Genomic DNA sequencing of freshwater mussel using the minion

Abstract: Freshwater mussels (Unionida) belong to phylum Mollusca and live in freshwater habitats, such as lakes and rivers. Freshwater mussels have high capacity for water purification and play an important role in calcium recycling. There is not much information about the freshwater mussel genome due to lack of genomic sequences in the database, till now only four species have been sequenced and the only Swedish one is Margaritifera margaritifera. This study aim was to usenanopore sequencing technology to sequence the genomic DNA of a freshwater mussel. The data about the genomic sequence is helpful in identification of their species and give a better understanding towards the genomics and transcriptomics, it also could help in the development of multi-biomarker panels for an early assessment of water pollution. In this study the DNA used was extracted from the foot tissues, and different tissue homogenization methods were tested to find the best approach. The genomic DNA was sequenced by using Oxford nanopore MinION device, and the reads were assembled and polished using multiple software through bioinformatic analysis. The number of reads from sequencing the DNA covered only 13.5x of the estimated genome size of the freshwater mussel, while the required coverage for a complete genome assembly is 20x-25x or higher. Due to low coverage and fragmentation, a partial sequence of the genomic DNA was obtained. This indicates that nanopore sequencing could be used, but additional sequencing runs are needed to get enough coverage to assemble a complete genomic DNA of the freshwater mussel.