Abstract
BackgroundSpliceosomal introns are a common feature of eukaryotic genomes. To approach a comprehensive understanding of intron evolution on Earth, studies should look beyond repeatedly studied groups such as animals, plants, and fungi. The slime mold Dictyostelium belongs to a supergroup of eukaryotes not covered in previous studies.ResultsWe found 441 precise intron losses in Dictyostelium discoideum and 202 precise intron losses in Dictyostelium purpureum. Consistent with these observations, Dictyostelium discoideum was found to have significantly more copies of reverse transcriptase genes than Dictyostelium purpureum. We also found that the lost introns are significantly further from the 5′ end of genes than the conserved introns. Adjacent introns were prone to be lost simultaneously in Dictyostelium discoideum. In both Dictyostelium species, the exonic sequences flanking lost introns were found to have a significantly higher GC content than those flanking conserved introns. Together, these observations support a reverse-transcription model of intron loss in which intron losses were caused by gene conversion between genomic DNA and cDNA reverse transcribed from mature mRNA. We also identified two imprecise intron losses in Dictyostelium discoideum that may have resulted from genomic deletions. Ninety-eight putative intron gains were also observed. Consistent with previous studies of other lineages, the source sequences were found in only a small number of cases, with only two instances of intron gain identified in Dictyostelium discoideum.ConclusionsAlthough they diverged very early from animals and fungi, Dictyostelium species have similar mechanisms of intron loss.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0567-y) contains supplementary material, which is available to authorized users.
Highlights
Spliceosomal introns are a common feature of eukaryotic genomes
Intron loss genes are significantly enriched in 98 Gene Ontology (GO) categories and putative intron gain genes are significantly enriched in 97 GO categories (P < 0.01, Additional file 2: Table S2)
They share 46 common GO categories. From these GO enrichments, we could not see any implications on the mechanisms of intron loss and gain
Summary
Spliceosomal introns are a common feature of eukaryotic genomes. To approach a comprehensive understanding of intron evolution on Earth, studies should look beyond repeatedly studied groups such as animals, plants, and fungi. Ma et al BMC Evolutionary Biology (2015) 15:286 reverse transcription process frequently aborts, producing incomplete cDNA molecules Recombination of these cDNAs with genomic DNA would cause a preferential loss of introns from the 3′ end of genes. As the repair process generally requires microhomology between the break sites, this model predicts that there should be short direct repeats at the two ends of the lost intron. Short direct repeats at the splice sites of lost introns have been detected in plants and invertebrates [25,26,27], supporting the third model Another prediction of the third model, imprecise intron loss, has not been observed to have a high frequency in most eukaryotic lineages [28]
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