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Open AccessArticle

Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites

by Yaqing Ou 1,* and James O. McInerney 1,2,*
1
Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK
2
School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
*
Authors to whom correspondence should be addressed.
Genes 2019, 10(9), 648; https://doi.org/10.3390/genes10090648
Received: 29 July 2019 / Revised: 18 August 2019 / Accepted: 23 August 2019 / Published: 28 August 2019
(This article belongs to the Special Issue Tools for Population and Evolutionary Genetics)
The formation of new genes by combining parts of existing genes is an important evolutionary process. Remodelled genes, which we call composites, have been investigated in many species, however, their distribution across all of life is still unknown. We set out to examine the extent to which genomes from cells and mobile genetic elements contain composite genes. We identify composite genes as those that show partial homology to at least two unrelated component genes. In order to identify composite and component genes, we constructed sequence similarity networks (SSNs) of more than one million genes from all three domains of life, as well as viruses and plasmids. We identified non-transitive triplets of nodes in this network and explored the homology relationships in these triplets to see if the middle nodes were indeed composite genes. In total, we identified 221,043 (18.57%) composites genes, which were distributed across all genomic and functional categories. In particular, the presence of composite genes is statistically more likely in eukaryotes than prokaryotes. View Full-Text
Keywords: composite genes; sequence similarity networks; odds ratio test composite genes; sequence similarity networks; odds ratio test
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Ou, Y.; McInerney, J.O. Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites. Genes 2019, 10, 648.

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