analysis of the equol biosynthesis gene cluster

Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19

Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections

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