title: Intron evolution in Neurospora: the role of mutational bias and selection.
abstract: We used comparative and population genomics to study intron evolutionary dynamics in the fungal model genus Neurospora. For our investigation, we used well-annotated genomes of N. crassa, N. discreta, and N. tetrasperma, and 92 resequenced genomes of N. tetrasperma from natural populations. By analyzing the four well-annotated genomes, we identified 9495 intron sites in 7619 orthologous genes. Our data supports nonhomologous end joining (NHEJ) and tandem duplication as mechanisms for intron gains in the genus and the RT-mRNA process as a mechanism for intron loss. We found a moderate intron gain rate (5.78-6.89 × 10(-13) intron gains per nucleotide site per year) and a high intron loss rate (7.53-13.76 × 10(-10) intron losses per intron sites per year) as compared to other eukaryotes. The derived intron gains and losses are skewed to high frequencies, relative to neutral SNPs, in natural populations of N. tetrasperma, suggesting that selection is involved in maintaining a high intron turnover. Furthermore, our analyses of the association between intron population-level frequency and genomic features suggest that selection is involved in shaping a 5' intron position bias and a low intron GC content. However, intron sequence analyses suggest that the gained introns were not exposed to recent selective sweeps. Taken together, this work contributes to our understanding of the importance of mutational bias and selection in shaping the intron distribution in eukaryotic genomes.
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden; Department of Molecular Evolution, Biomedical Centre, Uppsala University, SE-751 24 Uppsala, Sweden.
authors.forename: Yu
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden;
authors.forename: Carrie A
authors.initials: CA
authors.lastname: Whittle
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden;
authors.forename: Pádraic
authors.initials: P
authors.lastname: Corcoran
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden; hanna.johannesson@ebc.uu.se.
authors.forename: Hanna
authors.initials: H
authors.lastname: Johannesson
mesh_terms: D059766:DNA End-Joining Repair; D004271:DNA, Fungal / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D005787:Gene Frequency; D005828:Genetics, Population; D016681:Genome, Fungal; D007438:Introns; D009154:Mutation; D009491:Neurospora / Q000145:classification / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012333:RNA, Messenger / Q000235:genetics; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D004271:DNA, Fungal; D004272:DNA, Mitochondrial; D012333:RNA, Messenger