title: Patterns of intron gain and loss in fungi.
abstract: Little is known about the patterns of intron gain and loss or the relative contributions of these two processes to gene evolution. To investigate the dynamics of intron evolution, we analyzed orthologous genes from four filamentous fungal genomes and determined the pattern of intron conservation. We developed a probabilistic model to estimate the most likely rates of intron gain and loss giving rise to these observed conservation patterns. Our data reveal the surprising importance of intron gain. Between about 150 and 250 gains and between 150 and 350 losses were inferred in each lineage. We discuss one gene in particular (encoding 1-phosphoribosyl-5-pyrophosphate synthetase) that displays an unusually high rate of intron gain in multiple lineages. It has been recognized that introns are biased towards the 5' ends of genes in intron-poor genomes but are evenly distributed in intron-rich genomes. Current models attribute this bias to 3' intron loss through a poly-adenosine-primed reverse transcription mechanism. Contrary to standard models, we find no increased frequency of intron loss toward the 3' ends of genes. Thus, recent intron dynamics do not support a model whereby 5' intron positional bias is generated solely by 3'-biased intron loss.
authors.affiliation: Department of Biology, Massachusetts Institute of Technology Cambridge, Massachusetts, USA.
authors.forename: Cydney B
authors.initials: CB
authors.lastname: Nielsen
authors.forename: Brad
authors.initials: B
authors.lastname: Friedman
authors.forename: Bruce
authors.initials: B
authors.lastname: Birren
authors.forename: Christopher B
authors.initials: CB
authors.lastname: Burge
authors.forename: James E
authors.initials: JE
authors.lastname: Galagan
mesh_terms: D000241:Adenosine / Q000235:genetics; D000595:Amino Acid Sequence; D000818:Animals; D001233:Aspergillus nidulans / Q000235:genetics; D001483:Base Sequence; D017173:Caenorhabditis elegans; D005091:Exons; D005670:Fusarium / Q000235:genetics; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D016678:Genome; D016681:Genome, Fungal; D007438:Introns; D020082:Magnaporthe / Q000235:genetics; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009492:Neurospora crassa / Q000378:metabolism; D011108:Polymers; D011336:Probability; D012268:Ribose-Phosphate Pyrophosphokinase / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D014158:Transcription, Genetic
chemical_list: D011108:Polymers; C069424:polyadenosine; D012268:Ribose-Phosphate Pyrophosphokinase; D000241:Adenosine