MITObim

MITObim reconstructs complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data through a baiting and iterative mapping approach.

Key Features:

• Distantly Related Reference Capability: The method functions even when only distantly related mitochondrial genomes are available as starting-reference sequences.
• Mitochondrial Barcode Seed Capability: The method functions even when only mitochondrial barcode sequences are available as seeds.
• Metagenomic and Pooled Data Compatibility: The approach is applicable to metagenomic and pooled data sets as demonstrated using simulated data.
• Computational Efficiency: The method recovers mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in less than 24 hours using a standard desktop computer.

Scientific Applications:

• Non-Model Organism Mitochondrial Genomics: Enables mitochondrial genome reconstruction for species with little or no existing mitochondrial sequence information.
• Parasite-Host Systems: Demonstrated in case studies using NGS data sets of monogenean ectoparasites Gyrodactylus thymalli and Gyrodactylus derjavinoides and their teleost hosts Thymallus thymallus and Oncorhynchus mykiss.
• Alternative to Long-Range PCR: Provides a fast in silico alternative to laborious conventional strategies relying on initial long-range PCR.

Methodology:

The method uses mitochondrial baiting and iterative mapping from next-generation sequencing reads.