Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Meng, Guanliang, Li, Yiyuan, Yang, Chentao, Liu, Shanlin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
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
_version_ 1783428304503570432
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
work_keys_str_mv AT mengguanliang mitozatoolkitforanimalmitochondrialgenomeassemblyannotationandvisualization
AT liyiyuan mitozatoolkitforanimalmitochondrialgenomeassemblyannotationandvisualization
AT yangchentao mitozatoolkitforanimalmitochondrialgenomeassemblyannotationandvisualization
AT liushanlin mitozatoolkitforanimalmitochondrialgenomeassemblyannotationandvisualization