title: Reliability of mitochondrial DNA in an acanthocephalan: the problem of pseudogenes.
abstract: The utility of mitochondrial DNA as a molecular marker for evolutionary studies is well recognized. However, several problems can arise when using mitochondrial DNA, one of which is the presence of nuclear mitochondrial pseudogenes, or Numts. Pseudogenes of cytochrome oxidase I were preferentially amplified from Acanthocephalus lucii (Acanthocephala) using a universal PCR approach. To verify the presence and abundance of pseudogenes, length heterogeneity analysis of the PCR fragments was performed. PCR products obtained with universal primers often contained fragments of different sizes. Cloned sequences from universal PCR products nearly always contained sequence abnormalities such as indels and/or stop codons. Based on these sequences, new primers were developed to specifically target mitochondrial DNA. Sequences obtained with these specific primers lacked abnormalities. Phylogenetic analysis produced a single most parsimonious tree in which pseudogenes obtained with universal primers grouped together as did putative mitochondrial DNA sequences obtained with specific primers. The pattern of codon bias observed in the pseudogenes suggests a single nuclear integration event from the mitochondria. This is the first reported occurrence of pseudogenes in an acanthocephalan, and it demonstrates the potential dangers associated with the use of universal primers.
authors.affiliation: Department of Biological and Environmental Science, POB 35, University of Jyväskylä, FI-40014 Jyvaskyla, Finland. dabenesh@cc.jyu.fi
authors.forename: Daniel P
authors.initials: DP
authors.lastname: Benesh
authors.forename: Tiina
authors.initials: T
authors.lastname: Hasu
authors.forename: Lotta-Riina
authors.initials: LR
authors.lastname: Suomalainen
authors.forename: E Tellervo
authors.initials: ET
authors.lastname: Valtonen
authors.forename: Marja
authors.initials: M
authors.lastname: Tiirola
mesh_terms: D000049:Acanthocephala / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D017931:DNA Primers; D004272:DNA, Mitochondrial / Q000032:analysis*; D003576:Electron Transport Complex IV / Q000235:genetics*; D005838:Genotype; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D011544:Pseudogenes
chemical_list: D017931:DNA Primers; D004272:DNA, Mitochondrial; D003576:Electron Transport Complex IV