RNA editing by targeted insertion and deletion of uridine is crucial to generate translatable mRNAs from the cryptogenes of the mitochondrial genome of kinetoplastids. This type of editing consists of a stepwise cascade of reactions generally proceeding from 3' to 5' on a transcript, resulting in a population of partially edited as well as pre-edited and completely edited molecules for each mitochondrial cryptogene of these protozoans. Often, the number of uridines inserted and deleted exceed the number of nucleotides that are genome-encoded. Thus, analysis of kinetoplastid mitochondrial transcriptomes has proven frustratingly complex. Here we present our analysis of Leptomonas pyrrhocoris mitochondrial cDNA deep sequencing reads using T-Aligner, our new tool which allows comprehensive characterization of RNA editing, not relying on targeted transcript amplification and on prior knowledge of final edited products. T-Aligner implements a pipeline of read mapping, visualization of all editing states and their coverage, and assembly of canonical and alternative translatable mRNAs. We also assess T-Aligner functionality on a more challenging deep sequencing read input from Trypanosoma cruzi. The analysis reveals that transcripts of cryptogenes of both species undergo very complex editing that includes the formation of alternative open reading frames and whole categories of truncated editing products.
Bibliographical noteFunding Information:
M.D.L. and P.F.]; Russian Foundation for Basic Research [14-04-01717 to A.A.K. and E.S.G.]; American Heart Association [16SDG26420019 to S.L.Z.]; University of Minnesota Genomics Center Pilot Project Award to S.L.Z.; S.L.Z. received an Alexander Dubcˇek Fund travel fellowship (University of Minnesota). Funding for open access charge: American Heart Association [16SDG26420019 to S.L.Z.]; University of Ostrava (Rector’s Award to P.F.). Conflict of interest statement. None declared.
European Research Council CZ [LL1601 to J.L.]; Czech Science Foundation [15-21974S to J.L., 17-10656S to V.Y., 16-18699S to J.L. and V.Y.]; University of Ostrava IRP project “New research directions in the Life Science Research Centre”; Moravian–Silesian Region [research programs 2013–2014 and 2015, DT01-021358 to V.Y. and P.F.]; Czech Ministry of Education, Youth and Sports [LO1208 “TEWEP” to V.Y.]; Russian Science Foundation [transcrip-tomic library sequencing was supported by 14-50-00029 to
© The Author(s) 2017.