Mechanisms of Intron Loss and Gain in the Fission Yeast Schizosaccharomyces

Tao Zhu,Deng-Ke Niu,Jürg Bähler

doi:10.1371/journal.pone.0061683

Abstract

The fission yeast, Schizosaccharomyces pombe, is an important model species with a low intron density. Previous studies showed extensive intron losses during its evolution. To test the models of intron loss and gain in fission yeasts, we conducted a comparative genomic analysis in four Schizosaccharomyces species. Both intronization and de-intronization were observed, although both were at a low frequency. A de-intronization event was caused by a degenerative mutation in the branch site. Four cases of imprecise intron losses were identified, indicating that genomic deletion is not a negligible mechanism of intron loss. Most intron losses were precise deletions of introns, and were significantly biased to the 3′ sides of genes. Adjacent introns tended to be lost simultaneously. These observations indicated that the main force shaping the exon-intron structures of fission yeasts was precise intron losses mediated by reverse transcriptase. We found two cases of intron gains caused by tandem genomic duplication, but failed to identify the mechanisms for the majority of the intron gain events observed. In addition, we found that intron-lost and intron-gained genes had certain similar features, such as similar Gene Ontology categories and expression levels.

Highlights

Spliceosomal intron densities vary greatly among different organisms [1,2,3,4]
By consulting the orthologous genes in the six outgroup fungal species, we identified putative cases of intron loss and 62 putative cases of intron gain (Tables S2–S3), as well as 156 putative cases of intronization and de-intronization
We found an A to T mutation in the branch site of gene SPOG_00055 in S. cryophilus (Figure 3D)

Summary

Introduction

Spliceosomal intron densities vary greatly among different organisms [1,2,3,4]. losses and gains of introns in evolution have been confirmed by numerous studies, their mechanisms have not been fully revealed [5,6,7,8,9,10,11,12].Three models of intron loss have been proposed: the reverse transcription (RT) model, the genomic deletion model, and the model of non-homologous end joining (NHEJ) repair of double strand breaks [7,8,9]. In Neurospora crassa and Aspergillus, the biased position of intron loss has been observed in a comparative analysis among distantly related species [18], but not in analyses of closely related species [20,22]. In both Arabidopsis and Drosophila, conflicting results have been reported [10,23,24,25,26]

Methods

Results

Conclusion