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

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).

Evolutionary genomics reveals variation in structure and genetic content implicated in virulence and lifestyle in the genusGaeumannomyces

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De Novo Genome assembly of the Caucasian dwarf gobyKnipowitschiacf.caucasica, a new alien Gobiidae invading the River Rhine

“…Moreover, we extracted the mitochondrial genome from the assembly by using MitoHiFi 3.2 (Uliano-Silva et al, 2023) with MitoFinder (Allio et al, 2020).…”

Genome evolution is surprisingly predictable after initial hybridization

“…The mitochondrial genome was assembled from the adapter-filtered hifi reads using MitoHiFi (v3.2; [72]) with default parameters and using the X. maculatus mitochondrial genome as a reference. We used BLASTn [73] searches to identify and subsequently remove mitochondrial contaminant sequences present in the nuclear genome, which were present on only 6 contigs that were all less than 40 kb in length.…”