Exceptionally High Density of NUMTs in the Honeybee Genome

Abstract

The available genome sequences of 4 insects (the fruit fly, the African malaria mosquito, the flour beetle, and the honeybee) are used to compare the amount of mitochondrial DNA transferred to the nuclear genome (NUMTs). The data from the beetle and the bee show frequent transfer of NUMTs, whereas NUMTs in the 2 other insects are rare. The density of NUMTs in the honeybee (>1.0 bp transferred DNA per 1 kb of the nuclear sequence) is the highest in any animal studied, about ten times higher than in humans and comparable to the densities in plant genomes. The density of NUMTs in the beetle (0.056 bp/kb) is of the same order of magnitude as that in humans. The analysis of the honeybee genome indicates that NUMTs originate from all parts of the mitochondrial genome, that about two-thirds of the nuclear copies result from secondary transpositions within the nuclear genome, that the copies are significantly associated to "mariner" type transposons, and that the NUMTs consist mainly of short and fragmented copies.

The mitochondrial genome of the Mediterranean flour moth, Ephestia kuehniella (Lepidoptera: Pyralidae), and identification of invading mitochondrial sequences (numts) in the W chromosome

“…Recorded numt densities in other nuclear genomes are also mostly in the order of 0.001-0.01 bp/kbp but vary from 0 in the mosquito, Anopheles gambiae to 1.7 bp/kbp in the model plant species, Arabidopsis thaliana (Richly & Leister, 2004;Pamilo et al, 2007). Thus the numt density of the Ephestia W chromosome is more than 4× that of the highest density recorded to date in a nuclear genome.…”

Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified

“…Richly and Leister (10) surveyed numts in sequenced eukaryotic genomes and found that the number of numts ranges from none in the mosquito Anopheles gambiae to Ͼ500 in human. Although there are little or no reported cases of numts in groups such as f lies (10), chicken (26), and fishes (10), a large number of eukaryotic clades including plants (29), birds (30), nonavian reptiles (31), mammals (12,20), and arthropods (8,11,13,(17)(18)(19) were shown to have numts. In our study, the variation is not only clade-specific, but also species-specific and population-specific.…”

“…A BLAST search of mitochondrial sequences in the published nuclear genomes suggests that nearly 99% of the mitochondrial sequences were transferred to different parts of the nucleus in both human and mouse (10). Pamilo et al (13) reported Ͼ2,000 possible numts in the honey bee genome and found a similarly large number of numt copies in the flour beetle genome. These findings collectively indicate that numts are extremely pervasive in nature and that there may be a large number of species with unrealized numts of the COI gene in the nucleus.…”

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

“…Later, Pamilo et al (2007) searched for pseudogenes in four insect species, D. melanogaster; A. gambiae; Apis mellifera Linnaeus, 1758 (Hymenoptera : Apidae) and Tribolium castaneum (Herbst, 1797) (Coleoptera : Tenebrionidae), and suggested that the rate of transfer of mitochondrial genes to the nuclear DNA in Apis mellifera and Tribolium castaneum is high with respect to the dipterans sampled. After analyzing the number of NUMTs (>2000) and the relationship between the number of base-pairs transferred per 1 Kb of nuclear sequence (>1.0) in their samples, they also concluded that A. mellifera has the greatest number of NUMTs in the animal kingdom.…”