Abstract
This is the first study in which the Daphnia magna (D. magna) 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 D. magna 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 D. magna, 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 TRNA-MET 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.
Highlights
Daphnia, commonly known as the water flea, are small crustaceans usually inhabiting freshwater ponds and lakes on all continents of the globe
The total length of the NUMT sequences in the linkage groups corresponded to the number of fragments on individual LG (Table 1)
The total length of NUMTs in the D. magna genome was 44.391 base pairs, which accounted for 0.042% of the length of the nuclear genome
Summary
Commonly known as the water flea, are small crustaceans usually inhabiting freshwater ponds and lakes on all continents of the globe. It has long been used as a model for the elucidation of animal responses and adaptations to environmental changes [1]. Its sensitive behavioral and physiological responses are parameters used as biomarkers of the effect induced by various substances [1,2,3,4,5,6,7,8] It has been used for reproduction tests, acute toxicity studies, and chronic toxicity tests in the OECD Guidelines [9,10]. Low- and high-density genetic linkage maps were obtained, in which they assembled the whole genome sequence of D. magna
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