When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis.
Gene and intron prediction are essential for accurate inferences about genome evolution. Recently, two genome-wide studies searched for recent intron gains in humans, reaching very different conclusions: either of a complete absence of intron gain since early mammalian evolution, or of creation of numerous introns by genomic duplication in repetitive regions. We discuss one possible explanation: the underappreciated phenomenon of "template switching", by which reverse transcriptase may create artifactual splicing-like events in the preparation of cDNA/EST libraries, may cause complications in searches for newly gained introns in repetitive regions. We report large numbers of apparent template switching in transcript sequences from the intron-poor protists Trichomonas vaginalis and Giardia lamblia. Supplementary material for this article can be found on the BioEssays website (http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html).
Roy
Scott William
SW
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. scottwroy@gmail.com
Irimia
Manuel
M
D000483:Alleles; D000818:Animals; D001483:Base Sequence; D016054:DNA, Protozoan / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D023281:Genomics; D016829:Giardia lamblia / Q000235:genetics / Q000378:metabolism; D006801:Humans; D007438:Introns; D008957:Models, Genetic; D008969:Molecular Sequence Data; D012326:RNA Splicing / Q000235:genetics*; D012194:RNA-Directed DNA Polymerase / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic; D014246:Trichomonas vaginalis / Q000235:genetics / Q000378:metabolism
D016054:DNA, Protozoan; D012194:RNA-Directed DNA Polymerase