Comparative genomic analysis of fungal genomes reveals intron-rich ancestors

Jason E Stajich¹^,2 , Fred S Dietrich¹ and Scott W Roy¹^,3

¹Department of Molecular Genetics and Microbiology, Center for Genome Technology, Institute for Genome Science and Policy, Duke University, Durham, NC 27710, USA

²Miller Institute for Basic Research and Department of Plant and Microbial Biology, 111 Koshland Hall #3102, University of California, Berkeley, CA 94720-3102, USA

³National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA

author email corresponding author email

Genome Biology 2007, 8:R223doi:10.1186/gb-2007-8-10-r223


Published:	19 October 2007

Subject areas: Evolution, Genome studies, Bioinformatics

Abstract

Background

Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from transcripts before protein translation. Many facets of spliceosomal intron evolution, including age, mechanisms of origins, the role of natural selection, and the causes of the vast differences in intron number between eukaryotic species, remain debated. Genome sequencing and comparative analysis has made possible whole genome analysis of intron evolution to address these questions.

Results

We analyzed intron positions in 1,161 sets of orthologous genes across 25 eukaryotic species. We find strong support for an intron-rich fungus-animal ancestor, with more than four introns per kilobase, comparable to the highest known modern intron densities. Indeed, the fungus-animal ancestor is estimated to have had more introns than any of the extant fungi in this study. Thus, subsequent fungal evolution has been characterized by widespread and recurrent intron loss occurring in all fungal clades. These results reconcile three previously proposed methods for estimation of ancestral intron number, which previously gave very different estimates of ancestral intron number for eight eukaryotic species, as well as a fourth more recent method. We do not find a clear inverse correspondence between rates of intron loss and gain, contrary to the predictions of selection-based proposals for interspecific differences in intron number.

Conclusion

Our results underscore the high intron density of eukaryotic ancestors and the widespread importance of intron loss through eukaryotic evolution.