MitoHiFi

MitoHiFi assembles and annotates mitochondrial genomes from high-throughput sequencing data, extracting mitochondrial sequences from ultraconserved element (UCE) target-enrichment and other sequencing datasets to support phylogenetic and evolutionary analyses.

Key Features:

• UCE integration: Extracts mitochondrial sequences from UCE target-enrichment sequencing and links mtDNA with thousands of nuclear UCE markers for combined analyses.
• Metagenomic assemblers: Evaluates and uses IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity to assemble UCEs and mtDNA loci, with MetaSPAdes highlighted for broad effectiveness.
• Automated annotation: Automates mitogenome annotation to produce annotated mitochondrial genomes from assembled contigs.
• Species confirmation and mitonuclear discordance detection: Confirms species identity using CO1 barcoding and identifies potential mitonuclear discordances, including cases producing single-contig mitochondrial assemblies (296 cases reported).
• Scalability and cross-dataset applicability: Scales to process hundreds of UCE libraries and is applicable to other sequence capture methods, transcriptomic datasets, and whole-genome shotgun sequencing across diverse taxa.
• Empirical validation: Demonstrated on 501 Formicidae UCE libraries to expand available ant mitogenomes.

Scientific Applications:

• Phylogenomics: Combines mitogenomes and nuclear UCE markers to improve phylogenetic inference and resolve species relationships.
• Mitonuclear studies: Detects mitonuclear discordance and supports analyses of mitochondrial–nuclear genome interactions and evolutionary dynamics.
• Species identification and barcoding: Enables CO1-based species confirmation from large sequencing libraries.
• Comparative mitogenomics: Facilitates annotation and comparative analyses of mitochondrial function and evolution across taxa.

Methodology:

Extracts mitochondrial signals from UCE and other sequencing libraries, assembles UCEs and mtDNA loci using metagenomic assemblers (IDBA-UD, MEGAHIT, MetaSPAdes, Trinity), performs automated mitogenome annotation, and applies CO1 barcoding for species confirmation.