Resolving widespread incomplete and uneven archaeal classifications based on a rank-normalized genome-based taxonomy

Chuvochina, Maria; Mussig, Aaron J.; Chaumeil, Pierre-Alain; Davín, Adrián; Waite, David W.; Whitman, William B.; Parks, Donovan H.; Hugenholtz, Philip

doi:10.1101/2020.03.01.972265

Cited by 24 publications

(32 citation statements)

References 78 publications

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“…Notably, the topology of our complete phylogenetic tree (Fig. 2a) within the archaeal clade is mostly consistent with the tree obtained in a preliminary analysis of a larger set of archaeal genomes and a larger marker gene set ( 26 ). Taking into account these observations and the fact that we used the largest set of Asgard archaea and other archaea compared to all previous phylogenetic analyses, the appearance of the 3D topology in our tree indicates that the origin of eukaryotes from within Asgard cannot be considered a settled issue.…”

Section: Resultssupporting

confidence: 84%

Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes

Liu

Makarova

Huang

et al. 2020

Preprint

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Comparative analysis of 162 (nearly) complete genomes of Asgard archaea, including 75 not reported previously, substantially expands the phylogenetic and metabolic diversity of the superphylum Asgard, with six additional phyla proposed. Phylogenetic analysis of universally conserved genes does not strongly support the origin of eukaryotes from within Asgard but rather, leans towards a three-domain topology, with eukaryotes branching outside archaea. Using sensitive methods for protein domains detection on the extended set of Asgard genomes results in a major expansion of the set of homologs of eukaryote signature proteins (ESPs). However, almost all Asgard ESPs show patchy phyletic distributions, large variations in the number of paralogs and variable domain architectures, suggestive of highly dynamic evolution via horizontal gene transfer (HGT), gene loss, gene duplication and domain shuffling. The results appear to be best compatible with an evolutionary scenario in which the conserved core of eukaryote genes involved in informational processes originates from an as yet unknown ancestral lineage deep within or outside the currently characterized archaeal diversity. Such hypothetical ancestors could have accumulated components of the mobile archaeal 'eukaryome' via extensive HGT, eventually, giving rise to eukaryote-like cells. Our reconstruction of the metabolic networks for the extant and ancestral Asgard archaea reveals three distinct lifestyles, anaerobic heterotrophy, facultative aerobic heterotrophy, and chemolithotrophy, and suggests that the common ancestor of Asgard archaea was an acetogenic myxotroph capable of both production and consumption of hydrogen. These findings could be best compatible with different versions of the syntrophic hypothesis for eukaryogenesis, depending on the exact relationship between Asgard and eukaryotes.

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Section: Resultssupporting

confidence: 84%

Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes

Liu

Makarova

Huang

et al. 2020

Preprint

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“…Briefly, the NCBI taxonomy associated with every fungal genome was obtained from the NCBI Taxonomy FTP site on January 17, 2020. PhyloRank linearly interpolates the RED values of every internal node according to lineage-specific rates of evolution under the constraints of the root being defined as zero and the RED of all present taxa being defined as one 57,79 .…”

Section: Red Indexmentioning

confidence: 99%

A genome-scale phylogeny of Fungi; insights into early evolution, radiations, and the relationship between taxonomy and phylogeny

Steenwyk

Chang

et al. 2020

Preprint

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Phylogenomic studies based on genome-scale amounts of data have greatly improved understanding of the tree of life. Despite their diversity, ecological significance, and biomedical and industrial importance, large-scale phylogenomic studies of Fungi are lacking. Furthermore, several evolutionary relationships among major fungal lineages remain controversial, especially those at the base of the fungal phylogeny. To begin filling these gaps and assess progress toward a genome-scale phylogeny of the entire fungal kingdom, we compiled a phylogenomic data matrix of 290 genes from the genomes of 1,644 fungal species that includes representatives from most major fungal lineages; we also compiled 11 additional data matrices by subsampling genes or taxa based on filtering criteria previously shown to improve phylogenomic inference. Analyses of these 12 data matrices using concatenation- and coalescent-based approaches yielded a robust phylogeny of the kingdom in which ∼85% of internal branches were congruent across data matrices and approaches used. We found support for several relationships that have been historically contentious (e.g., for the placement of Wallemiomycotina (Basidiomycota), as sister to Agaricomycotina), as well as evidence for polytomies likely stemming from episodes of ancient diversification (e.g., at the base of Basidiomycota). By examining the relative evolutionary divergence of taxonomic groups of equivalent rank, we found that fungal taxonomy is broadly aligned with genome sequence divergence, but also identified lineages, such as the subphylum Saccharomycotina, where current taxonomic circumscription does not fully account for their high levels of evolutionary divergence. Our results provide a robust phylogenomic framework to explore the tempo and mode of fungal evolution and directions for future fungal phylogenetic and taxonomic studies.

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“…Our results have shown that formatting and correcting taxonomy and other metadata are critical components of reference database generation and management prior to applications for sequence classification, e.g., to standardize taxonomic ranks across entries [87]. We have already implemented functions in RESCRIPt to format the popular SILVA rRNA gene and NCBI GenBank databases, and are planning future support for parsing and editing other taxonomy formats, as well as mapping between these formats [71].…”

Section: The Curation Problemmentioning

confidence: 99%

“…These curational efforts result in a well integrated suite of biological information that can be interrogated through a variety of means and data types [25,88]. The GTDB extracts and curates data from both NCBI-RefSeq and NCBI-GenBank to generate a phylogeny of archaea and bacteria from roughly 120 ubiquitous single-copy proteins [23,87]. This phylogeny is used to inform microbial taxonomy, especially in cases where a given taxonomy is observed to be polyphyletic.…”

Section: The Evaluation Problemmentioning

confidence: 99%

“…In this case, a conservative approach is used to remove polyphyletic groups and normalize taxonomic ranks according to their relative evolutionary divergence. Any remaining polyphyletic groups are then flagged as a "regions of instability" in the hopes that future in-depth analyses will result in a stable set of classifiable taxa [23,87]. The efforts by NCBI and GTDB enables researchers to not only more accurately classify uncultured microbes, but also place them into ecological and evolutionary context based on their nearest phylogenetic and taxonomic neighbors.…”

Section: The Evaluation Problemmentioning

confidence: 99%

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RESCRIPt: Reproducible sequence taxonomy reference database management for the masses

Robeson

O’Rourke

Kaehler

et al. 2020

Preprint

105

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BackgroundNucleotide sequence and taxonomy reference databases are critical resources for widespread applications including marker-gene and metagenome sequencing for microbiome analysis, diet metabarcoding, and environmental DNA (eDNA) surveys. Reproducibly generating, managing, using, and evaluating nucleotide sequence and taxonomy reference databases creates a significant bottleneck for researchers aiming to generate custom sequence databases. Furthermore, database composition drastically influences results, and lack of standardizations limits cross-study comparisons. To address these challenges, we developed RESCRIPt, a software package for reproducible generation and management of reference sequence taxonomy databases, including dedicated functions that streamline creating databases from popular sources, and functions for evaluating, comparing, and interactively exploring qualitative and quantitative characteristics across reference databases.ResultsTo highlight the breadth and capabilities of RESCRIPt, we provide several examples for working with popular databases for microbiome profiling (SILVA, Greengenes, NCBI-RefSeq, GTDB), eDNA, and diet metabarcoding surveys (BOLD, GenBank), as well as for genome comparison. We show that bigger is not always better, and reference databases with standardized taxonomies and those that focus on type strains have quantitative advantages, though may not be appropriate for all use cases. Most databases appear to benefit from some curation (quality filtering), though sequence clustering appears detrimental to database quality. Finally, we demonstrate the breadth and extensibility of RESCRIPt for reproducible workflows with a comparison of global hepatitis genomes.ConclusionsRESCRIPt provides tools to democratize the process of reference database acquisition and management, enabling researchers to reproducibly and transparently create reference materials for diverse research applications. RESCRIPt is released under a permissive BSD-3 license at https://github.com/bokulich-lab/RESCRIPt.

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Resolving widespread incomplete and uneven archaeal classifications based on a rank-normalized genome-based taxonomy

Cited by 24 publications

References 78 publications

Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes

Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes

A genome-scale phylogeny of Fungi; insights into early evolution, radiations, and the relationship between taxonomy and phylogeny

RESCRIPt: Reproducible sequence taxonomy reference database management for the masses

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