Freshwater mussels are members of phylum Mollusca, which live in freshwater habitats such as lakes and rivers. Freshwater mussels are essential ecologically in the aquatic ecosystems, they have a high capacity for water purification and play a significant role in calcium recycling. The genomic DNA of many freshwater mussels' species has not yet been sequenced. Knowledge of such a sequence can be useful in the development of a multi-biomarker panel to identify water pollution, and it also helps to develop a method to identify freshwater mussels' species according to their genomic DNA. This study aims to use nanopore sequencing technology to sequence the genomic DNA of Anodonta anatina, a species of freshwater mussel common in Europe. The DNA used in this experiment was extracted from the foot tissues, and two tissue homogenization methods were tested in this experiment to determine the best approach. The genomic DNA was sequenced by using Oxford nanopore MinION device, and the reads were assembled and polished using multiple software tools. The reads obtained from sequencing the DNA cover 3.5x of the estimated genome size of Anodonta anatina. 20x coverage is required for a complete genome assembly, and due to the low coverage, only a partial sequence of the genomic DNA was obtained during this experiment. This indicates that nanopore sequencing could be used to sequence the genome of freshwater mussels, but further sequencing runs are required to get enough coverage to assemble the whole genomic DNA.
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:his-18874 |
| Date | January 2020 |
| Creators | Shikh Khaled, Saad |
| Publisher | Högskolan i Skövde, Institutionen för biovetenskap |
| Source Sets | DiVA Archive at Upsalla University |
| Language | English |
| Detected Language | English |
| Type | Student thesis, info:eu-repo/semantics/bachelorThesis, text |
| Format | application/pdf |
| Rights | info:eu-repo/semantics/openAccess |
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