Mitogenome sequence accuracy using different elucidation methods.
Mitogenome sequences are highly desired because they are used in several biological disciplines. Their elucidation has been facilitated through the development of massive parallel sequencing, accelerating their deposition in public databases. However, sequencing, assembly and annotation methods migh...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2017-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5491103?pdf=render |
| _version_ | 1818155858279792640 |
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| author | Renata Velozo Timbó Roberto Coiti Togawa Marcos M C Costa David A Andow Débora P Paula |
| author_facet | Renata Velozo Timbó Roberto Coiti Togawa Marcos M C Costa David A Andow Débora P Paula |
| author_sort | Renata Velozo Timbó |
| collection | DOAJ |
| description | Mitogenome sequences are highly desired because they are used in several biological disciplines. Their elucidation has been facilitated through the development of massive parallel sequencing, accelerating their deposition in public databases. However, sequencing, assembly and annotation methods might induce variability in their quality, raising concerns about the accuracy of the sequences that have been deposited in public databases. In this work we show that different sequencing methods (number of species pooled in a library, insert size and platform) and assembly and annotation methods generated variable completeness and similarity of the resulting mitogenome sequences, using three species of predaceous ladybird beetles as models. The identity of the sequences varied considerably depending on the method used and ranged from 38.19 to 90.1% for Cycloneda sanguinea, 72.85 to 91.06% for Harmonia axyridis and 41.15 to 93.60% for Hippodamia convergens. Dissimilarities were frequently found in the non-coding A+T rich region, but were also common in coding regions, and were not associated with low coverage. Mitogenome completeness and sequence identity were affected by the sequencing and assembly/annotation methods, and high within-species variation was also found for other mitogenome depositions in GenBank. This indicates a need for methods to confirm sequence accuracy, and guidelines for verifying mitogenomes should be discussed and developed by the scientific community. |
| first_indexed | 2024-12-11T14:49:05Z |
| format | Article |
| id | doaj.art-0352785493b44342a14ea895e422a120 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-11T14:49:05Z |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-0352785493b44342a14ea895e422a1202022-12-22T01:01:32ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01126e017997110.1371/journal.pone.0179971Mitogenome sequence accuracy using different elucidation methods.Renata Velozo TimbóRoberto Coiti TogawaMarcos M C CostaDavid A AndowDébora P PaulaMitogenome sequences are highly desired because they are used in several biological disciplines. Their elucidation has been facilitated through the development of massive parallel sequencing, accelerating their deposition in public databases. However, sequencing, assembly and annotation methods might induce variability in their quality, raising concerns about the accuracy of the sequences that have been deposited in public databases. In this work we show that different sequencing methods (number of species pooled in a library, insert size and platform) and assembly and annotation methods generated variable completeness and similarity of the resulting mitogenome sequences, using three species of predaceous ladybird beetles as models. The identity of the sequences varied considerably depending on the method used and ranged from 38.19 to 90.1% for Cycloneda sanguinea, 72.85 to 91.06% for Harmonia axyridis and 41.15 to 93.60% for Hippodamia convergens. Dissimilarities were frequently found in the non-coding A+T rich region, but were also common in coding regions, and were not associated with low coverage. Mitogenome completeness and sequence identity were affected by the sequencing and assembly/annotation methods, and high within-species variation was also found for other mitogenome depositions in GenBank. This indicates a need for methods to confirm sequence accuracy, and guidelines for verifying mitogenomes should be discussed and developed by the scientific community.http://europepmc.org/articles/PMC5491103?pdf=render |
| spellingShingle | Renata Velozo Timbó Roberto Coiti Togawa Marcos M C Costa David A Andow Débora P Paula Mitogenome sequence accuracy using different elucidation methods. PLoS ONE |
| title | Mitogenome sequence accuracy using different elucidation methods. |
| title_full | Mitogenome sequence accuracy using different elucidation methods. |
| title_fullStr | Mitogenome sequence accuracy using different elucidation methods. |
| title_full_unstemmed | Mitogenome sequence accuracy using different elucidation methods. |
| title_short | Mitogenome sequence accuracy using different elucidation methods. |
| title_sort | mitogenome sequence accuracy using different elucidation methods |
| url | http://europepmc.org/articles/PMC5491103?pdf=render |
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