Mitochondrial pseudogenes in insect DNA barcoding: differing points of view on the same issue

Abstract

Molecular tools have been used in taxonomy for the purpose of identification and classification of living organisms. Among these, a short sequence of the mitochondrial DNA, popularly known as DNA barcoding, has become very popular. However, the usefulness and dependability of DNA barcodes have been recently questioned because mitochondrial pseudogenes, non-functional copies of the mitochondrial DNA incorporated into the nuclear genome, have been found in various taxa. When these paralogous sequences are amplified together with the mitochondrial DNA, they may go unnoticed and end up being analyzed as if they were orthologous sequences. In this contribution the different points of view regarding the implications of mitochondrial pseudogenes for entomology are reviewed and discussed. A discussion of the problem from a historical and conceptual perspective is presented as well as a discussion of strategies to keep these nuclear mtDNA copies out of sequence analyzes. Keywords: COI, molecular, NUMTs. LEITE, L.A.R. Pseudogenes mitocondriais no DNA barcoding em insetos: diferentes pontos de vista sobre a mesma questão. Biota Neotrop. 12(3): http://www.biotaneotropica.org.br/v12n3/pt/abstract?thematicreview+bn02412032012Resumo: Ferramentas moleculares têm sido utilizadas para os estudos referentes à identificação e classificação dos organismos vivos. Entre estes, uma curta sequência do DNA mitocondrial, popularmente conhecida como DNA barcoding, tornou-se muito popular. No entanto, a utilidade e confiabilidade dos códigos de barras de DNA têm sido recentemente questionadas porque pseudogenes mitocondriais, cópias não-funcionais do DNA mitocondrial incorporados ao genoma nuclear, foram encontrados em vários táxons. Quando estas sequências parálogas são amplificadas juntamente com o DNA mitocondrial, podem passar despercebidas e acabam sendo analisadas como se fossem seqüências ortólogas. Nesta contribuição objetivou-se revisar e discutir os diferentes pontos de vista sobre as implicações de pseudogenes mitocondriais para entomologia. Discutimos também o problema através de uma perspectiva histórica e conceitual, abordando estratégias para eliminar ou evitar a presença dessas cópias nucleares em meio às sequências funcionais de DNA. Palavras-chave: COI, molecular, NUMTs.

Insecticide resistance and genetic variability in natural populations of Aedes (Stegomyia) aegypti (Diptera: Culicidae) from Colombia

“…Samples containing mixtures of mtDNA and NUMT sequences are expected to significantly affect the outcome of genealogy-and frequencybased analyses. This is because mtDNA and NUMTs have separate genealogies and thus different evolutionary histories (GONÇALVES et al 2012, RIBEIRO 2012. To reduce the error caused by NUMTs in the samples two analyses were carried out: 1.…”

How much is known about the genetic diversity of the Asian tiger mosquito? A systematic review

“…These sequences complicate the employment of mtDNA as a molecular marker in genetic studies. In insects, because of the relative small genome size, high copy number of NUMTs sequences may interfere in effective separation of mtDNA from its nuclear paralogs 52,94 . This has been evident among 85 sequenced eukaryotic genomes where the NUMTs sequences were found to have different mitochondrial origin 95 .…”

“…The mtDNA is a type of marker used for the recognition of cryptic species, phylogenetic studies and/or genetic structure of populations [48][49][50] . One of the disadvantages of using mtDNA in population and phylogenetic studies is the presence of nuclear mitochondrial pseudogenes (NUMTs) [51][52] . NUMTs are non-functional copies of mitochondrial sequences that have become incorporated into the nuclear genome 53 .…”

Species delimitation in the Grayling genus Pseudochazara (Lepidoptera, Nymphalidae, Satyrinae) supported by DNA barcodes

“…– Pseudogenes or Wolbachia infections: both are common in invertebrates, particularly in arthropods (Bensasson et al 2011, Gerth et al 2014, Leite 2012, Ritter et al 2013). As the vast majority of the haplotypes in the ‘ mamurra ’ and ‘ pelopea ’ clades originate from the BOLD database it is impossible to check or correct for this potential error.…”