Mechanisms of intron loss and gain in the fission yeast Schizosaccharomyces

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.

Figure 1. Phylogenetic relationship of the fission yeasts and six outgroup fungal species.

The tree was constructed from a study on comparative genomics of fission yeasts and the NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy). It is not scaled according to phylogenetic distances.

Figure 2. Detection of intronization and de-intronization.

Both intronization and de-intronization are characterized by introns neighboring large gaps while the surrounding coding regions remain well aligned. These two can be distinguished by the presence or absence of the introns in other outgroup species (A). The conserved surrounding coding regions are marked in yellow and the exonized or intronized regions are marked in red. Introns are represented as stars. The protein alignments show a case of intronization in S. pombe (B) and a case of de-intronization in S. cryophilus (C). Intron phases are marked as 0, 1, 2 or ∼ (absence of an intron). Species names abbreviations: S. cryophilus (Scry), S. octosporus (Soct), S. pombe (Spom), and S. japonicus (Sjap).

Figure 3. Intronization and de-intronization events in fission yeasts.

A) Intronization occurred in the SPBC29A10.02 gene of S. pombe. The intronized region is marked by underlining and variations in splice sites are marked in gray. Alignment of gene SPBC29A10.02 with its related EST is shown below. B) De-intronization occurred in the SPOG_00055 gene of S. cryophilus. Alignment of SPOG_00055 with its orthologs shows a de-intronization event, with the exonized region marked by underlining. Alignment of gene SPOG_00055 with its related EST is shown below. C) The consensus sequence (YTRAY) of branch sites in fission yeasts. Branch site sequences were detected using ICAT and consensus sequences were generated using Weblogo . D) The degraded branch sites of SPOG_00055 compared with its orthologous intron regions. The branch sites predicted by ICAT are marked by underlining and the consensus regions in the branch sites are in bold. Mutations are marked in gray. The introns are shown in lower case while exonic sequences are presented in upper case. Species name abbreviations: S. cryophilus (Scry), S. octosporus (Soct), S. pombe (Spom), and S. japonicus (Sjap).

Figure 4. Cases of imprecise intron deletion in fission yeasts.

The alignments of DNA sequences around imprecise intron deletion regions are shown. Exon sequences are shown in upper case while intron sequences are shown in lower case. Exonic sequence indels accompanying intron loss are marked in red. Internal regions in long intron sequences are marked by “//”. Species name abbreviations: S. cryophilus (Scry), S. octosporus (Soct), S. pombe (Spom), and S. japonicus (Sjap).

Figure 5. Adjacent introns tend to be lost together in fission yeasts.

The probability distribution of all possible numbers of adjacent lost intron pairs is shown, with the observed pattern marked by a circle. The probabilities exceeding the observed numbers of lost intron pairs were small and, therefore, adjacent introns tend to be lost together more frequently than by chance. Lost introns are categorized by A) S. pombe, B) S. japonicus, C) Ancestor of S. cryophilus, S. octosporus and S. pombe, D) Ancestor of S. cryophilus and S. octosporus.

Figure 6. Intron gain caused by tandem genomic duplication in fission yeasts.

A) Gained introns and surrounding exon sequences. To show each tandem repeat unit clearly, they are shown in different colors. The cryptic splice sites (AGGC) in tandem repeat units are marked in bold. B) Alignment of the intron-gained genes with their supporting ESTs. C) Alignments of the repeat sequences. They are not fully identical. The introns are shown in lower case while exonic sequences are shown in upper case.