Primates and mouse NumtS in the UCSC Genome Browser
<p>Abstract</p> <p>Background</p> <p>NumtS (Nuclear MiTochondrial Sequences) are mitochondrial DNA sequences that, after stress events involving the mitochondrion, colonized the nuclear genome. Accurate mapping of NumtS avoids contamination during mtDNA PCR amplificatio...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-03-01
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| Series: | BMC Bioinformatics |
| _version_ | 1818934692961845248 |
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| author | Calabrese Francesco Maria Simone Domenico Attimonelli Marcella |
| author_facet | Calabrese Francesco Maria Simone Domenico Attimonelli Marcella |
| author_sort | Calabrese Francesco Maria |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>NumtS (Nuclear MiTochondrial Sequences) are mitochondrial DNA sequences that, after stress events involving the mitochondrion, colonized the nuclear genome. Accurate mapping of NumtS avoids contamination during mtDNA PCR amplification, thus supplying reliable bases for detecting false heteroplasmies. In addition, since they commonly populate mammalian genomes (especially primates) and are polymorphic, in terms of presence/absence and content of SNPs, they may be used as evolutionary markers in intra- and inter-species population analyses.</p> <p>Results</p> <p>The need for an exhaustive NumtS annotation led us to produce the Reference Human NumtS compilation, followed, as reported in this paper, by those for chimpanzee, rhesus macaque and mouse ones. Identification of NumtS inside the UCSC Genome Browser and their inter-species comparison required the design and the implementation of NumtS tracks, starting from the compilation data. NumtS retrieval through the UCSC Genome Browser, in the species examined, is now feasible at a glance.</p> <p>Conclusions</p> <p>Analyses involving NumtS tracks, together with other genome element tracks publicly available at the UCSC Genome Browser, can provide deep insight into genome evolution and comparative genomics, thus improving studies dealing with the mechanisms that drove the generation of NumtS. In addition, the NumtS tracks constitute a useful tool in the design of mitochondrial DNA primers.</p> |
| first_indexed | 2024-12-20T05:08:19Z |
| format | Article |
| id | doaj.art-f20f1bf1db5544dcb2fc1d5c843b36b5 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-20T05:08:19Z |
| publishDate | 2012-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-f20f1bf1db5544dcb2fc1d5c843b36b52022-12-21T19:52:20ZengBMCBMC Bioinformatics1471-21052012-03-0113Suppl 4S1510.1186/1471-2105-13-S4-S15Primates and mouse NumtS in the UCSC Genome BrowserCalabrese Francesco MariaSimone DomenicoAttimonelli Marcella<p>Abstract</p> <p>Background</p> <p>NumtS (Nuclear MiTochondrial Sequences) are mitochondrial DNA sequences that, after stress events involving the mitochondrion, colonized the nuclear genome. Accurate mapping of NumtS avoids contamination during mtDNA PCR amplification, thus supplying reliable bases for detecting false heteroplasmies. In addition, since they commonly populate mammalian genomes (especially primates) and are polymorphic, in terms of presence/absence and content of SNPs, they may be used as evolutionary markers in intra- and inter-species population analyses.</p> <p>Results</p> <p>The need for an exhaustive NumtS annotation led us to produce the Reference Human NumtS compilation, followed, as reported in this paper, by those for chimpanzee, rhesus macaque and mouse ones. Identification of NumtS inside the UCSC Genome Browser and their inter-species comparison required the design and the implementation of NumtS tracks, starting from the compilation data. NumtS retrieval through the UCSC Genome Browser, in the species examined, is now feasible at a glance.</p> <p>Conclusions</p> <p>Analyses involving NumtS tracks, together with other genome element tracks publicly available at the UCSC Genome Browser, can provide deep insight into genome evolution and comparative genomics, thus improving studies dealing with the mechanisms that drove the generation of NumtS. In addition, the NumtS tracks constitute a useful tool in the design of mitochondrial DNA primers.</p> |
| spellingShingle | Calabrese Francesco Maria Simone Domenico Attimonelli Marcella Primates and mouse NumtS in the UCSC Genome Browser BMC Bioinformatics |
| title | Primates and mouse NumtS in the UCSC Genome Browser |
| title_full | Primates and mouse NumtS in the UCSC Genome Browser |
| title_fullStr | Primates and mouse NumtS in the UCSC Genome Browser |
| title_full_unstemmed | Primates and mouse NumtS in the UCSC Genome Browser |
| title_short | Primates and mouse NumtS in the UCSC Genome Browser |
| title_sort | primates and mouse numts in the ucsc genome browser |
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