GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

Chaumeil, Pierre-Alain; Mussig, Aaron J.; Hugenholtz, Philip; Parks, Donovan H.

doi:10.1093/bioinformatics/btz848

Cited by 3,636 publications

(3,324 citation statements)

References 20 publications

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“…Phylogenetic analysis of the partial 16S rRNA gene (904 bp) confirmed the position of rG16 within the Archaeoglobi ( Supplementary Figure 5 ). The average AAI between rG16 and other Archaeoglobi recovered from the Juan de Fuca Ridge (54.2% ± 0.7 AAI; Supplementary Figure 6 ) and relative evolutionary divergence 33,34 , suggest it is the first representative of a novel family within the Archaeoglobi 35 . The incongruencies between the genome tree and MCR phylogenies for rG16, Ca.…”

Section: Resultsmentioning

confidence: 98%

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi

Boyd

Jungbluth

Leu

et al. 2018

Preprint

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The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane and potentially propane. The number of archaeal clades encoding the MCR complex continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; rG16) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found in Candidatus Bathyarchaeota and Candidatus Syntrophoarchaeum MAGs. rG16 is basal to members of the class Archaeoglobi, and encodes the genes for β -oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed for Ca. Syntrophoarchaeum. rG16 also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. As the first Archaeoglobi with the MCR complex, rG16 extends our understanding of the evolution and distribution of novel MCR encoding lineages among the Archaea.

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Section: Resultsmentioning

confidence: 98%

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi

Boyd

Jungbluth

Leu

et al. 2018

Preprint

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“…The proposed quantitative species definition allows for the scalable and automated assignment of genomes to species clusters. We have incorporated these species clusters into the GTDB and GTDB-Tk (Chaumeil et al, 2019), an open source tool for the taxonomic classification of genome assemblies. These clusters encompass the nearly 150,000 public genomes within the NCBI Assembly database and will be updated with each GTDB release.…”

Section: Discussionmentioning

confidence: 99%

“…Trees were rooted by randomly selecting a genome from the sister lineage to the genus as determined from the topology of the GTDB R04-RS89 reference trees. The GTDB-Tk v0.3.2 (Chaumeil et al, 2019) 'de novo' workflow with default parameters was used to infer the trees. Briefly, genes were called using Prodigal v2.6.3 (Hyatt et al, 2010) and 120 bacterial or 122 archaeal marker genes identified and aligned using HMMER v3.1b (Eddy, 2011).…”

Section: Assessing Monophyly Of Species Clustersmentioning

confidence: 99%

Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy

Parks

Chuvochina

Chaumeil

et al. 2019

Preprint

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We recently introduced the Genome Taxonomy Database (GTDB), a phylogenetically consistent, genome-based taxonomy providing rank normalized classifications for nearly 150,000 genomes from domain to genus. However, nearly 40% of the genomes used to infer the GTDB reference tree lack a species name, reflecting the large number of genomes in public repositories without complete taxonomic assignments. Here we address this limitation by proposing 24,706 species clusters which encompass all publicly available bacterial and archaeal genomes when using commonly accepted average nucleotide identity (ANI) criteria for circumscribing species. In contrast to previous ANI studies, we selected a single representative genome to serve as the nomenclatural type for circumscribing each species with type strains used where available. We complemented the 8,792 species clusters with validly or effectively published names with 15,914 de novo species clusters in order to assign placeholder names to the growing number of genomes from uncultivated species. This provides the first complete domain to species taxonomic framework which will improve communication of scientific results. taxonomic framework where genomes have assignments at all ranks from domain to species (Parks et al., 2018).

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“…Their classification towards the most up-to-date Thaumarchaeota amoA and 16S rRNA gene databases 2, 43 was performed using BLASTn 45 . Initial classification of genome sequences was performed using classify_wf in the GTDB-Tk package 46 .…”

Section: Methodsmentioning

confidence: 99%

Gene duplication drives genome expansion in Thaumarchaeota

Sheridan

Raguideau

Quince

et al. 2020

Preprint

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13Ammonia-oxidising archaea of the phylum Thaumarchaeota are keystone species in global 14 nitrogen cycling. However, only three of the six known families of the terrestrially ubiquitous 15 order Nitrososphaerales possess representative genomes. Here we provide genomes for the 16 three remaining families and examine the impact of gene duplication, loss and transfer events 17 across the entire phylum. Much of the genomic divergence in this phylum is driven by gene 18 duplication and loss, but we also detected early lateral gene transfer that introduced 19 considerable proteome novelty. In particular, we identified two large gene transfer events into 20 Nitrososphaerales. The fate of gene families originating on these branches was highly lineage-21 specific, being lost in some descendant lineages, but undergoing extensive duplication in 22 others, suggesting niche-specific roles within soil and sediment environments. Overall, our 23 results suggest that lateral gene transfer followed by gene duplication drives Nitrososphaerales 24 evolution, highlighting a previously under-appreciated mechanism of genome expansion in 25 archaea. 26 27 73 provided a well-supported thaumarchaeotal phylogenomic tree (Figure 1), with most nodes 74 with UF bootstrap values > 95 % and SH-aLRT values > 95 %. This phylogenomic tree was 75 the best supported tree after comparison of several phylogenomic reconstruction 76 5methodologies (Supplementary Information: Extended phylogenomics). The tree is broadly 77 similar to previously published work 11 with some exceptions, mainly relating to poorly-78 supported basal branches in both trees (Supplementary Information: Extended phylogenomics). 79Previous classifications of Thaumarchaeota have been based on phylogenetic analyses of 80 the ammonia monooxygenase (amoA) gene, but this gene is not present in all members of the 81 phylum. We therefore suggest a phylum-wide thaumarchaeotal classification based on our 82 phylogenomic analysis that maintains maximum consistency with previous work while 83 incorporating the early-diverging lineages that lack amoA 2, 17, 18 (Table S2). Our genome dataset 84 of Thaumarchaeota represent a diverse phylum comprising 8 classes, 10 orders, 28 families, 31 85 genus and 103 species. While the classically used thaumarchaeotal nomenclature is congruent 86 with the taxonomic stratification, a few exceptions were observed. For example, the order 87 Nitrosopumilales encompasses Candidatus Nitrosotalea and Cenarchaeum, which were 88 previously suggested to represent orders of their own, and Nitrososphaerales contains a 89 minimum of 8 genera, with Ca. Nitrososphaera gargensis and Nitrososphaera viennensis and 90Ca. Nitrososphaera evergladensis belonging to different genera. 91 We also used the Genome Taxonomy Database Toolkit (GTDB-Tk) to evaluate the 92 genomic diversity of our 12 new MAGs. While one of these genomes (TH1173) is a close 93 relative of a published genome, MY3, the range of relative evolutionary divergence (RED) 19 94 values for the other 11 MA...

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GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

Cited by 3,636 publications

References 20 publications

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi

Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy

Gene duplication drives genome expansion in Thaumarchaeota

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