The complete mitogenome of <it>Cylindrus obtusus </it>(Helicidae, Ariantinae) using Illumina next generation sequencing
<p>Abstract</p> <p>Background</p> <p>This study describes how the complete mitogenome of a terrestrial snail, <it>Cylindrus obtusus </it>(Draparnaud, 1805) was sequenced without PCRs from a collection specimen that had been in 70% ethanol for 8 years. The mi...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-03-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/13/114 |
| _version_ | 1831748773594791936 |
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| author | Groenenberg Dick SJ Pirovano Walter Gittenberger Edmund Schilthuizen Menno |
| author_facet | Groenenberg Dick SJ Pirovano Walter Gittenberger Edmund Schilthuizen Menno |
| author_sort | Groenenberg Dick SJ |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>This study describes how the complete mitogenome of a terrestrial snail, <it>Cylindrus obtusus </it>(Draparnaud, 1805) was sequenced without PCRs from a collection specimen that had been in 70% ethanol for 8 years. The mitogenome was obtained with Illumina GAIIx shot gun sequencing. Although the used specimen was collected relatively recently and kept in a DNA-friendly preservative (not formalin as frequently used with old museum specimens), we believe that the exclusion of PCRs as facilitated by NGS (Next Generation Sequencing) removes a great obstacle in DNA sequencing of collection specimens. A brief comparison is made between our Illumina GAIIx approach and a similar study that made use of the Roche 454-FLX platform.</p> <p>Results</p> <p>The mtDNA sequence of <it>C. obtusus </it>is 14,610 bases in length (about 0.5 kb larger than other stylommatophoran mitogenomes reported hitherto) and contains the 37 genes (13 protein coding genes, two rRNAs and 22 tRNAs) typical for metazoans. Except for a swap between the position of tRNA-Pro and tRNA-Ala, the gene arrangement of <it>C. obtusus </it>is identical to that reported for <it>Cepaea nemoralis</it>. The 'aberrant' rearrangement of tRNA-Thr and <it>COIII </it>compared to that of other Sigmurethra (and the majority of gastropods), is not unique for <it>C</it>. <it>nemoralis </it>(subfamily Helicinae), but is also shown to occur in <it>C. obtusus </it>(subfamily Ariantinae) and might be a synapomorphy for the family Helicidae.</p> <p>Conclusions</p> <p>Natural history collections potentially harbor a wealth of information for the field of evolutionary genetics, but it can be difficult to amplify DNA from such specimens (due to DNA degradation for instance). Because NGS techniques do not rely on primer-directed amplification (PCR) and allow DNA to be fragmented (DNA gets sheared during library preparation), NGS could be a valuable tool for retrieving DNA sequence data from such specimens. A comparison between Illumina GAIIx and the Roche 454 platform suggests that the former might be more suited for <it>de novo </it>sequencing of mitogenomes.</p> |
| first_indexed | 2024-12-21T21:57:33Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T21:57:33Z |
| publishDate | 2012-03-01 |
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| spelling | doaj.art-76631107f1eb4348a24158abfe884ca22022-12-21T18:48:55ZengBMCBMC Genomics1471-21642012-03-0113111410.1186/1471-2164-13-114The complete mitogenome of <it>Cylindrus obtusus </it>(Helicidae, Ariantinae) using Illumina next generation sequencingGroenenberg Dick SJPirovano WalterGittenberger EdmundSchilthuizen Menno<p>Abstract</p> <p>Background</p> <p>This study describes how the complete mitogenome of a terrestrial snail, <it>Cylindrus obtusus </it>(Draparnaud, 1805) was sequenced without PCRs from a collection specimen that had been in 70% ethanol for 8 years. The mitogenome was obtained with Illumina GAIIx shot gun sequencing. Although the used specimen was collected relatively recently and kept in a DNA-friendly preservative (not formalin as frequently used with old museum specimens), we believe that the exclusion of PCRs as facilitated by NGS (Next Generation Sequencing) removes a great obstacle in DNA sequencing of collection specimens. A brief comparison is made between our Illumina GAIIx approach and a similar study that made use of the Roche 454-FLX platform.</p> <p>Results</p> <p>The mtDNA sequence of <it>C. obtusus </it>is 14,610 bases in length (about 0.5 kb larger than other stylommatophoran mitogenomes reported hitherto) and contains the 37 genes (13 protein coding genes, two rRNAs and 22 tRNAs) typical for metazoans. Except for a swap between the position of tRNA-Pro and tRNA-Ala, the gene arrangement of <it>C. obtusus </it>is identical to that reported for <it>Cepaea nemoralis</it>. The 'aberrant' rearrangement of tRNA-Thr and <it>COIII </it>compared to that of other Sigmurethra (and the majority of gastropods), is not unique for <it>C</it>. <it>nemoralis </it>(subfamily Helicinae), but is also shown to occur in <it>C. obtusus </it>(subfamily Ariantinae) and might be a synapomorphy for the family Helicidae.</p> <p>Conclusions</p> <p>Natural history collections potentially harbor a wealth of information for the field of evolutionary genetics, but it can be difficult to amplify DNA from such specimens (due to DNA degradation for instance). Because NGS techniques do not rely on primer-directed amplification (PCR) and allow DNA to be fragmented (DNA gets sheared during library preparation), NGS could be a valuable tool for retrieving DNA sequence data from such specimens. A comparison between Illumina GAIIx and the Roche 454 platform suggests that the former might be more suited for <it>de novo </it>sequencing of mitogenomes.</p>http://www.biomedcentral.com/1471-2164/13/114 |
| spellingShingle | Groenenberg Dick SJ Pirovano Walter Gittenberger Edmund Schilthuizen Menno The complete mitogenome of <it>Cylindrus obtusus </it>(Helicidae, Ariantinae) using Illumina next generation sequencing BMC Genomics |
| title | The complete mitogenome of <it>Cylindrus obtusus </it>(Helicidae, Ariantinae) using Illumina next generation sequencing |
| title_full | The complete mitogenome of <it>Cylindrus obtusus </it>(Helicidae, Ariantinae) using Illumina next generation sequencing |
| title_fullStr | The complete mitogenome of <it>Cylindrus obtusus </it>(Helicidae, Ariantinae) using Illumina next generation sequencing |
| title_full_unstemmed | The complete mitogenome of <it>Cylindrus obtusus </it>(Helicidae, Ariantinae) using Illumina next generation sequencing |
| title_short | The complete mitogenome of <it>Cylindrus obtusus </it>(Helicidae, Ariantinae) using Illumina next generation sequencing |
| title_sort | complete mitogenome of it cylindrus obtusus it helicidae ariantinae using illumina next generation sequencing |
| url | http://www.biomedcentral.com/1471-2164/13/114 |
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