Intron gain by tandem genomic duplication: a novel case and a modification of the traditional model
- Published
- Accepted
- Subject Areas
- Computational Biology, Evolutionary Studies, Genomics
- Keywords
- intron gain, tandem genomic duplication, splicing, RdRp, Solanum tuberosum
- Copyright
- © 2015 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
- 2015. Intron gain by tandem genomic duplication: a novel case and a modification of the traditional model. PeerJ PrePrints 3:e1439v1 https://doi.org/10.7287/peerj.preprints.1439v1
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 mechanism(s) of intron gain because the evolutionary traces might have not been erased by randomly accumulated mutations. However, the mechanism(s) of intron gain remain unclear due to the presence of a 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. However, successful recognition and splicing of an intron require many more signals than those at the two splicing sites. We found that the second intron of the potato RNA-dependent RNA polymerase gene PGSC0003DMG402000361 is absent in the orthologous genes of other Solanaceae plants, and sequence similarity showed that the major part of the new intron is a direct duplication of the 3' side of the upstream intron. In addition to the new intron, a downstream exonic segment of 168bp has also been duplicated. Most of the splicing signals were inherited 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 modified version of the tandem genomic duplication model, termed as the partial duplication of the preexisting intron/exon structure.
Author Comment
This is a submission to PeerJ for review.
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.