MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

2023/07/18 by Marcela Uliano‐Silva, João Gabriel R. N. Ferreira, Ksenia Krasheninnikova +22 · 53 citations
Biochemistry, Genetics and Molecular Biology · #Genomics and Phylogenetic Studies #Mitochondrial Function and Pathology #Protist diversity and phylogeny

paper · pdf · doi:10.1186/s12859-023-05385-y

openalex publication_date 2023/07/18 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30

Abstract

BACKGROUND: PacBio high fidelity (HiFi) sequencing reads are both long (15-20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and contiguous genomes. In eukaryotes the mitochondrial genome is sequenced alongside the nuclear genome often at very high coverage. A dedicated tool for mitochondrial genome assembly using HiFi reads is still missing. RESULTS: MitoHiFi was developed within the Darwin Tree of Life Project to assemble mitochondrial genomes from the HiFi reads generated for target species. The input for MitoHiFi is either the raw reads or the assembled contigs, and the tool outputs a mitochondrial genome sequence fasta file along with annotation of protein and RNA genes. Variants arising from heteroplasmy are assembled independently, and nuclear insertions of mitochondrial sequences are identified and not used in organellar genome assembly. MitoHiFi has been used to assemble 374 mitochondrial genomes (368 Metazoa and 6 Fungi species) for the Darwin Tree of Life Project, the Vertebrate Genomes Project and the Aquatic Symbiosis Genome Project. Inspection of 60 mitochondrial genomes assembled with MitoHiFi for species that already have reference sequences in public databases showed the widespread presence of previously unreported repeats. CONCLUSIONS: MitoHiFi is able to assemble mitochondrial genomes from a wide phylogenetic range of taxa from Pacbio HiFi data. MitoHiFi is written in python and is freely available on GitHub ( https://github.com/marcelauliano/MitoHiFi ). MitoHiFi is available with its dependencies as a Docker container on GitHub (ghcr.io/marcelauliano/mitohifi:master).

Citations

• MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics
• Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
• NCBI Taxonomy: a comprehensive update on curation, resources and tools
• GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
• Towards complete and error-free genome assemblies of all vertebrate species

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