Abstract
BackgroundTo a greater or lesser extent, eukaryotic nuclear genomes contain fragments of their mitochondrial genome counterpart, deriving from the random insertion of damaged mtDNA fragments. NumtS (Nuclear mt Sequences) are not equally abundant in all species, and are redundant and polymorphic in terms of copy number. In population and clinical genetics, it is important to have a complete overview of NumtS quantity and location. Searching PubMed for NumtS or Mitochondrial pseudo-genes yields hundreds of papers reporting Human NumtS compilations produced by in silico or wet-lab approaches. A comparison of published compilations clearly shows significant discrepancies among data, due both to unwise application of Bioinformatics methods and to a not yet correctly assembled nuclear genome. To optimize quantification and location of NumtS, we produced a consensus compilation of Human NumtS by applying various bioinformatics approaches.ResultsLocation and quantification of NumtS may be achieved by applying database similarity searching methods: we have applied various methods such as Blastn, MegaBlast and BLAT, changing both parameters and database; the results were compared, further analysed and checked against the already published compilations, thus producing the Reference Human Numt Sequences (RHNumtS) compilation. The resulting NumtS total 190.ConclusionThe RHNumtS compilation represents a highly reliable reference basis, which may allow designing a lab protocol to test the actual existence of each NumtS. Here we report preliminary results based on PCR amplification and sequencing on 41 NumtS selected from RHNumtS among those with lower score. In parallel, we are currently designing the RHNumtS database structure for implementation in the HmtDB resource. In the future, the same database will host NumtS compilations from other organisms, but these will be generated only when the nuclear genome of a specific organism has reached a high-quality level of assembly.
Highlights
To a greater or lesser extent, eukaryotic nuclear genomes contain fragments of their mitochondrial genome counterpart, deriving from the random insertion of damaged mtDNA fragments
We report preliminary results based on PCR amplification and sequencing on 41 NumtS selected from Reference Human Numt Sequences (RHNumtS) among those with lower score
We used Blastn and MegaBlast, the versions most frequently adopted in reports on human NumtS compilation
Summary
To a greater or lesser extent, eukaryotic nuclear genomes contain fragments of their mitochondrial genome counterpart, deriving from the random insertion of damaged mtDNA fragments. In greater or lesser abundance, eukaryotic nuclear genomes contain fragments of their mitochondrial (mt) genome counterpart, deriving from "random" insertion of damaged mtDNA fragments [1]. It seems obvious that the genomic region where the mt sequence is inserted may be involved in further recombination events, generating duplication of the mt fragment In some organisms, such as primates, the same mt region occurs several times along the nuclear genome, but only detailed evolutionary analysis may help in identifying "duplicated" NumtS, because recombination and mutation occurring after duplication may well mask the latter event. Once this problem is solved, each NumtS may be associated with a given copy number, this may differ even among tissues or cells of the same individual. Further examples of polymorphic NumtS are reported in "The case of siblings" [15] and the Ricchetti compilation [16]
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