title: Cross-kingdom patterns of alternative splicing and splice recognition.
abstract: BACKGROUND
  Variations in transcript splicing can reveal how eukaryotes recognize intronic splice sites. Retained introns (RIs) commonly appear when the intron definition (ID) mechanism of splice site recognition inconsistently identifies intron-exon boundaries, and cassette exons (CEs) are often caused by variable recognition of splice junctions by the exon definition (ED) mechanism. We have performed a comprehensive survey of alternative splicing across 42 eukaryotes to gain insight into how spliceosomal introns are recognized.
  
  
  RESULTS
  All eukaryotes we studied exhibit RIs, which appear more frequently than previously thought. CEs are also present in all kingdoms and most of the organisms in our analysis. We observe that the ratio of CEs to RIs varies substantially among kingdoms, while the ratio of competing 3' acceptor and competing 5' donor sites remains nearly constant. In addition, we find the ratio of CEs to RIs in each organism correlates with the length of its introns. In all 14 fungi we examined, as well as in most of the 9 protists, RIs far outnumber CEs. This differs from the trend seen in 13 multicellular animals, where CEs occur much more frequently than RIs. The six plants we analyzed exhibit intermediate proportions of CEs and RIs.
  
  
  CONCLUSIONS
  Our results suggest that most extant eukaryotes are capable of recognizing splice sites via both ID and ED, although ED is most common in multicellular animals and ID predominates in fungi and most protists.
authors.affiliation: The Broad Institute of MIT and Harvard, Cambridge Center, Cambridge, MA 02142, USA. amcguire@broad.mit.edu
authors.forename: Abigail M
authors.initials: AM
authors.lastname: McGuire
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Pearson
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Neafsey
authors.forename: James E
authors.initials: JE
authors.lastname: Galagan
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D001483:Base Sequence; D019143:Evolution, Molecular; D005091:Exons; D020224:Expressed Sequence Tags; D016678:Genome; D007438:Introns; D010802:Phylogeny; D022821:RNA Splice Sites; D014158:Transcription, Genetic
chemical_list: D022821:RNA Splice Sites