A quick, direct method that can differentiate expressed mitochondrial genes from their nuclear pseudogenes

Current Biology : CB
R V ColluraC B Stewart

Abstract

Direct sequencing of mitochondrial DNA (mtDNA) following amplification using the polymerase chain reaction (PCR) has found widespread use in population genetic and phylogenetic research over the past few years. Recently, nuclear copies of mitochondrial genes have been reported in diverse eukaryotic species, often confounding such research (reviewed in [2,3]). Under certain circumstances, nuclear pseudogenes can be amplified more efficiently than the intended mtDNA target, even when using as template mtDNA that has been purified by gradient centrifugation. If the transfer of the gene copy to the nucleus happened recently, it can be difficult-if not impossible-to identify the legitimate mitochondrial sequence. Here, we present a simple method that can identify expressed mitochondrial genes, using the cytochrome b gene of the particularly problematical proboscis monkey as an example. Because mtDNA is transcribed and processed into polyadenylated mRNAs reverse transcription coupled to PCR can be used to amplify the expressed mitochondrial version. This method produced an unambiguous sequence for the proboscis monkey mitochondrial cytochrome b gene; in contrast, traditional DNA-based PCR methods produced ambiguous sequence, because ...Continue Reading

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