Abstract
The role of spliceosomal intronic structures played in evolution has only begun to be elucidated. Comparative genomic analyses of fungal snoRNA sequences, which are often contained within introns and/or exons, revealed that about one-third of snoRNA-associated introns in three major snoRNA gene clusters manifested polymorphisms, likely resulting from intron loss and gain events during fungi evolution. Genomic deletions can clearly be observed as one mechanism underlying intron and exon loss, as well as generation of complex introns where several introns lie in juxtaposition without intercalating exons. Strikingly, by tracking conserved snoRNAs in introns, we found that some introns had moved from one position to another by excision from donor sites and insertion into target sties elsewhere in the genome without needing transposon structures. This study revealed the origin of many newly gained introns. Moreover, our analyses suggested that intron-containing sequences were more prone to sustainable structural changes than DNA sequences without introns due to intron's ability to jump within the genome via unknown mechanisms. We propose that splicing-related structural features of introns serve as an additional motor to propel evolution.
Highlights
Spliceosomal introns, one of the hallmarks of eukaryotic genomes, exist in eukaryotic protein-coding genes [1,2,3,4] and non-protein-coding genes [5,6]
Previous studies of intron loss and gain mainly focused on protein-coding genes [7,8,9,10], which are subjected to huge natural selection pressure because small changes in nucleotide sequences in exons tend to drastically alter protein structures and functions
Several lines of evidence suggest that half or more of mammalian transcriptomes consist of non-coding RNAs, many of which are subjected to splicing [11,12,13]
Summary
Spliceosomal introns, one of the hallmarks of eukaryotic genomes, exist in eukaryotic protein-coding genes [1,2,3,4] and non-protein-coding genes [5,6]. Previous studies of intron loss and gain mainly focused on protein-coding genes [7,8,9,10], which are subjected to huge natural selection pressure because small changes in nucleotide sequences in exons (lost or gained) tend to drastically alter protein structures and functions. The presence of conserved non-coding RNAs in introns of non-coding genes has facilitated tracking of intron loss and gain events. By comparing conserved snoRNAs in introns, an alternative mechanism for intron loss through widespread degeneration of splicing signals (de-intronization) was uncovered in Saccharomyces [15], demonstrating the power of studying intron loss and gain in non-coding RNA genes. Based on these findings we propose a novel evolution mechanism, i.e., intronic structures serve as an additional motor to propel evolution
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