Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites
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...
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doaj-c37f28c8672c47dbb4ffa766bbbd2ec32020-11-25T02:01:02ZengMDPI AGGenes2073-44252019-08-0110964810.3390/genes10090648genes10090648Eukaryote Genes Are More Likely than Prokaryote Genes to Be CompositesYaqing Ou0James O. McInerney1Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UKDivision of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UKThe 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.https://www.mdpi.com/2073-4425/10/9/648composite genessequence similarity networksodds ratio test |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yaqing Ou James O. McInerney |
spellingShingle |
Yaqing Ou James O. McInerney Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites Genes composite genes sequence similarity networks odds ratio test |
author_facet |
Yaqing Ou James O. McInerney |
author_sort |
Yaqing Ou |
title |
Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites |
title_short |
Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites |
title_full |
Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites |
title_fullStr |
Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites |
title_full_unstemmed |
Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites |
title_sort |
eukaryote genes are more likely than prokaryote genes to be composites |
publisher |
MDPI AG |
series |
Genes |
issn |
2073-4425 |
publishDate |
2019-08-01 |
description |
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. |
topic |
composite genes sequence similarity networks odds ratio test |
url |
https://www.mdpi.com/2073-4425/10/9/648 |
work_keys_str_mv |
AT yaqingou eukaryotegenesaremorelikelythanprokaryotegenestobecomposites AT jamesomcinerney eukaryotegenesaremorelikelythanprokaryotegenestobecomposites |
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1724959217775804416 |