MitoCOMON: A whole mitochondrial DNA sequencing by universal primer design and long overlapping amplicons assembly

Mitochondrial DNA sequences are used for various biological and ecological research, but in most cases short regions of some marker genes are used for species or individual differentiation. Recent development of long-read sequencing technology enables acquisition of longer regions of mitochondrial DNA, but the performance rarely exceeds that of short marker sequences partly because of the scarcity of the reference sequences of mitochondrial DNA in databases covering such longer regions. Thus, a new method or pipeline was in demand for promoting scientists to sequence and deposit more whole mitochondrial DNA sequence. In this work, we present a pipeline for both designing a common primer set targeting species in a specific taxonomic clade and for assembling whole mitochondrial DNA sequence amplified by the designed primer set.