Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history

Abstract

Background K-mer-based methods have greatly advanced in recent years, largely driven by the realization of their biological significance and by the advent of next-generation sequencing. Their speed and their independence from the annotation process are major advantages. Their utility in the study of the mobilome has recently emerged and they seem a priori adapted to the patchy gene distribution and the lack of universal marker genes of viruses and plasmids. To provide a framework for the interpretation of results from k-mer based methods applied to archaea or their mobilome, we analyzed the 5-mer DNA profiles of close to 600 archaeal cells, viruses and plasmids. Archaea is one of the three domains of life. Archaea seem enriched in extremophiles and are associated with a high diversity of viral and plasmid families, many of which are specific to this domain. We explored the dataset structure by multivariate and statistical analyses, seeking to identify the underlying factors. Results For cells, the 5-mer profiles were inconsistent with the phylogeny of archaea. At a finer taxonomic level, the influence of the taxonomy and the environmental constraints on 5-mer profiles was very strong. These two factors were interdependent to a significant extent, and the respective weights of their contributions varied according to the clade. A convergent adaptation was observed for the class Halobacteria, for which a strong 5-mer signature was identified. For mobile elements, coevolution with the host had a clear influence on their 5-mer profile. This enabled us to identify one previously known and one new case of recent host transfer based on the atypical composition of the mobile elements involved. Beyond the effect of coevolution, extrachromosomal elements strikingly retain the specific imprint of their own viral or plasmid taxonomic family in their 5-mer profile. Conclusion This specific imprint confirms that the evolution of extrachromosomal elements is driven by multiple parameters and is not restricted to host adaptation. In addition, we detected only recent host transfer events, suggesting the fast evolution of short k-mer profiles. This calls for caution when using k-mers for host prediction, metagenomic binning or phylogenetic reconstruction.

Ksak: A high-throughput tool for alignment-free phylogenetics

“…Efficient counting of k -mers is the basis for k -mer based statistical tools. In recent years, a variety of applications with many methods to count k -mers were developed ( Crusoe et al, 2015 ; Bize et al, 2021 ; Cattaneo et al, 2022 ). Given the fact that the most useful k for alignment-free phylogenetics is relatively small, typically <10, we implemented a neat yet ultra-efficient algorithm to count k -mer frequency (see Supplementary Figure 2 for an illustrated example), which mathematically transforms a k -mer to its index based on the powers of 4.…”

Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis

“…k-mer frequency is another important variable that was shown to strongly correlate with codon usage frequencies 36 . To test how k-mer frequencies could influence the codon and AA usage distances of our test samples we estimated frequencies of different short k-mers starting from k = 2 to k = 10 (except k = 3) (details in material and methods) and correlated the distances in k-mer usage frequencies with our previously estimated codon/AA usage distances among the test samples.…”

“…GC content is another crucial variable that can shape the codon usage pattern of microorganisms just like gene expression 7 , 34 , 35 , 46 . Recent studies suggested that despite their compositional diversity environmental samples show distinctive distributions in their oligonucleotide signature 36 , 47 . Consequently, k-mer-based comparison of sequence signatures gained wide popularity to evaluate relationships between different metagenomic samples 47 .…”

Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins

“…Gaussian mixture models using two distributions were fitted 129 to the k-mer content of all windows, to classify these as belonging to either the core genome or transferred elements. This deviation in k-mer spectra has been explored in the context of the archaeal mobilome and contains information on the ecological niche and evolutionary history of DNA sequences 130 .…”