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

By C. Hahn, L. Bachmann, Bastien Chevreux. Nucleic Acids Research, 2013

1,799 citations recorded by the source corpus.

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.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/be05a17671aa4729bd42ff6d7be0f9fa906386f8

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Citations in the corpus

NOVOPlasty: de novo assembly of organelle genomes from whole genome data (2016, methodology): “Due to a lack of reliable and user-friendly open-source software for the assembly of mitochondrial and, especially, plastid genomes, many researchers select the CLC payfor-use assembler (1,9,23,24).”
MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics (2019, methodology): “For comparison purposes, we also ran MiTO biM (Hahn et al., 2013) to extract mitochondrial sequences from the 501 UCE raw sequenc - ing data.”
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization (2019, methodology): “The two frequently-used mitogenome assembly software,MITObim (25) andNOVOPlasty (26), require closelyrelated mitochondrial fragments as seeds to anchor short reads and build initial datasets.”
GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes (2018, result): “…and taking target genome(s) or sequence(s) as the seed; the initial target-associated reads (seed-mapped reads) are treated as “ baits ” to get more target-associated reads through multiple extension iterations, which is similar in concept to those of the MITObim [29] and IOGA [21] pipelines.”
How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research (2014, methodology): “Software has been developed to automate assembling mt genomes from NGS reads using either a previously sequenced, close relative as a reference genome, or using individual mt genes from the target species as ‘seeds’ for iterative assembly (Hahn et al., 2013).”
Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes (2020, methodology): “…the development of different toolkits solely optimized for assembling (GetOrganelle: Jin et al., 2019; FastPlast: McKain and Wilson, 2017; MITObim: Hahn et al., 2013), annotating (Plann: Huang and Crong, 2015; MITOS: Bernt et al., 2013), and analyzing organelle genomes (Chlorobox: Tillich et …”
NOVOPlasty: de novo assembly of organelle genomes from whole genome data. (2016, methodology): “Due to a lack of reliable and user-friendly open-source software for the assembly of mitochondrial and, especially, plastid genomes, many researchers select the CLC pay-for-use assembler (1,9,23,24).”