A new strategy to infer circularity applied to four new complete frog mitogenomes

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Mitochondrial genomes (mitogenomes) are vital for evolutionary studies.
• Complete mitogenome assembly is challenging, especially without closely related references.
• Previous methods lacked robust circularity inference.

Purpose of the Study:

• To present a novel bioinformatics strategy for inferring sequence circularity and completing mitochondrial genome assembly.
• To validate the accuracy and sensitivity of the proposed method using permutation tests.
• To provide a reliable method for assembling mitogenomes from short genomic reads.

Main Methods:

• Applied a baiting and iterative mapping strategy followed by a new ad hoc mapping strategy.
• Utilized Bowtie2 alignment scores and a novel 'connectivity' metric for quality assessment.
• Performed permutation tests with mutation simulations to evaluate circularity inference sensitivity.

Main Results:

• Successfully assembled four complete frog mitochondrial genomes from four genera (Bufonidae, Dendrobatidae, Scaphiopodidae).
• The novel method demonstrated high sensitivity in detecting circularity, with low false positive rates (2%).
• Assembled mitogenomes showed species-specific variations in size, gene content, and arrangement, consistent with their clades.

Conclusions:

• The developed bioinformatics strategy offers a robust approach for complete mitogenome assembly and circularity inference.
• This method is particularly valuable for studies lacking closely related reference genomes.
• The findings contribute to advancing genomic research in amphibians and other taxa.