title: Alternative splicing acting as a bridge in evolution.
abstract: BACKGROUND
  Alternative splicing (AS) regulates diverse cellular and developmental functions through alternative protein structures of different isoforms. Alternative exons dominate AS in vertebrates; however, very little is known about the extent and function of AS in lower eukaryotes. To understand the role of introns in gene evolution, we examined AS from a green algal and five fungal genomes using a novel EST-based gene-modeling algorithm (COMBEST).
  
  
  METHODS
  AS from each genome was classified with COMBEST that maps EST sequences to genomes to build gene models. Various aspects of AS were analyzed through statistical methods. The interplay of intron 3n length, phase, coding property, and intron retention (RI) were examined with Chi-square testing.
  
  
  RESULTS
  With 3 to 834 times EST coverage, we identified up to 73% of AS in intron-containing genes and found preponderance of RI among 11 types of AS. The number of exons, expression level, and maximum intron length correlated with number of AS per gene (NAG), and intron-rich genes suppressed AS. Genes with AS were more ancient, and AS was conserved among fungal genomes. Among stopless introns, non-retained introns (NRI) avoided, but major RI preferred 3n length. In contrast, stop-containing introns showed uniform distribution among 3n, 3n+1, and 3n+2 lengths. We found a clue to the intron phase enigma: it was the coding function of introns involved in AS that dictates the intron phase bias.
  
  
  CONCLUSIONS
  Majority of AS is non-functional, and the extent of AS is suppressed for intron-rich genes. RI through 3n length, stop codon, and phase bias bridges the transition from functionless to functional alternative isoforms.
authors.affiliation: 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China.
authors.forename: Kemin
authors.initials: K
authors.lastname: Zhou
authors.affiliation: 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China.
authors.forename: Asaf
authors.initials: A
authors.lastname: Salamov
authors.affiliation: 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China.
authors.forename: Alan
authors.initials: A
authors.lastname: Kuo
authors.affiliation: 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China.
authors.forename: Andrea L
authors.initials: AL
authors.lastname: Aerts
authors.affiliation: 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China.
authors.forename: Xiangyang
authors.initials: X
authors.lastname: Kong
authors.affiliation: 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
keywords: Alternative splicing (AS); fungal genome; intron retention (RI)