ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies

Léonard, Raphaël R.; Leleu, Marie; Vlierberghe, Mick Van; Cornet, Luc; Kerff, Frédéric; Baurain, Denis

doi:10.7717/peerj.11348

Cited by 6 publications

(7 citation statements)

References 49 publications

(63 reference statements)

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“…We first reduced the number of genomes based on genomic signatures [ 27 ] to regroup similar genomes into genome clusters with a prerelease version of our new software ToRQuEMaDA [ 28 ]. Briefly, for five different k-mer sizes (from 2 to 6-nt), we computed the frequency of each word in each genome using the program compseq from the EMBOSS software package [ 29 ].…”

Section: Methodsmentioning

confidence: 99%

“…To choose the best combination of methods and parameters, the available taxonomic information was used to evaluate the quality of the clustering. Briefly, we computed how many different taxa of each rank (phylum, class, order, family, genus, species) were found in each individual cluster or each set of clusters and chose the combination that best separated the higher-level taxa (phylum, class, order, family) while merging the lower-level taxa (genus, species) [ 28 ]. This led us to settle on the following set of methods and parameters: 6-nt k-mer, 900 clusters, Pearson distance and ascending hierarchical clustering algorithm.…”

Section: Methodsmentioning

confidence: 99%

“…This led us to settle on the following set of methods and parameters: 6-nt k-mer, 900 clusters, Pearson distance and ascending hierarchical clustering algorithm. Then, we selected a single representative for each cluster, based on the quality of genome annotations, as evaluated by the number of gene names devoid of uninformative words like “hypothetical”, “putative”, “unknown” etc [ 28 ]. After including a few other well-characterized genomes (e.g., Streptomyces coelicolor A3(2), Escherichia coli O127:H6 str.…”

Section: Methodsmentioning

confidence: 99%

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Was the Last Bacterial Common Ancestor a Monoderm after All?

Léonard

Sauvage

Lupo

et al. 2022

Genes

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The very nature of the last bacterial common ancestor (LBCA), in particular the characteristics of its cell wall, is a critical issue to understand the evolution of life on earth. Although knowledge of the relationships between bacterial phyla has made progress with the advent of phylogenomics, many questions remain, including on the appearance or disappearance of the outer membrane of diderm bacteria (also called Gram-negative bacteria). The phylogenetic transition between monoderm (Gram-positive bacteria) and diderm bacteria, and the associated peptidoglycan expansion or reduction, requires clarification. Herein, using a phylogenomic tree of cultivated and characterized bacteria as an evolutionary framework and a literature review of their cell-wall characteristics, we used Bayesian ancestral state reconstruction to infer the cell-wall architecture of the LBCA. With the same phylogenomic tree, we further revisited the evolution of the division and cell-wall synthesis (dcw) gene cluster using homology- and model-based methods. Finally, extensive similarity searches were carried out to determine the phylogenetic distribution of the genes involved with the biosynthesis of the outer membrane in diderm bacteria. Quite unexpectedly, our analyses suggest that all cultivated and characterized bacteria might have evolved from a common ancestor with a monoderm cell-wall architecture. If true, this would indicate that the appearance of the outer membrane was not a unique event and that selective forces have led to the repeated adoption of such an architecture. Due to the lack of phenotypic information, our methodology cannot be applied to all extant bacteria. Consequently, our conclusion might change once enough information is made available to allow the use of an even more diverse organism selection.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Was the Last Bacterial Common Ancestor a Monoderm after All?

Léonard

Sauvage

Lupo

et al. 2022

Genes

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“…Three local mirrors of NCBI RefSeq were used during this study: 1) an archaeal database composed of the 819 whole genomes that were available on March 7, 2019, 2) a bacterial database of 598 representative genomes selected by the ToRQuEMaDA pipeline (Léonard et al 2021) and 3) a prokaryotic database of 80,490 genomes, already used in (Lupo et al 2022). To assemble the bacterial database, ToRQuEMaDA was run in June 2018, according to a ‘direct’ strategy and using the following parameters: dist-metric set to JI (Jaccard Index), dist-threshold set to 0.86, clustering-mode set to ‘loose’, and pack size set to 200.…”

Section: Methodsmentioning

confidence: 99%

Origin and Evolution of Pseudomurein Biosynthetic Gene Clusters

Lupo

Roomans

Royen

et al. 2022

Preprint

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The peptidoglycan (PG; or murein) is a mesh-like structure, which is made of glycan polymers connected by short peptides and surrounds the cell membrane of nearly all bacterial species. In contrast, there is no PG counterpart that would be universally found in Archaea, but rather various polymers that are specific to some lineages. Methanopyrales and Methanobacteriales are two orders of Euryarchaeota that harbor pseudomurein (PM) in their cell-wall, a structural analogue of the bacterial PG. Owing to the differences between PG and PM biosynthesis, some have argued that the origin of both polymers is not connected. However, recents studies have revealed that the genomes of PM-containing Archaea encode homologues of the bacterial genes involved in PG biosynthesis, even though neither their specific functions nor the relationships within the corresponding inter-domain phylogenies have been investigated so far. In this work, we devised a bioinformatic pipeline to identify all potential proteins for PM biosynthesis in Archaea without relying on a candidate gene approach. After anin silicocharacterization of their functional domains, the taxonomic distribution and evolutionary relationships of the collected proteins were studied in detail in Archaea and Bacteria through HMM similarity searches and phylogenetic inference of the Mur domain-containing family, the ATP-grasp superfamily and the MraY-like family. Our results notably show that the extant archaeal muramyl ligases are ultimately of bacterial origin, but likely diversified through a mixture of horizontal gene transfer and gene duplication. Moreover, structural modeling of these enzymes allowed us to propose a tentative function for each of them in pentapeptide elongation. While our work clarifies the genetic determinants behind PM biosynthesis in Archaea, it also raises the question of the architecture of the cell wall in the last universal common ancestor.

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“…Taxonomic affiliation is based on a MEGAN -like algorithm [ 37 ] that infers a last common ancestor (LCA) from the set of reference sequences best matching each contig or transcript of the evaluated dataset. Forty-Two can be used on prokaryotic or eukaryotic datasets, depending on the reference database considered, RiboDB [ 38 , 39 ] or a set of manually curated eukaryotic alignments [ 40 ], respectively. Recently, an inter-domain dataset has been assembled.…”

Section: Overview Of Algorithmsmentioning

confidence: 99%

Contamination detection in genomic data: more is not enough

Cornet

Baurain

2022

Genome Biol

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The decreasing cost of sequencing and concomitant augmentation of publicly available genomes have created an acute need for automated software to assess genomic contamination. During the last 6 years, 18 programs have been published, each with its own strengths and weaknesses. Deciding which tools to use becomes more and more difficult without an understanding of the underlying algorithms. We review these programs, benchmarking six of them, and present their main operating principles. This article is intended to guide researchers in the selection of appropriate tools for specific applications. Finally, we present future challenges in the developing field of contamination detection.

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ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies

Cited by 6 publications

References 49 publications

Was the Last Bacterial Common Ancestor a Monoderm after All?

Was the Last Bacterial Common Ancestor a Monoderm after All?

Origin and Evolution of Pseudomurein Biosynthetic Gene Clusters

Contamination detection in genomic data: more is not enough

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