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

Overview of attention for article published in BMC Biology, October 2016
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Title
A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70 % rule
Published in
BMC Biology, October 2016
DOI 10.1186/s12915-016-0315-9
Pubmed ID
Authors

Chuan Ku, William F. Martin

Abstract

The 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. Here 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. Our 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.

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The data shown below were compiled from readership statistics for 188 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 2 1%
France 2 1%
South Africa 1 <1%
Finland 1 <1%
Czechia 1 <1%
United Kingdom 1 <1%
Mexico 1 <1%
Unknown 179 95%

Demographic breakdown

Readers by professional status Count As %
Researcher 41 22%
Student > Ph. D. Student 27 14%
Student > Master 19 10%
Student > Bachelor 19 10%
Professor > Associate Professor 10 5%
Other 36 19%
Unknown 36 19%
Readers by discipline Count As %
Agricultural and Biological Sciences 73 39%
Biochemistry, Genetics and Molecular Biology 53 28%
Environmental Science 4 2%
Immunology and Microbiology 3 2%
Computer Science 2 1%
Other 11 6%
Unknown 42 22%