Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome of Daphnia Magna

Abstract Background: This is the first study in which the Daphnia magna (D. magna) nuclear genome deposited in the GenBank data-base was analyzed for pseudogene sequences of mitochondrial origin. The first complete information about the genome of D. magna was published by Lee et al. in 2019. To date, there is no information about pseudogenes localized in the genome of D. magna . The aim of the present study was to identify NUMTs, their length, homology, and location for potential use in evolutionary studies and to check whether their occurrence causes co-amplification during mitochondrial genome analyses.Results: Bioinformatic analysis showed 1909 fragments of the mitochondrial genome of D. magna , of which 1630 fragments were located in ten linkage groups (LG) of the nuclear genome (nDNA). The most frequently occurring fragments of the mtDNA sequence in the nuclear genome included ND2 (115), ND3 (113), and TRNA-CYS (110)). However, the highest number of NUMTs was observed for the D-loop (147). 253 fragments showed 100% homology (from 16 to 46 bp) with mtDNA gene sequences. The sequence homology for TRNA-MET was 100% for all 6 NUMTs (from 16 to 18 bp). The overall length of NUMTs in the nDNA was 44.391 bp (from 16 to 182 bp), which accounted for 0.042% of the entire genome.Conclusions: The best-matched NUMTs covering more than 90% of the mtDNA gene sequence have been identified for the TRNA-ARG (95%), TRNA-GLU (97%), and TRNA-THR (95%) genes, and they may be included in the functional nuclear tRNA genes. Using the product of total DNA isolation in mtDNA studies, coamplification of nDNA fragments is unlikely in the case of amplification of the whole tRNA genes as well as fragments of other genes and the D-loop with a length exceeding 200 bp. It was observed that TRNA-MET fragments had the highest level of sequence homology, which means that they could be evolutionarily the youngest. The lowest degree of homology was found in the pseudogene derived from the mtDNA D-loop sequence. It may probably be the oldest element of mitochondrial DNA incorporated into the nuclear genome; however, further analysis is necessary.