The RHNumtS compilation: Features and bioinformatics approaches to locate and quantify Human NumtS
<p>Abstract</p> <p>Background</p> <p>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 abunda...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2008-06-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/9/267 |
| _version_ | 1811287751125893120 |
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| author | Saccone Cecilia Romeo Giovanni Gasparre Giuseppe Castellana Stefano Lascaro Daniela Attimonelli Marcella |
| author_facet | Saccone Cecilia Romeo Giovanni Gasparre Giuseppe Castellana Stefano Lascaro Daniela Attimonelli Marcella |
| author_sort | Saccone Cecilia |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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 <it>in silico </it>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-04-13T03:23:56Z |
| format | Article |
| id | doaj.art-5ea890b9846a45398a80e66cc0167e57 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T03:23:56Z |
| publishDate | 2008-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-5ea890b9846a45398a80e66cc0167e572022-12-22T03:04:42ZengBMCBMC Genomics1471-21642008-06-019126710.1186/1471-2164-9-267The RHNumtS compilation: Features and bioinformatics approaches to locate and quantify Human NumtSSaccone CeciliaRomeo GiovanniGasparre GiuseppeCastellana StefanoLascaro DanielaAttimonelli Marcella<p>Abstract</p> <p>Background</p> <p>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 <it>in silico </it>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2164/9/267 |
| spellingShingle | Saccone Cecilia Romeo Giovanni Gasparre Giuseppe Castellana Stefano Lascaro Daniela Attimonelli Marcella The RHNumtS compilation: Features and bioinformatics approaches to locate and quantify Human NumtS BMC Genomics |
| title | The RHNumtS compilation: Features and bioinformatics approaches to locate and quantify Human NumtS |
| title_full | The RHNumtS compilation: Features and bioinformatics approaches to locate and quantify Human NumtS |
| title_fullStr | The RHNumtS compilation: Features and bioinformatics approaches to locate and quantify Human NumtS |
| title_full_unstemmed | The RHNumtS compilation: Features and bioinformatics approaches to locate and quantify Human NumtS |
| title_short | The RHNumtS compilation: Features and bioinformatics approaches to locate and quantify Human NumtS |
| title_sort | rhnumts compilation features and bioinformatics approaches to locate and quantify human numts |
| url | http://www.biomedcentral.com/1471-2164/9/267 |
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