Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites

Abstract

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.

Glycoconjugate pathway connections revealed by sequence similarity network analysis of the monotopic phosphoglycosyl transferases

“…Protein fusions comprise at least 4% of the monoPGT superfamily, the remaining sequences being small and large monoPGTs (38% and 47%, respectively) and sequences which could not be categorized into families based on sequence alone (11%). A recent comprehensive study of fusion event frequency across genomes from all three domains of life has revealed that, although there is a wide range among the 90 genomes characterized, on average, bacterial genomes include 14% fusion proteins (46). Additionally, the frequency of fusion proteins is higher for metabolic enzymes, possibly supporting shuttling of pathway intermediates.…”