Ubiquitous internal gene duplication and intron creation in eukaryotes

Gao, Xiang; Lynch, Michael

doi:10.1073/pnas.0911093106

Cited by 45 publications

(42 citation statements)

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“…Another mechanism that is related to the exon intronization model also suffers from the fact that size changes of the encoded proteins ensue. Duplication of intragenic segments (encompassing intronic and flanking exon sequences) may lead to activation of latent splice sites [42], thus creating novel introns or exons (that are flanked by novel introns). Dissenting from the Rogers [39] model, here the splice signals of novel introns reside in dispersed, complex repeats rather than in expanded AGGT repetitions.…”

Section: (1) Intron Generation Via Transposon Insertionmentioning

confidence: 99%

Intron creation and DNA repair

Ragg

2010

Cell. Mol. Life Sci.

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The genesis of the exon-intron patterns of eukaryotic genes persists as one of the most enigmatic questions in molecular genetics. In particular, the origin and mechanisms responsible for creation of spliceosomal introns have remained controversial. Now the issue appears to have taken a turn. The formation of novel introns in eukaryotes, including some vertebrate lineages, is not as rare as commonly assumed. Moreover, introns appear to have been gained in parallel at closely spaced sites and even repeatedly at the same position. Based on these discoveries, novel hypotheses of intron creation have been developed. The new concepts posit that DNA repair processes are a major source of intron formation. Here, after summarizing the current views of intron gain mechanisms, I review findings in support of the DNA repair hypothesis that provides a global mechanistic scenario for intron creation. Some implications on our perception of the mosaic structure of eukaryotic genes are also discussed.

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Section: (1) Intron Generation Via Transposon Insertionmentioning

confidence: 99%

Intron creation and DNA repair

Ragg

2010

Cell. Mol. Life Sci.

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“…This result is in stark contrast to the comparative studies of their highly conserved orthologous genes, which found very few or no intron gains at all (Coulombe-Huntington & Majewski 2007;Fawcett et al 2012;Roy et al 2003;Yang et al 2013). Considering the high frequency of internal gene duplications, which is 0.0010.013 duplications/gene per million years (Gao & Lynch 2009), it can be stated that intron gain by segmental duplication may be an important force shaping the eukaryotic gene structure.…”

Section: Resultsmentioning

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“…Due to this methodology, the frequency of intron gain by segmental duplication might have been underestimated previously. To be consistent with this idea, a study that specifically explored intron gains by segmental duplications revealed tens of new introns in humans, mice, and A. thaliana (Gao & Lynch 2009). This result is in stark contrast to the comparative studies of their highly conserved orthologous genes, which found very few or no intron gains at all (Coulombe-Huntington & Majewski 2007;Fawcett et al 2012;Roy et al 2003;Yang et al 2013).…”

Section: Resultsmentioning

confidence: 92%

“…Each of them might account for some cases of intron gain in evolution. Segmental duplication containing entire introns would be more likely to increase the intron number of genes and also has been observed previously (Gao & Lynch 2009). In the present paper, we confine our discussion to the creation of new introns rather than the propagation of preexisting introns.…”

Section: Resultsmentioning

confidence: 93%

“…Collemare et al (2013) claimed that the abundance of introns in extant eukaryotic genomes could not be explained by traditional models of intron gain, but can be possible by a new model, the insertion of introner-like elements (van der Burgt et al 2012). Among the traditional models, intron gain by tandem genomic duplication is not expected to occur rarely, because frequent internal gene duplications are observed (Gao & Lynch 2009). …”

Section: Introductionmentioning

confidence: 99%

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Supplemental Information 1: Transcriptome Data Supporting the Annotation of the Target Intron and Genome Sequencing Data Suppor

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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.3

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Evaluation of Models of the Mechanisms Underlying Intron Loss and Gain in Aspergillus Fungi

2010

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Although intron loss and gain have been widely observed, their mechanisms are still to be determined. In four Aspergillus genomes, we found 204 cases of intron loss and 84 cases of intron gain. Using this data, we tested common hypotheses of intron loss or gain. Statistical analysis showed that adjacent introns tend to be lost simultaneously and small introns were preferentially lost, supporting the model of mRNA-mediated intron loss. The lost introns reside in internal regions of genes, which is inconsistent with the traditional version of the model (partial length cDNAs are reverse transcribed from 3' ends of mRNAs), but consistent with an alternate version (partial length cDNAs are produced by self-primed reverse transcription). The latter version was not supported by examination of the abundance of T-rich segments in mRNAs. Preferential loss of internal introns might be explained by highly efficient recombination at internal regions of genes. Among the 84 cases of intron gain, we found a significantly higher frequency of short direct repeats near exon-intron boundary than in conserved introns, supporting the double-strand break repair model. We also found possible source sequences for two cases of intron gain, one by gene conversion and one by insertion of a mitochondrial sequence during double-strand break repair. Source sequences for most gained introns could not be identified and the possible reasons were discussed. In the four Aspergillus genomes studied, we did not find evidence of frequent parallel intron gains.

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Ubiquitous internal gene duplication and intron creation in eukaryotes

Cited by 45 publications

References 46 publications

Intron creation and DNA repair

Intron creation and DNA repair

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Evaluation of Models of the Mechanisms Underlying Intron Loss and Gain in Aspergillus Fungi

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