Journal Article

Intron Gains and Losses in the Evolution of <i>Fusarium</i> and <i>Cryptococcus</i> Fungi

Daniel Croll and Bruce A. McDonald

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 4, issue 11, pages 1148-1161
Published in print January 2012 |
Published online October 2012 | e-ISSN: 1759-6653 | DOI: http://dx.doi.org/10.1093/gbe/evs091

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The presence of spliceosomal introns in eukaryotic genes poses a major puzzle for the study of genome evolution. Intron densities vary enormously among distant lineages. However, the mechanisms driving intron gains are poorly understood and very few intron gains and losses have been documented over short evolutionary time spans. Fungi emerged recently as excellent models to study intron evolution and “reverse splicing” was found to be a major driver of recent intron gains in a clade of ascomycete fungi. We screened a total of 38 genomes from two fungal clades important in medicine and agriculture to identify intron gains and losses both within and between species. We detected 86 and 198 variable intron positions in the Cryptococcus and Fusarium clades, respectively. Some genes underwent extensive changes in their exon–intron structure, with up to six variable intron positions per gene. We identified a very recently gained intron in a group of tomato-infecting strains belonging to the F. oxysporum species complex. In the human pathogen C. gattii, we found recent intron losses in subtypes of the species. The two studied fungal clades provided evidence for extensive changes in their exon–intron structure within and among closely related species. We show that both intronization of previously coding DNA and insertion of exogenous DNA are the major drivers of intron gains.

Keywords: spliceosomal introns; intron gains; Fusarium; Cryptococcus; population genomics

Journal Article.  8715 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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