A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70 % rule

Abstract

BackgroundThe literature harbors many claims for lateral gene transfer (LGT) from prokaryotes to eukaryotes. Such claims are typically founded in analyses of genome sequences. It is undisputed that many genes entered the eukaryotic lineage via the origin of mitochondria and the origin of plastids. Claims for lineage-specific LGT to eukaryotes outside the context of organelle origins and claims of continuous LGT to eukaryotic lineages are more problematic. If eukaryotes acquire genes from prokaryotes continuously during evolution, then sequenced eukaryote genomes should harbor evidence for recent LGT, like prokaryotic genomes do.ResultsHere we devise an approach to investigate 30,358 eukaryotic sequences in the context of 1,035,375 prokaryotic homologs among 2585 phylogenetic trees containing homologs from prokaryotes and eukaryotes. Prokaryote genomes reflect a continuous process of gene acquisition and inheritance, with abundant recent acquisitions showing 80–100 % amino acid sequence identity to their phylogenetic sister-group homologs from other phyla. By contrast, eukaryote genomes show no evidence for either continuous or recent gene acquisitions from prokaryotes. We find that, in general, genes in eukaryotic genomes that share ≥70 % amino acid identity to prokaryotic homologs are genome-specific; that is, they are not found outside individual genome assemblies.ConclusionsOur analyses indicate that eukaryotes do not acquire genes through continual LGT like prokaryotes do. We propose a 70 % rule: Coding sequences in eukaryotic genomes that share more than 70 % amino acid sequence identity to prokaryotic homologs are most likely assembly or annotation artifacts. The findings further uncover that the role of differential loss in eukaryote genome evolution has been vastly underestimated.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-016-0315-9) contains supplementary material, which is available to authorized users.

Massive horizontal transfer of transposable elements in insects

“…In contrast, the study of HT in eukaryotes is less documented, but has been increasingly investigated. The majority of genes horizontally acquired by eukaryotes come from bacteria, but the extent to which these transfers have contributed to eukaryote evolution is still unclear (3,4). Gene transfers from eukaryote to eukaryote appear to be largely limited to filamentous organisms, such as oomycetes and fungi (5,6).…”

Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

“…Any protein with an AI>0 and ≥70% identity are put apart in a category of possible contaminants. In a recent paper [66], Ku and Martin defined what they called the 70% rule, above which candidate HGT of prokaryote origin to eukaryotes are more likely to represent contamination than actual HGT. This rule holds at the nucleotide level and for prokaryote to eukaryote transfers.…”

Symbiogenesis, gradualism, and mitochondrial energy in eukaryote origin

“…At the other end of the spectrum is the symbiogenic proposition that eukaryotes do not acquire genes via outright LGT either from other eukaryotes or from prokaryotes except at endosymbiotic events (the origin of mitochondria, the origin of primary plastids, the origin of secondary plastids) (21,83,130,147). We can see cumulative effects of LGT in prokaryotic genomes (148).…”