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 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 in general, however a dearth of transcriptomic data at the time prohibited systematic study of these questions. Methods. 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. Results. 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 are closely packed together, revealing striking economy in the implementation of a seemingly inherently uneconomical molecular mechanism. Discussion. 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.

A chromosome-scale reference genome for Giardia intestinalis WB

“…For multi-copy genes, synteny between the two versions were examined to determine the most appropriate geneid for the gene, an attempt to keep the synteny consistent between the two versions of genomes. www.nature.com/scientificdata www.nature.com/scientificdata/ Introns in Giardia have been published in different papers 2,26,27 , but were not curated and integrated in the genome. In this version of annotation, we integrated all the 8 cis-spliced introns and 5 trans-spliced introns (Table 1).…”

Global Lysine Acetylation and 2-Hydroxyisobutyrylation Profiling Reveals the Metabolism Conversion Mechanism in Giardia lamblia

“…Although it is a true eukaryotic cell, it displays several prokaryotic properties, such as lack of mitochondria and peroxisomes ( 51 , 52 ). In evolutionary terms, G. lamblia is more divergent from yeast than yeast is from man, and elements that are conserved from G. lamblia to man are therefore likely to reflect universal eukaryotic cell functions ( 53 ). G. lamblia is the most divergent eukaryote examined to date, and tools have been recently developed to study genes in detail ( 54 ).…”