title: Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication.
abstract: BACKGROUND
  Positions 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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  Recent 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.
authors.affiliation: Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Lehmann
authors.forename: Carina
authors.initials: C
authors.lastname: Eisenhardt
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Veiko
authors.initials: V
authors.lastname: Krauss
mesh_terms: D000818:Animals; D001483:Base Sequence; D055028:Comparative Genomic Hybridization; D004330:Drosophila / Q000235:genetics*; D019143:Evolution, Molecular; D017344:Genes, Insect; D007438:Introns; D008969:Molecular Sequence Data; D010802:Phylogeny; D022821:RNA Splice Sites; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D020080:Tandem Repeat Sequences
chemical_list: D022821:RNA Splice Sites