Anomalous Phylogenetic Behavior of Ribosomal Proteins in Metagenome-Assembled Asgard Archaea

Abstract

Metagenomic studies permit the exploration of microbial diversity in a defined habitat and binning procedures enable phylogenomic analyses, taxon description and even phenotypic characterizations in the absence of morphological evidence. Such lineages include asgard archaea, which were initially reported to represent archaea with eukaryotic cell complexity, although the first images of such an archaeon show simple cells with prokaryotic characteristics. However, these metagenome-assembled genomes (MAGs) might suffer from data quality problems not encountered in sequences from cultured organisms due to two common analytical procedures of bioinformatics: assembly of metagenomic sequences and binning of assembled sequences on the basis of innate sequence properties and abundance across samples. Consequently, genomic sequences of distantly related taxa, or domains, can in principle be assigned to the same MAG and result in chimeric sequences. The impacts of low-quality or chimeric MAGs on phylogenomic and metabolic prediction remain unknown. Debates that asgard archaeal data are contaminated with eukaryotic sequences are overshadowed by the lack of evidence indicating that individual asgard MAGs stem from the same chromosome. Here we show that universal proteins including ribosomal proteins of asgard archaeal MAGs fail to meet the basic phylogenetic criterion fulfilled by genome sequences of cultured archaea investigated to date: these proteins do not share common evolutionary histories to the same extent as pure culture genomes (PCGs) do, pointing to a chimeric nature of asgard archaeal MAGs. Our analysis suggests that some asgard archaeal MAGs represent unnatural constructs, genome-like patchworks of genes resulting from assembly and/or the binning process.

Gene Duplications Are At Least 50 Times Less Frequent than Gene Transfers in Prokaryotic Genomes

“…Chromosome-encoded protein sequences for 5,655 prokaryotic genomes were downloaded from NCBI ( Pruitt et al 2007 ), version September 2016 (see supplementary table 1 for detailed species composition). The genomes were selected based on assembly to chromosome-level, and RefSeq status ( O’Leary et al 2016 ), while discarding metagenome-assembled genomes to avoid phylogenetic errors resulting from sequence contaminations ( Garg et al 2021 ). We then performed all-vs-all BLAST searches ( Altschul et al 1990 ) with BlastP, version 2.5.0, using default parameters and selected all reciprocal best hits with e-value ≤ 10 −10 .…”

Reconciling Asgardarchaeota Phylogenetic Proximity to Eukaryotes and Planctomycetes Cellular Features in the Evolution of Life

“…The pattern of inconclusive phylogenies is pointing toward wrong premises of 2D-centric analyses. This is supported by the anomalous phylogenetic behavior of ribosomal proteins in Asgard metagenome-assembled genomes ( Garg et al 2021 ).…”

The Asgard Archaeal-Unique Contribution to Protein Families of the Eukaryotic Common Ancestor Was 0.3%

“…3 b ) are strange as well, because protein length across pro- and eukaryotes is usually well conserved ( Xu et al 2006 ). This could hint at an assembly and/or binning issue, which was also observed regarding the anomalous phylogenetic behavior of their ribosomal proteins and concatenated gene trees ( Da Cunha et al 2018 ; Garg et al 2021 ). If not, it is a biological phenomenon absent in other sequenced prokaryotes that requires explaining.…”