Re-evaluation of nuclear mitochondrial pseudogenes (NUMTs) and heteroplasmy in the Japanese spiny lobster Panulirus japonicus

Abstract

The Japanese spiny lobster Panulirus japonicus has been reported to harbor a numbers of nuclear mitochondrial pseudogenes (NUMTs) and heteroplasmy. However, distinguishing phylogenetically young NUMTs, heteroplasmy, and PCR-cloning artefacts may be challenging. In addition, greater degradation for mtDNA than nuclear DNA in elderly tissue specimens may promote amplification of NUMTs. In this study, we performed clone library-based nucleotide sequence analysis of the partial mtDNA COI gene using genomic DNA and cDNA obtained from fresh tissues of the Japanese spiny lobster and genomic DNA obtained from three crustacean and three fish species. Minor nucleotide substitutions between clones in an individual were ubiquitously observed in all species examined including the lobster cDNA, suggesting that most of these were artefacts. Rarely, a few clones were most likely to have originated from heteroplasmic copies, as they had skewed nucleotide substitutions at the third codon. The Japanese spiny lobster is more likely than others to detect NUMTs, while the detection of NUMTs may be somewhat suppressed using genomic DNA obtained from fresh tissue.