MITGARD

MITGARD recovers mitochondrial genomes from RNA-sequencing (RNA-seq) and next-generation sequencing (NGS) datasets to extract mitochondrial DNA (mtDNA) for phylogenetic and evolutionary analyses.

Key Features:

• Reference-guided read identification: Identifies mitochondrial sequence reads by aligning RNA-seq reads to a phylogenetically related reference genome.
• Contig assembly and mtDNA extraction: Assembles mitochondrial reads into contiguous sequences (contigs) and extracts complete mitochondrial genomes (mtDNA).
• Reference flexibility and divergence tolerance: Recovers entire mitogenomes using congeneric references diverged up to 30 million years ago (MYA) and reconstructs most mitochondrial genes for references diverged between 30–60 MYA.
• Low-depth performance: Reconstructs mitochondrial genomes across diverse eukaryotic taxa even in scenarios with low sequencing depth.
• RNA-seq/NGS integration: Leverages mitochondrial mRNA sequences co-sequenced with target transcriptomes from RNA-seq and other NGS experiments.
• Phylogenetic and barcoding support: Produces mitogenomic sequences suitable for phylogenetic inference and DNA barcoding analyses.
• Contamination detection compatibility: Enables downstream detection of cross-contamination in datasets using third-party tools.

Scientific Applications:

• Phylogenetic reconstruction: Supports estimation of phylogenetic trees, including case studies such as the snake genus Bothrops.
• Biodiversity and evolutionary studies: Facilitates recovery of mitogenomes across diverse eukaryotic species for comparative and evolutionary analyses.
• Species identification (barcoding): Provides mitochondrial sequences for species identification and barcoding workflows.
• Quality control and contamination screening: Aids in detecting cross-contamination in RNA-seq datasets when combined with third-party tools.

Methodology:

Identifying mitochondrial reads by alignment to a phylogenetically related reference genome, assembling those reads into contigs, and extracting complete mtDNA from RNA-seq/NGS data.