Abstract
BackgroundEukaryotic nuclear genomes contain fragments of mitochondrial DNA called NumtS (Nuclear mitochondrial Sequences), whose mode and time of insertion, as well as their functional/structural role within the genome are debated issues. Insertion sites match with chromosomal breaks, revealing that micro-deletions usually occurring at non-homologous end joining loci become reduced in presence of NumtS. Some NumtS are involved in recombination events leading to fragment duplication. Moreover, NumtS are polymorphic, a feature that renders them candidates as population markers. Finally, they are a cause of contamination during human mtDNA sequencing, leading to the generation of false heteroplasmies.ResultsHere we present RHNumtS.2, the most exhaustive human NumtSome catalogue annotating 585 NumtS, 97% of which were here validated in a European individual and in HapMap samples. The NumtS complete dataset and related features have been made available at the UCSC Genome Browser. The produced sequences have been submitted to INSDC databases. The implementation of the RHNumtS.2 tracks within the UCSC Genome Browser has been carried out with the aim to facilitate browsing of the NumtS tracks to be exploited in a wide range of research applications.ConclusionsWe aimed at providing the scientific community with the most exhaustive overview on the human NumtSome, a resource whose aim is to support several research applications, such as studies concerning human structural variation, diversity, and disease, as well as the detection of false heteroplasmic mtDNA variants. Upon implementation of the NumtS tracks, the application of the BLAT program on the UCSC Genome Browser has now become an additional tool to check for heteroplasmic artefacts, supported by data available through the NumtS tracks.
Highlights
Eukaryotic nuclear genomes contain fragments of mitochondrial DNA called nuclear mitochondrial sequences (NumtS) (Nuclear mitochondrial Sequences), whose mode and time of insertion, as well as their functional/structural role within the genome are debated issues
HSP_NumtS showing evident neighbourhood on both nuclear and mitochondrial genomes were merged in a single NumtS according to the criteria described in the Methods section
NumtS covering the D-loop region were returned by BLASTN as different High Scoring Pairs (HSPs), as in the rCRS EMBL/GenBank/DDBJ
Summary
Eukaryotic nuclear genomes contain fragments of mitochondrial DNA called NumtS (Nuclear mitochondrial Sequences), whose mode and time of insertion, as well as their functional/structural role within the genome are debated issues. NumtS are polymorphic, a feature that renders them candidates as population markers. They are a cause of contamination during human mtDNA sequencing, leading to the generation of false heteroplasmies. Fragments of mtDNA that give rise to nuclear mitochondrial sequences (NumtS) are found in many proposed [4,5]. Some NumtS display a highly polymorphic behaviour, as they can occur in homo- or heterozygosis, or be absent in different individuals at specific loci. These features render them candidates as population markers, as already suggested [16]
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