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.
Highlights
Spliceosomal introns are the characteristic feature of eukaryotic nuclear genes, their origin and subsequent accumulation during evolution remain obscure
Using the RNA-Seq data, we examined the available annotations of the RNA-dependent RNA polymerase (RdRp) genes in S. lycopersicum, S. pennellii, N. benthamiana, and C. annuum
A comparison of the annotations clearly showed that the second introns of S. tuberosum and S. commersonii are absent from the other Solanaceae genomes (Fig. 2)
Summary
Spliceosomal introns are the characteristic feature of eukaryotic nuclear genes, their origin and subsequent accumulation during evolution remain obscure. Intron gains by tandem genomic duplication should not occur at a low frequency because internal gene duplications are commonly observed (Gao & Lynch, 2009). This model was originally advanced by Rogers (1989), who suggested that the tandem duplication of an exonic segment harboring the AGGT sequence generates two splice sites for the new intron: 5′-GT and 3′-AG. In the Arabidopsis TOUCH3 gene, Knowles & McLysaght (2006) observed two tandem internal gene duplications that duplicated an entire preexisting intron along with the exonic sequences on both sides of the intron.
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