Evolution of yeast noncoding RNAs reveals an alternative mechanism for widespread intron loss.
The evolutionary forces responsible for intron loss are unresolved. Whereas research has focused on protein-coding genes, here we analyze noncoding small nucleolar RNA (snoRNA) genes in which introns, rather than exons, are typically the functional elements. Within the yeast lineage exemplified by the human pathogen Candida albicans, we find--through deep RNA sequencing and genome-wide annotation of splice junctions--extreme compaction and loss of associated exons, but retention of snoRNAs within introns. In the Saccharomyces yeast lineage, however, we find it is the introns that have been lost through widespread degeneration of splicing signals. This intron loss, perhaps facilitated by innovations in snoRNA processing, is distinct from that observed in protein-coding genes with respect to both mechanism and evolutionary timing.
Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143-2200, USA.
Quinn M
QM
Mitrovich
Brian B
BB
Tuch
Francisco M
FM
De La Vega
Christine
C
Guthrie
Alexander D
AD
Johnson
D017398:Alternative Splicing; D002176:Candida albicans / Q000235:genetics*; D019143:Evolution, Molecular; D005091:Exons; D016681:Genome, Fungal; D007438:Introns; D058977:Molecular Sequence Annotation; D022821:RNA Splice Sites / Q000235:genetics; D012326:RNA Splicing; D012331:RNA, Fungal / Q000235:genetics*; D020537:RNA, Small Nucleolar / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017423:Sequence Analysis, RNA; D015003:Yeasts / Q000235:genetics*
D022821:RNA Splice Sites; D012331:RNA, Fungal; D020537:RNA, Small Nucleolar