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Abstract
BackgroundIt is widely accepted that orthologous genes have lost or gained introns throughout evolution. However, the specific mechanisms that generate these changes have proved elusive. Introns are known to affect nearly every level of gene expression. Therefore, understanding their mechanism of evolution after their initial fixation in eukaryotes is pertinent to understanding the means by which organisms develop greater regulation and complexity.ResultsTo investigate possible mechanisms of intron gain and loss, we identified 189 intron gain and 297 intron loss events among 11 Drosophila species. We then investigated these events for signatures of previously proposed mechanisms of intron gain and loss. This work constitutes the first comprehensive study into the specific mechanisms that may generate intron gains and losses in Drosophila. We report evidence of intron gain via transposon insertion; the first intron loss that may have occurred via non-homologous end joining; intron gains via the repair of a double strand break; evidence of intron sliding; and evidence that internal or 5' introns may not frequently be deleted via the self-priming of reverse transcription during mRNA-mediated intron loss. Our data also suggest that the transcription process may promote or result in intron gain.ConclusionOur findings support the occurrence of intron gain via transposon insertion, repair of double strand breaks, as well as intron loss via non-homologous end joining. Furthermore, our data suggest that intron gain may be enabled by or due to transcription, and we shed further light on the exact mechanism of mRNA-mediated intron loss.
Highlights
It is widely accepted that orthologous genes have lost or gained introns throughout evolution
Within the final dataset of 353 orthologs, we identified 189 intron gains and 287 intron losses with 112 gains and 94 losses located at ancestral nodes (Figure 1) and 77 gains and 193 losses located within a single species (Table 1)
Mechanisms of Intron Loss Reverse Transcriptase-Mediated Intron Loss Because RTMIL leaves behind no distinct mechanistic signatures, it is only possible to determine its prevalence by analyzing intron deletion biases
Summary
It is widely accepted that orthologous genes have lost or gained introns throughout evolution. Introns are known to affect nearly every level of gene expression Understanding their mechanism of evolution after their initial fixation in eukaryotes is pertinent to understanding the means by which organisms develop greater regulation and complexity. By identifying orthologs, aligning gene sequences, and coupling intron absences/ presences with known species phylogenies, numerous studies have identified the number of intron gains and losses that have occurred among species throughout evolution [1,2,3,4,5,6,7,8,9,10,11]. The genomic deletion of introns may occur via various molecular mechanisms and may produce precise or imprecise intron losses. The prevalence of each proposed mechanism of intron loss is unknown
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