Protein‐Coding Segments: Evolution of Exon–Intron Gene Structure

Abstract

Abstract Many eukaryotic genes are disrupted by noncoding regions of deoxyribonucleic acid (DNA) of variable sizes called introns, giving the genes an exon–intron structure. Origin and evolution of introns is an important, long‐standing problem. The availability of multiple, complete genome sequences allows one to address many fundamental evolutionary questions. Analysis of orthologous genes from completely sequenced eukaryotic genomes revealed numerous shared intron positions in orthologous genes between animals, fungi, plants and protists. The data on intron positions were used as the starting point for evolutionary reconstruction with various phylogenetic methods. These methods reconstructed intron‐rich ancestors but in many cases inferred lineage‐specific high levels of intron loss and gain. These results indicate that numerous introns were present already at the earliest stages of evolution of eukaryotes and are compatible with the hypothesis that the original, catastrophic intron invasion accompanied the emergence of the eukaryotic cells. Key concepts: The exon–intron gene structure is highly dynamic. Orthologous genes from distant eukaryotic species share up to 25–30% intron positions. Intron gains and losses might occur during limited time spans. The Last Eukaryotic Common Ancestor was intron‐rich. In the course of evolution, the splice signal shifts from exons to introns. The scenario of the origin and evolution of introns that is best compatible with the results of comparative genomics goes as follows: self‐splicing introns since the earliest stages of life's evolution followed by numerous spliceosomal introns invading genes of the emerging eukaryotes and subsequent lineage‐specific loss and gain of spliceosomal introns.