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Project properties |
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| Title | Environmental DNA metabarcoding from North Sea samples using MinION DNA sequencing |
| Group | Marine Animal Ecology |
| Project type | thesis |
| Credits | 24-36 |
| Supervisor(s) | Reindert Nijland |
| Examiner(s) | Tinka Murk |
| Contact info | reindert.nijland@wur.nl |
| Begin date | 2019/01/01 |
| End date | 2024/12/31 |
| Description | To monitor biodiversity in the North Sea, usually samples are taken either by fishing gear or grabs, or through direct collection by divers. A new method that adds to this is studying DNA that is present in the water column, so called environmental DNA (eDNA). However, eDNA analysis so far been a rather costly procedure requiring Next Generation sequencing approaches and therefore large service providers and often long waiting times.
Recently, a new DNA sequencing device has become available, the MinION, developed by Oxford Nanopore technologies. This device is no larger than a MARS-bar and can be run from a standard laptop. It has the opportunity to revolutionise DNA sequencing, as it allows DNA sequencing virtually anywhere, including on a research vessels or other remote places. The obtained sequencing data is available in real time. Another large advantage of nanopore sequencing is that the read-length is only limited by the length of the input DNA, in contrast to classical next gen sequencing where the maximum read length is about 400 bases. This enables the use of other and much longer meta-barcodes that used up until know. In this project we will establish the use of the MinION for sequencing of environmental DNA (eDNA) to assess biodiversity, with samples obtained directly from seawater, or after washing of mixed benthos sample. Using either direct sequencing or amplification with universal metabarcode primers, we aim to identify which species are present in these samples. Next to the technical challenges in obtaining sufficient amounts of eDNA and sequence data, there are also challenges is developing a bioinformatics analysis pipeline that can reliably identify the marine species based on the obtained DNA sequences and barcodes. This project provides opportunities for both molecular biology as well as bioinformatics student, providing you are willing to work on both sides of the project, with the emphasis depending on the interest and background of the student. |
| Used skills | Molecular biology, Population genetics, Bioinformatics |
| Requirements | Molecular biology laboratory skills, affinity for/experience with bioinformatics |