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A spectrum of verticality across genes

Falk S. P. Nagies, Julia Brueckner , Fernando D. K. Tria, William F. Martin

Abstract

Lateral gene transfer (LGT) has impacted prokaryotic genome evolution, yet the extent to which LGT compromises vertical evolution across individual genes and individual phyla is unknown, as are the factors that govern LGT frequency across genes. Estimating LGT frequency from tree comparisons is problematic when thousands of genomes are compared, because LGT becomes difficult to distinguish from phylogenetic artefacts. Here we report quantitative estimates for verticality across all genes and genomes, leveraging a well-known property of phylogenetic inference: phylogeny works best at the tips of trees. From terminal (tip) phylum level relationships, we calculate the verticality for 19,050,992 genes from 101,422 clusters in 5,655 prokaryotic genomes and rank them by their verticality. Among functional classes, translation, followed by nucleotide and cofactor biosynthesis, and DNA replication and repair are the most vertical. The most vertically evolving lineages are those rich in ecological specialists such as Acidithiobacilli, Chlamydiae, Chlorobi and Methanococcales. Lineages most affected by LGT are the α-, β-, γ-, and δ- classes of Proteobacteria and the Firmicutes. The 2,587 eukaryotic clusters in our sample having prokaryotic homologues fail to reject eukaryotic monophyly using the likelihood ratio test. The low verticality of α-proteobacterial and cyanobacterial genomes requires only three partners—an archaeal host, a mitochondrial symbiont, and a plastid ancestor—each with mosaic chromosomes, to directly account for the prokaryotic origin of eukaryotic genes. In terms of phylogeny, the 100 most vertically evolving prokaryotic genes are neither representative nor predictive for the remaining 97% of an average genome. In search of factors that govern LGT frequency, we find a simple but natural principle: Verticality correlates strongly with gene distribution density, LGT being least likely for intruding genes that must replace a preexisting homologue in recipient chromosomes. LGT is most likely for novel genetic material, intruding genes that encounter no competing copy.

Introduction

Prokaryotes undergo recombination that is facilitated by the mechanisms of lateral gene transfer (LGT) [1,2]—transformation, conjugation, transduction, and gene transfer agents [3]. These mechanisms introduce DNA into the cell for recombination and do not obey taxonomic boundaries, species or otherwise. Over time they generate pangenomes [4,5] that are superimposed upon vertical evolution of a conserved core. About 30 genes are present in all genomes [6–9], a few more are nearly universal [10], many are found only in strains of one species [5], but the vast majority of genes are distributed between those extremes according to a power law [11]. Previous work has shown that LGT is subject to natural barriers [12,13], that LGT affects core metabolism less than it affects peripheral metabolism [14] and that LGT is affected by regulatory interaction networks [15]. LGT generates collections of genes in each genome that are of different evolutionary age [16], transferred genes are non-randomly associated [17,18], and major events of gene flux have occurred during evolution [9,19]. In principle, each gene should be transferable, because the mechanisms that introduce DNA into the cell are not selective with regard to the nature of sequences introduced, notwithstanding the CRISPR activity associated with phage defense [20]. If all genes are transferrable, what determines verticality?

Methods

Prokaryotic dataset

Protein sequences for 5,655 prokaryotic genomes were downloaded from NCBI [68] (version September 2016; see S3 Table for detailed species composition). We performed all-vs-all BLAST searches (BlastP version 2.5.0 with default parameters) and selected all reciprocal best hits with e-value ≤ 10−10. The protein pairs were aligned with the Needleman-Wunsch algorithm (EMBOSS needle) and the pairs with global identity values < 25% were discarded. The retained global identity pairs were used for clustering using Markov clustering algorithm (MCL) version 12–068, changing default parameters for pruning (-P 180000, -S 19800, -R 25200). Clusters distributed in at least 4 genomes spanning 2 prokaryotic phyla were retained, resulting in 101,422 used clusters in total. Sequence alignments for each cluster were generated using MAFFT with the iterative refinement method that incorporates local pairwise alignment information (L-INS-i; version 7.130). The resulting alignments were used to reconstruct maximum-likelihood trees with RAxML version 8.2.8 (parameters: -m PROTCATWAG -p 12345) (S9 Table). The trees were rooted with the Minimal Ancestor Deviation method (MAD).

Discussion

Even though gene evolution in prokaryotes has substantial lateral components, rRNA-based investigations and some protein phylogenetic studies tend to recover groups that microbiologists recognized long before molecular systematics. Hence the groups are in some cases real and there must be a vertical component to prokaryote evolution. The vertical component has, however, been difficult to quantify across lineages. Equally elusive have been estimates for verticality itself, yet suitable methods to quantify that component have been obscure, as have means to quantify verticality across prokaryotic genes. Quantification of discordance in tree comparisons represents one approach [66] to estimate LGT or lack thereof, but its utility is limited when large genome samples are involved, because the number of possible trees exceeds the number that a computer can examine by hundreds of orders of magnitude for trees containing 60 leaves or more. By exploiting the common wisdom that phylogeny works better at the tips of trees than at their deeper branches, we have obtained robust estimates of verticality.

Acknowledgments

We thank the central computing unit, ZIM, at the University of Düsseldorf for providing the computational platform for these analyses.

Citation: Nagies FSP, Brueckner J, Tria FDK, Martin WF (2020) A spectrum of verticality across genes. PLoS Genet 16(11): e1009200. https://doi.org/10.1371/journal.pgen.1009200.

Editor: Takashi Gojobori, National Institute of Genetics, JAPAN.

Received: July 31, 2020; Accepted: October 16, 2020; Published: November 2, 2020

Copyright: © 2020 Nagies et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: Files for S9 Table are available on the repository of our university: http://dx.doi.org/10.25838/d5p-12. The other supplementary files are provided with the manuscript and Supporting Information.

Funding: This study was supported by the European Research Council (666053), the Volkswagen Foundation (93 046), and the Moore-Simons Project on the Origin of the Eukaryotic Cell (9743) which were awarded to WFM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

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