Intron gain by tandem genomic duplication: a novel case and a new version of the model
- Published
- Accepted
- Subject Areas
- Bioinformatics, Computational Biology, Evolutionary Studies, Genomics
- Keywords
- intron gain, tandem genomic duplication, splicing, RdRp, Solanum tuberosum
- Copyright
- © 2016 Ma et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2016. Intron gain by tandem genomic duplication: a novel case and a new version of the model. PeerJ PrePrints 4:e1439v2 https://doi.org/10.7287/peerj.preprints.1439v2
Abstract
Origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. Recently gained introns would be especially useful for the study of the mechanisms of intron gain because randomly accumulated mutations might erase the evolutionary traces. The mechanisms of intron gain remain unclear due to the presence of very few solid cases. A widely cited model of intron gain is tandem genomic duplication, in which the duplication of an AGGT-containing exonic segment provides the GT and AG splicing sites for the new intron. We found that the second intron of the potato RNA-dependent RNA polymerase gene PGSC0003DMG402000361 originated mainly from a direct duplication of the 3′ side of the upstream intron. The 5' splicing site of this new intron was recruited from the upstream exonic sequence. In addition to the new intron, a downstream exonic segment of 178 bp also arose from duplication. Most of the splicing signals were inherited directly from the parental intron/exon structure, including a putative branch site, the polypyrimidine tract, the 3′ splicing site, two putative exonic splicing enhancers and the GC contents differentiated between the intron and exon. We propose a new version of the tandem genomic duplication model, termed as the partial duplication of the preexisting intron/exon structure. This new version and the widely cited version are not mutually exclusive.
Author Comment
An error in the previous version has been corrected. Indeed, the duplication was not accompanied by recruitment of a small exogenous segment. The 5' end of the novel is recruited from the upstream exon.The whole manuscript has been improved. This is an updated version a preprint submission to PeerJ Preprints.
Supplemental Information
Transcriptome data supporting the annotation of the target intron and genome sequencing data supporting the assembly of the region
Table S1: The RNA-Seq reads mapped crossing the exon-exon boundary of the target intron; Table S2: The WGS reads mapped crossing the boundaries of the two duplicates.