Abstract
BackgroundPositions of spliceosomal introns are often conserved between remotely related genes. Introns that reside in non-conserved positions are either novel or remnants of frequent losses of introns in some evolutionary lineages. A recent gain of such introns is difficult to prove. However, introns verified as novel are needed to evaluate contemporary processes of intron gain.ResultsWe identified 25 unambiguous cases of novel intron positions in 31 Drosophila genes that exhibit near intron pairs (NIPs). Here, a NIP consists of an ancient and a novel intron position that are separated by less than 32 nt. Within a single gene, such closely-spaced introns are very unlikely to have coexisted. In most cases, therefore, the ancient intron position must have disappeared in favour of the novel one. A survey for NIPs among 12 Drosophila genomes identifies intron sliding (migration) as one of the more frequent causes of novel intron positions. Other novel introns seem to have been gained by regional tandem duplications of coding sequences containing a proto-splice site.ConclusionsRecent intron gains sometimes appear to have arisen by duplication of exonic sequences and subsequent intronization of one of the copies. Intron migration and exon duplication together may account for a significant amount of novel intron positions in conserved coding sequences.
Highlights
Positions of spliceosomal introns are often conserved between remotely related genes
Using the intron distributions among Drosophila and the arthropod outgroup species Glossina morsitans, Aedes aegypti, Anopheles gambiae, Culex pipiens, Bombyx mori, Tribolium castaneum, Apis mellifera, Nasonia vitripennis, Acyrthosiphon pisum, Pediculus humanus, Daphnia pulex and Ixodes scapularis, we discovered that at least 25 intron positions of the 31 near intron pair (NIP) have arisen during Drosophila radiation
After an automatic NIP extraction alignment procedure, we obtained 122 NIP regions containing two or more near introns (NIP distance < 50 nt). These were manually inspected for splice site, alignment and conservation validity, resulting in regions comprising NIPs
Summary
Positions of spliceosomal introns are often conserved between remotely related genes. Recent gains of introns inside of conserved coding sequences (CDS), often equated with the usage of novel intron positions, appear to be a rare and poorly understood phenomenon [6]. A near intron pair (NIP) consists of two intron positions that exist in orthologous genes at nearby locations. Exon sizes smaller than about 50 nt are relatively rare [16] and in general functionally detrimental [17]. Such nearby introns typically exclude each other within a single gene. By using NIPs to determine the time at which the younger introns were gained, it can be avoided to erroneously identify those introns as novel that have been lost independently in multiple lineages
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