Transcriptomic analysis of diplomonad parasites reveals a trans-spliced intron in a helicase gene in Giardia

Abstract

Gene expression is the central preoccupation of molecular biology, thus newly discovered facets of gene expression are of great interest. Recently, ourselves and others reported that in the diplomonad protist Giardia 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 the G. lamblia transcriptome and across diplomonad diversity, however a dearth of transcriptomic data at the time prohibited systematic study of these questions. Here, I leverage newly available transcriptomic data from G. lamblia and the related diplomonad Spironucleus salmonicida to search for trans-spliced introns. My computational pipeline recovers all four previously reported trans-spliced introns in G. lamblia, suggesting good sensitivity. Scrutiny of thousands of potential cases revealed only a single additional trans-spliced intron in G. lamblia, in the p68 helicase gene, and no cases in S. salmonicida. The p68 intron differs from the previously reported trans-spliced introns in its high degree of streamlining: the core features of G. lamblia trans-spliced introns closely packed together, revealing striking efficiency in the implementation of a seemingly inherently inefficient molecular mechanism. These results serve to circumscribe the role of trans-splicing both in terms of genes effected and taxonomically. Future work should focus on the molecular mechanisms, evolutionary origins and phenotypic implications of this intriguing phenomenon.