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

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• PacBio HiFi sequencing offers long and highly accurate reads, revolutionizing genome assembly.
• Eukaryotic mitochondrial genomes are often sequenced with high coverage alongside nuclear genomes.
• A specialized tool for mitochondrial genome assembly using HiFi reads was previously unavailable.

Purpose of the Study:

• To develop a dedicated tool, MitoHiFi, for assembling mitochondrial genomes from PacBio HiFi reads.
• To enable accurate annotation of protein and RNA genes within assembled mitochondrial genomes.
• To identify and exclude nuclear insertions of mitochondrial DNA from organellar genome assembly.

Main Methods:

• MitoHiFi accepts raw reads or assembled contigs as input.
• The tool outputs mitochondrial genome sequences in FASTA format with gene annotations.
• It independently assembles variants from heteroplasmy and identifies nuclear mitochondrial sequences.

Main Results:

• MitoHiFi successfully assembled 374 mitochondrial genomes across Metazoa and Fungi for major genome projects.
• Analysis of 60 assemblies revealed widespread, previously unreported repeats in mitochondrial genomes.
• The tool demonstrated capability across a wide phylogenetic range of taxa.

Conclusions:

• MitoHiFi is effective for assembling mitochondrial genomes from PacBio HiFi data across diverse taxa.
• The software is freely available in Python and as a Docker container on GitHub.
• MitoHiFi contributes to more comprehensive and accurate mitochondrial genome sequencing efforts.