Comparative genomic analysis of fungal genomes reveals intron-rich ancestors
Open Access
- 19 October 2007
- journal article
- research article
- Published by Springer Nature in Genome Biology
- Vol. 8 (10), R223
- https://doi.org/10.1186/gb-2007-8-10-r223
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.Keywords
This publication has 58 references indexed in Scilit:
- Evidence of mRNA-Mediated Intron Loss in the Human-Pathogenic Fungus Cryptococcus neoformansEukaryotic Cell, 2006
- Rates of intron loss and gain: Implications for early eukaryotic evolutionProceedings of the National Academy of Sciences, 2005
- Automated generation of heuristics for biological sequence comparisonBMC Bioinformatics, 2005
- Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78Nature Biotechnology, 2004
- The Generic Genome Browser: A Building Block for a Model Organism System DatabaseGenome Research, 2002
- Intron evolution as a population-genetic processProceedings of the National Academy of Sciences, 2002
- The Chaperonin Genes of Jakobid and Jakobid-Like Flagellates: Implications for Eukaryotic EvolutionMolecular Biology and Evolution, 2002
- Frequent Intron Loss in the White Gene: A Cautionary Tale for PhylogeneticistsMolecular Biology and Evolution, 2002
- Molecular evolution: Recent cases of spliceosomal intron gain?Current Biology, 1998
- Improved tools for biological sequence comparison.Proceedings of the National Academy of Sciences, 1988