The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS.
BACKGROUND
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. 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.


RESULTS
Location 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.


CONCLUSIONS
The 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.
Dipartimento di Biochimica e Biologia Molecolare E, Quagliariello, Università di Bari, Via E, Orabona 4, 70126 Bari, Italy. daniela.lascaro@biologia.uniba.it
Daniela
D
Lascaro
Stefano
S
Castellana
Giuseppe
G
Gasparre
Giovanni
G
Romeo
Cecilia
C
Saccone
Marcella
M
Attimonelli
D002467:Cell Nucleus / Q000235:genetics; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods*; D004272:DNA, Mitochondrial / Q000235:genetics*; D030561:Databases, Nucleic Acid; D015894:Genome, Human; D054629:Genome, Mitochondrial; D023281:Genomics / Q000379:methods*; D006801:Humans; D032085:Isochores / Q000235:genetics; D016133:Polymerase Chain Reaction; D012016:Reference Values; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D004272:DNA, Mitochondrial; D032085:Isochores