Sequencing and reconstructing helminth mitochondrial genomes directly from genomic next-generation sequencing data

We present a detailed method for extraction of high-molecular weight genomic DNA suitable for numerous DNA sequencing applications, and a straightforward in silico approach for reconstructing novel mitochondrial (mt) genomes directly from total genomic DNA extracts derived next-generation sequencing (NGS) data sets. The in silico post-sequencing pipeline described is fast, accurate and highly efficient with modest runtime and memory requirements that can be performed using a standard desktop computer. The approach is particularly effective for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information currently available and overcomes the limitations of traditional strategies. The described methodologies are also applicable for metagenomics sequencing from mixed or pooled samples containing different species and subsequent specific assembly of mitochondrial genomes.