Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase

Abstract

The origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. However, the mechanisms underlying intron gain remain unclear because there are few proven cases of recently gained introns. In an RNA-dependent RNA polymerase (RdRp) gene, we found that a tandem duplication occurred after the divergence of potato and its wild relatives among other Solanum plants. The duplicated sequence crosses the intron-exon boundary of the first intron and the second exon. A new intron was detected at this duplicated region, and it includes a small previously exonic segment of the upstream copy of the duplicated sequence and the intronic segment of the downstream copy of the duplicated sequence. The donor site of this new intron was directly obtained from the small previously exonic segment. 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 differed between the intron and exon. In the widely cited model of intron gain by tandem genomic duplication, the duplication of an AGGT-containing exonic segment provides the GT and AG splicing sites for the new intron. Our results illustrate that the tandem duplication model of intron gain should be diverse in terms of obtaining the proper splicing signals.

Association Study of the 5′UTR Intron of the FAD2-2 Gene With Oleic and Linoleic Acid Content in Olea europaea L.

“…In this work, the hypothetical mechanisms concerning the origin and evolution of introns have not been explored, but the presence of two duplications within the 5′UTR intron led us to speculate other mechanisms could be occurred in the differentiation of FAD2 genes, such as the multiplication of a preexisting intron by tandem duplication or creation of a new intron by internal gene duplication (Gao and Lynch, 2009;Ma et al, 2016).…”

Tandem Exon Duplications Expanding the Alternative Splicing Repertoire

“…Tandem genomic duplications may affect entire genes, either protein-coding or non-coding, or only gene parts. In the latter case, the duplication leads to propagation of only a portion of the gene sequence, thus affecting the exon-intron structure [ 3 ]. The process where the same exon of a gene is duplicated or two or more exons from different genes are brought together ectopically is called exon shuffling [ 4 , 5 ].…”

Mechanizmy utraty i nabywania intronów spliceosomalnych

“…Część nukleotydów intronowych może pozostać w zmienionej sekwencji lub mogą zostać usunięte dodatkowe nukleotydy z eksonów flankujących intron. Jeżeli delecja nie powoduje zmiany ramki odczytu oraz nie wprowadza znaczących zmian w sekwencji aminokwasowej, to zmodyfikowana sekwencja bez intronu może stać się funkcjonalna [42,43].…”