Eukaryote-wide survey suggests unified proximate and ultimate models of de novo intron creation
Authors: Landen Gozashti 1,6; Scott Roy 2; Bryan Thornlow 3,5; Alexander Kramer 3,5; Manuel Ares Jr. 4; Russell Corbett-Detig 3,5
Affiliations: 1) Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA; 2) Department of Biology, San Francisco State University, San Francisco, CA; 3) Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA; 4) Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA; 5) Genomics Institute, University of California Santa Cruz, Santa Cruz, CA; 6) Museum of Comparative Zoology, Harvard University, Cambridge, MA
Keywords: Comparative genomics & genome evolution
The causes for the massive variation in intron numbers across eukaryotes have been debated for decades but remain poorly understood. Rapid intron loss and/or gain in some lineages contrasts with stasis in other lineages. Episodic intron gain could be explained by specialized transposons called Introners, if Introners are present in only a subset of organisms. Systematic searches for Introners across all available eukaryotic genomes identified 27,563 Introner-derived introns from 548 distinct families, with Introners found in 175/3325 (5.2%) of studied genomes. Unexpectedly, marine organisms were 6.5 times more likely to contain Introners, and 74% of Introner-containing marine genomes harbored multiple distinct Introner families. Overrepresentation in marine organisms could reflect higher rates of lateral gene transfer. While we find that Introners are efficiently splice, preferential presence in lowly-expressed genes suggests that new insertions are costly. Most Introner families exhibit one or more signatures of DNA-based propagation. However, observations of families with partial or absent signatures suggest possible additional alternative mechanisms. These results suggest unified proximal and ultimate causes of intron gain, with susceptibility to acquire weakly deleterious Introners by lateral gene transfer playing a major role in a taxon’s tendency to gain introns.