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      MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

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          Abstract

          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.

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          Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

          Christoph Hahn, Lutz Bachmann, Bastien Chevreux (2013)
          We present an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data—mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling (Thymallus thymallus) and Rainbow trout (Oncorhynchus mykiss). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24 h using a standard desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/chrishah/MITObim.
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            SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

            Ruibang Luo, Binghang Liu, Yinlong Xie … (2012)
            Background There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions. Findings To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome. Conclusions Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.
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              ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

              Jaime Huerta-Cepas, François Serra, Peer Bork (2016)
              The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 20 June 2019
                Publication date (Electronic): 13 March 2019
                Publication date PMC-release: 13 March 2019
                Volume: 47
                Issue: 11
                Page: e63
                Affiliations
                [1 ]BGI-Shenzhen, Shenzhen 518083, China
                [2 ]China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
                [3 ]Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
                [4 ]Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing 100193, China
                Author notes
                To whom correspondence should be addressed. Tel: +86 13873115450; Email: liushanlin@ 123456genomics.cn
                Author information
                http://orcid.org/0000-0002-6488-1527
                Article
                Publisher ID: gkz173
                DOI: 10.1093/nar/gkz173
                PMC ID: 6582343
                PubMed ID: 30864657
                SO-VID: 48a54c5a-85b7-44fe-b9b4-876e586d573a
                Copyright © © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
                License:

                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.

                History
                Date accepted : 08 March 2019
                Date revision received : 25 January 2019
                Date received : 21 November 2018
                Page count
                Pages: 7
                Funding
                Funded by: Free-oriented Project from Shenzhen Government
                Award ID: JCYJ20170817150755701
                Categories
                Subject: Methods Online

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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