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MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological studies. It becomes routine to utilize multiple genes on mitogenome or the entire mitogenomes to investigate phylogeny and biodiversity of focal groups with the onset of High Throughput Sequencing (HTS) technologi...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582343/ https://www.ncbi.nlm.nih.gov/pubmed/30864657 http://dx.doi.org/10.1093/nar/gkz173 |
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author | Meng, Guanliang Li, Yiyuan Yang, Chentao Liu, Shanlin |
author_facet | Meng, Guanliang Li, Yiyuan Yang, Chentao Liu, Shanlin |
author_sort | Meng, Guanliang |
collection | PubMed |
description | Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological studies. It becomes routine to utilize multiple genes on mitogenome or the entire mitogenomes to investigate phylogeny and biodiversity of focal groups with the onset of High Throughput Sequencing (HTS) technologies. We developed a mitogenome toolkit MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads. We evaluated its performance using a total of 50 samples of which mitogenomes are publicly available. The results showed that MitoZ can recover more full-length mitogenomes with higher accuracy compared to the other available mitogenome assemblers. Overall, MitoZ provides a one-click solution to construct the annotated mitogenome from HTS raw data and will facilitate large scale ecological and evolutionary studies. MitoZ is free open source software distributed under GPLv3 license and available at https://github.com/linzhi2013/MitoZ. |
format | Online Article Text |
id | pubmed-6582343 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-65823432019-06-21 MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization Meng, Guanliang Li, Yiyuan Yang, Chentao Liu, Shanlin Nucleic Acids Res Methods Online Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological studies. It becomes routine to utilize multiple genes on mitogenome or the entire mitogenomes to investigate phylogeny and biodiversity of focal groups with the onset of High Throughput Sequencing (HTS) technologies. We developed a mitogenome toolkit MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads. We evaluated its performance using a total of 50 samples of which mitogenomes are publicly available. The results showed that MitoZ can recover more full-length mitogenomes with higher accuracy compared to the other available mitogenome assemblers. Overall, MitoZ provides a one-click solution to construct the annotated mitogenome from HTS raw data and will facilitate large scale ecological and evolutionary studies. MitoZ is free open source software distributed under GPLv3 license and available at https://github.com/linzhi2013/MitoZ. Oxford University Press 2019-06-20 2019-03-13 /pmc/articles/PMC6582343/ /pubmed/30864657 http://dx.doi.org/10.1093/nar/gkz173 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methods Online Meng, Guanliang Li, Yiyuan Yang, Chentao Liu, Shanlin MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization |
title | MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization |
title_full | MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization |
title_fullStr | MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization |
title_full_unstemmed | MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization |
title_short | MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization |
title_sort | mitoz: a toolkit for animal mitochondrial genome assembly, annotation and visualization |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582343/ https://www.ncbi.nlm.nih.gov/pubmed/30864657 http://dx.doi.org/10.1093/nar/gkz173 |
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