Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist

Abstract

One contribution of 17 to a theme issue 'Eukaryotic origins: progress and challenges'. While there is compelling evidence for the impact of endosymbiotic gene transfer (EGT; transfer from either mitochondrion or chloroplast to the nucleus) on genome evolution in eukaryotes, the role of interdomain transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear. Lateral gene transfers (LGTs) have been argued to be potential sources of phylogenetic information, particularly for reconstructing deep nodes that are difficult to recover with traditional phylogenetic methods. We sought to identify interdomain LGTs by using a phylogenomic pipeline that generated 13 465 single gene trees and included up to 487 eukaryotes, 303 bacteria and 118 archaea. Our goals include searching for LGTs that unite major eukaryotic clades, and describing the relative contributions of LGT and EGT across the eukaryotic tree of life. Given the difficulties in interpreting single gene trees that aim to capture the approximately 1.8 billion years of eukaryotic evolution, we focus on presence -absence data to identify interdomain transfer events. Specifically, we identify 1138 genes found only in prokaryotes and representatives of three or fewer major clades of eukaryotes (e.g. Amoebozoa, Archaeplastida, Excavata, Opisthokonta, SAR and orphan lineages). The majority of these genes have phylogenetic patterns that are consistent with recent interdomain LGTs and, with the notable exception of EGTs involving photosynthetic eukaryotes, we detect few ancient interdomain LGTs. These analyses suggest that LGTs have probably occurred throughout the history of eukaryotes, but that ancient events are not maintained unless they are associated with endosymbiotic gene transfer among photosynthetic lineages.

Changing ideas about eukaryotic origins

“…There is good evidence for both sources (reviewed in [32,[35][36][37]), but disagreement about their relative importance [38,39]. Katz [40] presents an analysis of patterns of gene presence and absence in the context of an extremely broad sampling of eukaryotic diversity to identify candidate prokaryote to eukaryote HGT. Her analyses identify over a thousand transfers into eukaryotes, but most are restricted to one or a few closely related genomes.…”

Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes

“…In contrast, eukaryotic HGT was long thought to be extremely rare, and limited to few microbial taxa (Eisen, 2000; Andersson, 2005). However, in recent years, the number of described events of eukaryotic HGT has increased exponentially, suggesting it is more widespread than previously anticipated (Andersson, 2005, 2009; Keeling and Palmer, 2008; Laura, 2015; Soucy et al, 2015). However, we still have, a very limited understanding of the mechanisms that underlie the transfer of genetic material in eukaryotes.…”

The plastid genome of some eustigmatophyte algae harbours a bacteria-derived six-gene cluster for biosynthesis of a novel secondary metabolite

“…Such conflicting or unclear results are commonly observed in phylogenetic analyses concerning ancient HGT events, and, indeed, they rarely point with confidence to a particular bacterial taxon as a source of bacteria-derived eukaryotic genes (e.g. [54,55]).

Figure 4.Phylogenetic analysis of EboC protein sequences.

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