proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

Fullam, Anthony; Letunić, Ivica; Schmidt, Thomas Sebastian Benedikt; Ducarmon, Quinten R; Karcher, Nicolai; Khedkar, Supriya; Kuhn, Michael; Larralde, Martin; Maistrenko, Oleksandr M.; Malfertheiner, Lukas; Milanese, Alessio; Rodrigues, João F. Matias; Sanchis-López, Claudia; Schudoma, Christian; Szklarczyk, Damian; Sunagawa, Shinichi; Zeller, Georg; Huerta-Cepas, Jaime; Mering, Christian von; Bork, Peer; Mende, Daniel R.

doi:10.1093/nar/gkac1078

Cited by 28 publications

(22 citation statements)

References 61 publications

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“…Classification of rdhA -containing contigs as belonging to chromosomes, plasmids or viruses was performed using Genomad v.1.5.0 with default parameters 100 . Integrons, integrative conjugative element (ICEs), IS elements and transposons were identified using HMM searches of the proteins against the 68 marker HMM profiles by default, which are available on proMGE (http://promge.embl.de/) 101 .…”

Section: Methodsmentioning

confidence: 99%

Phylogenetically and structurally diverse reductive dehalogenases link biogeochemical cycles in deep-sea cold seeps

Han,

Peng,

Peng

et al. 2024

Preprint

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Reductive dehalogenation is crucial for halogen cycling and environmental remediation, yet its ecological role is incompletely understood, especially in deep-sea environments. To address this gap, we investigated the diversity of reductive dehalogenases (RDases) and ecophysiology of organohalide reducers in deep-sea cold seeps, which are environments rich in halogenated compounds. Through genome-resolved metagenomic analysis 165 global cold seep sediment samples, we identified four types of RDases, namely prototypical respiratory, transmembrane respiratory, and cytosolic RDases, and one novel clade. These RDases are encoded by physiologically diverse microbes across four archaeal and 36 bacterial phyla, significantly broadening the known diversity of organohalide reducers. Halogen geochemistry, metatranscriptomic data, and metabolomic profiling confirm that organohalides occur at as high as 18 mg/g in these sediments and are actively reduced by microorganisms. This process is tightly linked to other biogeochemical cycles, including carbon, hydrogen, nitrogen, sulfur, and trace elements. RDases from cold seeps have diverse N-terminal structures across different gene groups, and rdhA genes in these environments are mostly functionally constrained and conserved. Altogether, these findings suggest that reductive dehalogenation is a central rather than supplemental process in deep-sea environments, mediated by numerous diverse microbes and novel enzymes.

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Section: Methodsmentioning

confidence: 99%

Phylogenetically and structurally diverse reductive dehalogenases link biogeochemical cycles in deep-sea cold seeps

Han,

Peng,

Peng

et al. 2024

Preprint

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“…Assemblies, including gene annotations, were downloaded from RefSeq or Genbank. Although we ran GUNC on some assemblies ourselves, for the most part, we relied on previous classifications of assemblies as being non-chimeric, either from the GUNC website (https://grp-bork.embl-community.io/gunc/datasets.html) or from proGenomes3 (Fullam et al 2023).…”

Section: Methodsmentioning

confidence: 99%

A fast comparative genome browser for diverse bacteria and archaea

Price,

Arkin

2023

Preprint

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Genome sequencing has revealed an incredible diversity of bacteria and archaea, but there are no fast and convenient tools for browsing across these genomes. It is cumbersome to view the prevalence of homologs for a protein of interest, or the gene neighborhoods of those homologs, across the diversity of the prokaryotes. We developed a web-based tool, fast.genomics, that uses two strategies to support fast browsing across the diversity of prokaryotes. First, the database of genomes is split up. The main database contains one representative from each of the 6,377 genera that have a high-quality genome, and additional databases for each taxonomic order contain up to 10 representatives of each species. Second, homologs of proteins of interest are identified quickly by using accelerated searches, usually in a few seconds. Once homologs are identified, fast.genomics can quickly show their prevalence across taxa, view their neighboring genes, or compare the prevalence of two different proteins. Fast.genomics is available at https://fast.genomics.lbl.gov.

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“…The GTDB database provides the phylogenetic tree in plain Newick format, together with a massive data table including hundreds of columns informing different aspects of the genomes used to build the tree. Moreover, the ProGenomes database (Fullam et al, 2023; Parks et al, 2021) provides habitat information for many of the species included in the GTDB tree.…”

Section: Use Case Examplesmentioning

confidence: 99%

TreeProfiler: A command-line tool for computing and visualizing phylogenetic profiles against large trees

Deng,

Hernández-Plaza,

Huerta-Cepas

2023

Preprint

Self Cite

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Phylogenetic profiling is a common bioinformatics approach used to study the distribution of traits across species or, more broadly, along the topology of a phylogenetic tree. Originally proposed as a technique for establishing functional relationships between various genes through their correlated presence/absence patterns, phylogenetic profiling is currently considered a powerful exploration tool for investigating the evolutionary distribution of nearly any trait across both gene or species phylogenies. However, computing and visualizing phylogenetic profiles based on large trees is a laborious task. First, traits need to be mapped against tree nodes, which usually requires the implementation of ad hoc scripts or substantial manual work. Second, tree mapping is often limited to leaf nodes, neglecting the usefulness of profiling traits against internal tree nodes. Lastly, graphical exploration of large phylogenetic tree-based profiles is challenging, as plotting usually requires complex manual adjustments and most visualization tools cannot scale to the size and complexity of current datasets. To address these limitations, we have developed TreeProfiler, a command line tool designed to facilitate both the automated annotation of large trees using a wide range of data sources, and the visual exploration of these annotations as phylogenetic profiles. TreeProfiler enables seamless annotation of massive trees and data tables, including built-in support for functional data, taxonomic information, multiple sequence alignments and protein domain architectures. Importantly, TreeProfiler expands its annotation capabilities beyond tree leaves, enabling the annotation of internal nodes with summarized or consensus information under each branch. Additionally, TreeProfiler offers a predefined set of graphical layouts that are based on the ETE Toolkit v4.0 library. TreeProfiler offers unique capabilities that extend and facilitate the use of phylogenetic profiling techniques for a broad landscape of scenarios and for a wide community of researchers interested in evolutionary analysis. To demonstrate its value, we showcase TreeProfiler by automatically profiling multiple data sources across a large bacterial phylogeny including 45,555 species, and by exploring functional and taxonomic annotations over a large gene family tree. TreeProfiler is available at https://github.com/compgenomicslab/TreeProfiler.

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proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

Cited by 28 publications

References 61 publications

Phylogenetically and structurally diverse reductive dehalogenases link biogeochemical cycles in deep-sea cold seeps

Phylogenetically and structurally diverse reductive dehalogenases link biogeochemical cycles in deep-sea cold seeps

A fast comparative genome browser for diverse bacteria and archaea

TreeProfiler: A command-line tool for computing and visualizing phylogenetic profiles against large trees

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