ArticleNucleic acids research2013
Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads--a baiting and iterative mapping approach.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 971 papers.
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Who cites it
971 citing papers in PubMed.
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- Chromosome-level de novo assembly of the nuclear and mitochondrial genomes of Arcopilus aureus, a filamentous fungus with multifaceted ecological and economic roles.Scientific data · 2026Article
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- Characterization of Six Complete Mitochondrial Genomes and ITS Sequences fromInternational journal of molecular sciences · 2026Article
- SwarmGenomics: A Unified Pipeline for Individual-Based Whole-Genome Analyses.Molecular ecology resources · 2026Article
- Mosaic phenotypic evolution underlies the adaptive success of water-surface colonization in Gerromorpha.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The mitochondrial genome characteristics of Coronocyclus coronatus (Looss, 1900) and comparative analysis with other strongylid nematodes.Parasitology research · 2026Article
- Large-scale genomic phylogeography provides insights into evolutionary history and conservation priorities of the white-bellied pangolin (Phataginus tricuspis).Molecular biology and evolution · 2026Article
- Early hominin arrival in Southeast Asia triggered the evolution of major human malaria vectors.Scientific reports · 2026Article
- The Complete Mitochondrial Genome ofBiology · 2026Article
911 more citing papers are in PubMed but not listed here.
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
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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