MitoFinder

MitoFinder extracts and assembles mitogenomic data from high-throughput sequencing libraries, enabling automated large-scale recovery of mitochondrial genomes alongside targeted nuclear loci for phylogenomic studies.

Key Features:

• Automated mitogenome assembly: Assembles mitochondrial genomes from UCE libraries using multiple assemblers including IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity.
• Metagenomic assembler integration: Leverages metagenomic assemblers, particularly MetaSPAdes, to simultaneously assemble both UCE and mtDNA loci from the same sequencing data.
• Mitogenome annotation: Annotates assembled mitochondrial genomes to support downstream evolutionary analysis.
• CO1 barcoding identification: Enables species confirmation through mitochondrial CO1 barcode sequences extracted from assembled mitogenomic data.
• Single-contig mitogenome recovery: Retrieves complete circular mitochondrial genomes assembled as single contigs for phylogenomic analysis.
• Mitonuclear discordance testing: Facilitates comparison of mitochondrial and nuclear phylogenetic signals from the same samples.

Scientific Applications:

• Target enrichment phylogenomics: Recovers complementary mitogenomic data from UCE capture experiments to augment nuclear marker datasets.
• Species identification: Confirms species identity via CO1 barcoding from mitogenomic sequences co-captured in UCE libraries.
• Mitogenome-scale taxonomy: Dramatically increases available mitogenome resources for understudied taxa, as demonstrated by increasing ant mitogenome availability from 29 to 296 genomes.
• Mitonuclear phylogenetics: Tests for mitonuclear discordance by comparing mitochondrial and nuclear evolutionary signals from identical samples.
• Cross-platform mitogenomics: Applicable to other sequence capture methods, transcriptomic data, and whole genome shotgun sequencing across diverse taxa.

Methodology:

MitoFinder uses metagenomic assemblers to assemble both UCE and mtDNA loci from high-throughput sequencing data, with comparative evaluation of assemblers including IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity.