title: Transcriptomic analysis of diplomonad parasites reveals a trans-spliced intron in a helicase gene inGiardia.
abstract: BACKGROUND
  The mechanisms by which DNA sequences are expressed is the central preoccupation of molecular genetics. Recently, ourselves and others reported that in the diplomonad protistGiardia lamblia, the coding regions of several mRNAs are produced by ligation of independent RNA species expressed from distinct genomic loci. Such trans-splicing of introns was found to affect nearly as many genes in this organism as does classical cis-splicing of introns. These findings raised questions about the incidence of intron trans-splicing both across theG. lambliatranscriptome and across diplomonad diversity in general, however a dearth of transcriptomic data at the time prohibited systematic study of these questions.
  
  
  METHODS
  I leverage newly available transcriptomic data fromG. lambliaand the related diplomonadSpironucleus salmonicidato search for trans-spliced introns. My computational pipeline recovers all four previously reported trans-spliced introns inG. lamblia, suggesting good sensitivity.
  
  
  RESULTS
  Scrutiny of thousands of potential cases revealed only a single additional trans-spliced intron inG. lamblia, in the p68 helicase gene, and no cases inS. salmonicida. The p68 intron differs from the previously reported trans-spliced introns in its high degree of streamlining: the core features ofG. lambliatrans-spliced introns are closely packed together, revealing striking economy in the implementation of a seemingly inherently uneconomical molecular mechanism.
  
  
  CONCLUSIONS
  These results serve to circumscribe the role of trans-splicing in diplomonads both in terms of the number of genes effected and taxonomically. Future work should focus on the molecular mechanisms, evolutionary origins and phenotypic implications of this intriguing phenomenon.
authors.affiliation: Department of Biology, San Francisco State University , San Francisco , CA , United States.
authors.forename: Scott William
authors.initials: SW
authors.lastname: Roy
keywords: Genome complexity; Protist molecular biology; Trans-splicing