Numts and heteroplasmy disrupting mitochondrial markers on evolutionary studies
Elaine Aparecida Françoso, Elaine Aparecida Françoso , Paulo Ricardo Cseri , Maria Cristina Arias
Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil; Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil ; Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil ; Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil
While Numts are mitochondrial DNA (mtDNA) copies transferred to nucleus, the heteroplasmy is characterized by multiple copies of mitochondrial genome in the same individual. Although they are completely distinct phenomena, both can be primarily recognized by double picks in the electropherogram of presumably mitochondrial sequences. Numts and heteroplasmy are described as rare in the literature, but we truly believe that these events are neglected and their consequences on evolutionary studies are still unpredictable. The aim of this study was to isolate and characterize numts and heteroplasmy in bees, a group of extreme ecological, economical and scientific importance. For this, mitochondria were first isolated from the nucleus and their DNA were extracted separately. A portion of the Cytochrome C Oxidase I (COI) gene was PCR amplified using as template DNA from nuclear and mitochondrial fractions in an attempt to isolate numts and heteroplasmic sequences, respectively. PCR products were cloned and sequenced. Numts and heteroplasmy were confirmed in several bee species. COI numts were recovered in all Meliponini species tested. Reconstructing a phylogeny from Meliponini group, the origin of some numts was identified. In addition, we also found some numts deposited in GenBank erroneously identified as COI sequences. The heteroplasmy was confirmed in all bees tested, but the heteroplasmic sequence frequencies vary among species. For example, from 40 sequences of COI from the mtDNA of one single bee, Bombus morio, 23 different mitochondrial haplotypes were identified, a number much higher than expected. Numts and heteroplasmy can be, at the same time, an obstacle and a new tool for evolutionary analysis. Understanding the origin and the evolution of these molecular phenomena will be important for studies that use mtDNA as main marker in phylogenetic and phylogeographic analyses, population genetics, and molecular identification of species through DNA barcode.