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Original Research ARTICLE

Third, ten nucleotides were different between the duplicates Fig. In recent years, numerous spliced out sequences have been identified as originating in long noncoding RNAs and conclusively described as introns Derrien et al. Therefore, the production of functional proteins by spliced RNA molecules should not be considered as a prerequisite for identifying a sequence spliced out of RNA molecules as a new intron.

In this study, our search for evidence of intron gains is limited to whether the intron sequence occurred in the potato genome and whether the intron sequence has been removed from the mature mRNA.


This methodology underlies the objectives of our study. The first is a clear phylogeny that provides support for the intron gain, and the second is an identified source element for the gained intron. Because of the clear phylogeny and the identity of the source sequence, we consider the second intron of the potato gene PGSCDMG L to be a well-supported case of a newly gained intron.

Submission history

Accurate recognition and efficient splicing of an intron also requires a polypyrimidine tract, an adenine nucleotide at the branch site, and many other cis -acting regulatory motifs Schwartz et al. In addition, introns are often remarkably richer in A and U compared with exons Amit et al.

At first glance, it appears unlikely that a coding segment will have a full set of splicing signals. However, the intronization of coding regions has been observed in several different organisms, including animals and plants Irimia et al.

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These observations indicate that it is possible for certain coding sequences to contain a full set of cryptic splice signals. Furthermore, an experimental duplication of a coding segment of the vertebrate gene ATP2A2 , which harbors the AGGT sequence, has been shown to generate the new intron Hellsten et al. Therefore, a full set of the splicing signals required for active splicing is present in the coding sequence of the gene ATP2A2.

This case of intron gain indicates that the tandem duplication model should not be narrowly considered according to its original proposal 27 years ago Rogers, In the last common ancestor of domesticated potato S. L created a novel intron.

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However, the widely cited model of intron gain includes the tandem duplication of an exonic segment containing AGGT, which would create the GT and AG splicing sites. The case of intron gain observed here illustrates that the tandem duplication model of intron gain should be diversified so that the proper splicing signals can be obtained. Common use cases Typos, corrections needed, missing information, abuse, etc.

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Javascript is disabled in your browser. Please enable Javascript to view PeerJ. Share Twitter Facebook Email. Note that a Preprint of this article also exists, first published October 17, Introduction Although spliceosomal introns are the characteristic feature of eukaryotic nuclear genes, their origin and subsequent accumulation during evolution remain obscure. Download full-size image.

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DOI: Transcriptome data supporting the annotation of the target intron and genome sequencing data supporting the assembly of the region. I published in PeerJ and it is very fast, has good editors, has consistently given good quality and rigorous reviews of my work, and produces visually appealing manuscripts.

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Gain: A Novel of the American Century

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