Description and display conventions
NumtS (Nuclear mitochondrial sequences) are mitochondrial fragments inserted
in nuclear genomic sequences. The most credited hypothesis concerning their generation
suggests that in presence of mutagenic agents, or under stress conditions, fragments of
mtDNA escape from mitochondria, reach the nucleus and insert into chromosomes during
break repair; although NumtS can also derive from duplication of genomic fragments.
NumtS may be a cause of contamination during mtDNA sequencing and hence frequent false
low heteroplasmic evidences have been reported. The Bioinformatics group chaired
by M. Attimonelli (University of Bari, Italy) has produced the RPNumtS (Reference Pig
NumtS) compilation annotating Pig assembled NumtS. To allow the scientific community to
access the compilation and to perform genomics comparative analyses inclusive of the
NumtS data, the group has designed the Pig NumtS tracks described below.
The NumtS tracks show nuclear and mitochondrial regions, based on the High Score Pairs
(HSPs) obtained by aligning the mitochondrial reference genome (NC_012095) with the
susScr2 assembly of the pig genome.
- "NumtS (Nuclear mitochondrial Sequences)" Track
The "NumtS mitochondrial sequences" track shows the mapping of the HSPs returned by
BlastN on the nuclear genome. The shading of the items reflect the similarity returned
by BlastN, and the direction of the arrows is concordant with the strand of the
alignment. For every item, a link pointing to the mitochondrial mapping is provided,
thus allowing easier cross referencing between the NumtS subtracks.
- "NumtS assembled" Track
The "NumtS assembled" track shows items obtained by assembling HSPs annotated in the
"NumtS" track fulfilling the following conditions:
- The orientation of their alignments must be concordant.
- The distance between them must be less than 2 kb, on the mitochondrial genome
as well as on the nuclear genome.
Exceptions for the second condition arise when a long repetitive element is present between two HSPs.
- "NumtS on mitochondrion" Track
The "NumtS on mitochondrion" track shows the mapping of the HSPs on the mitochondrial
genome. The shading of the items reflects the similarity returned by BlastN, and the
direction of the arrows is concordant with the strand of the alignment.
For every, a link pointing to the nuclear mapping is provided.
- "Pig NumtS on mitochondrion SNP" Track
The "Pig NumtS SNP" shows the mapping of the HSPs on the mitochondrial genome, with
the SNPs which fall within, derived from comparison with the susScr2 assembly. No shading is provided here.
Methods
NumtS mappings were obtained by running Blast2seq (program: BlastN) between each chromosome
of the Pig Genome (susScr2 assembly) and the Pig mitochondrial reference sequence (AC: NC_012095),
fixing the e-value threshold to 1e-03. The assembling of the HSPs was performed with spreadsheet
interpolation and manual inspection. BED format is used for the first three annotation tracks,
while for the last one the SAM/BAM format is preferred.
Credits
These data were provided by Francesco Maria Calabrese, Dario Leonardo Balacco, Domenico Simone
and Marcella Attimonelli from the Department of of Biosciences, Biotechnology and Pharmacological
Sciences (University of Bari, Italy).
Manual inspection and format details have been carried out by Francesco Maria Calabrese,
Dario Leonardo Balacco and Domenico Simone.
References
Calabrese FM, Simone D, Attimonelli M.
Primates and mouse NumtS in the UCSC Genome Browser.
BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S15.
PMID: 22536961; PMC: PMC3314570
Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M.
The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human
NumtS.
BMC Genomics. 2008 Jun 3;9:267.
PMID: 18522722; PMC: PMC2447851
Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M.
The reference human nuclear mitochondrial sequences compilation validated and implemented on the
UCSC genome browser.
BMC Genomics. 2011 Oct 20;12:517.
PMID: 22013967; PMC: PMC3228558
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