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

This is the first study in which the ( ) nuclear genome (nDNA) obtained from the GenBank database was analyzed for pseudogene sequences of mitochondrial origin. To date, there is no information about pseudogenes localized in genome. This study aimed to identify NUMTs, their length, homology, and loc...

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Bibliographic Details
Published in:International journal of molecular sciences 2020-11, Vol.21 (22), p.8725
Main Authors: Kowal, Krzysztof, Tkaczyk, Angelika, Pierzchała, Mariusz, Bownik, Adam, Ślaska, Brygida
Format: Article
Language:English
Subjects:
Animals
BLAST
Cell Nucleus - genetics
Daphnia - genetics
Daphnia magna
Deoxyribonucleic acid
DNA
DNA, Mitochondrial - genetics
Evolution
Fragments
Genes
Genes, Mitochondrial - genetics
Genome - genetics
Genome, Mitochondrial - genetics
Genomes
Genomics
Homology
Mitochondria - genetics
Mitochondrial DNA
mtDNA
NUMT
Pseudogenes
Pseudogenes - genetics
RNA, Transfer - genetics
Sequence Analysis, DNA - methods
tRNA Met
water flea
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Summary:This is the first study in which the ( ) nuclear genome (nDNA) obtained from the GenBank database was analyzed for pseudogene sequences of mitochondrial origin. To date, there is no information about pseudogenes localized in genome. This study aimed 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 (mtDNA) analyses. Bioinformatic analysis showed 1909 fragments of the mtDNA of , of which 1630 were located in ten linkage groups (LG) of the nDNA. The best-matched NUMTs covering >90% of the gene sequence have been identified for two mt-tRNA genes, and they may be functional nuclear RNA molecules. Isolating the total DNA in mtDNA studies, co-amplification of nDNA fragments is unlikely in the case of amplification of the whole tRNA genes as well as fragments of other genes. It was observed that fragments had the highest level of sequence homology, thus they could be evolutionarily the youngest. The lowest homology was found in the D-loop-derived pseudogene. It may probably be the oldest NUMT incorporated into the nDNA; however, further analysis is necessary.
ISSN:1422-0067
1661-6596
1422-0067
DOI:10.3390/ijms21228725