Next generation of taxonomy – genome-skimming of worms from natural history collections

The rapid and correct assessment of biodiversity is mandatory for many ecological studies. Determining, for example, the response of an ecosystem to human impact and climate change is becoming more important than ever. However, taxonomic expertise is dwindling. To circumvent these problems it has been suggested that molecular data, as so called barcodes, is determined for each species. However, also this pragmatic approach is hampered by several challenges. Many species cannot be found easily anymore or have only been reported once, and recollection of such species may be very expensive. In addition, molecular taxonomic revisions have revealed a high degree of cryptic diversity. These days, the most cost-effective sequencing strategies are high-throughput methodologies allowing genome-skimming approaches. Such strategies may be very useful for the assessment of biodiversity as well. Genome-skimming approach allow a shallow determination of the targeted genomes and to obtain more sequence information than targeted gene approaches. The specimens present in museum’s collection would be a very valuable treasure trove for such studies. However, while the usage of dry-preserved material like bones, insects or plants is on a very good way, specimens preserved for longer times in ethanol or formalin (i.e., wet collections) face some challenges. Nonetheless, in medical cancer research some of the obstacles have been successfully solved.

Terebellides stroemi (Picture by Frederik Pleijel)

The aim of this master project is to apply these new methods to specimens of a worm, Terebellides stroemi, from wet collections and obtain genome data from historic material.

The species Terebellides stroemi is a sedentary animal filtering small food particles from the surrounding water. They have been described from all along the Norwegian coastline as well as throughout Europe. However, their taxonomy is highly disputed as a little as 15 species are recognized in Norwegian waters alone using molecular data. Such species are usually called cryptic species. However, individual counts are often small and finding these animals in their natural habitats can be challenging. On the other hand, museum’s collections such as those of the Natural History Museum Oslo comprise many specimens from populations along the entire Norwegian coastline and hence are very valuable sources for taxonomic revisions. This may also include molecular approaches.

Aim of this Master project:

The aim of this Master project is to establish methods of genome-skimming approaches using high-throughput sequencing technology for material obtained from the wet collection of the Natural History Museum Oslo, which have been preserved in historic times. Formalin-preservation of specimens may be a challenge. Therefore the project will employ new methods developed for medical research to circumvent these problems. The obtained data will be compared with data generated from reference material specifically preserved for molecular work for the same species.

Methods

You will extract genomic DNA from differently preserved specimens of Terebellides stroemi and thereby testing different extraction techniques and optimizing the extraction to maximize both quantity and quality of the genomic DNA. The genomes will be sequenced using a genome-skimming approach. The quality of the sequencing data will be related to the quality control measurements, which will be developed as part of the optimization step and includes, among others, PCR-based assessment of DNA quality. This allows the establishment of threshold values of quality and quantity of genomic DNA extracted from museum’s material for future studies. The assessment of the quality of the sequence data includes the grade of successful retrieval of the mitochondrial genome and the nuclear rRNA cluster from such historic samples. These bioinformatic retrieval methods will explore different bait approaches based on genomic information obtained from material specifically preserved for molecular work. Some field work may be necessary to obtain further reference samples.

Supervision and teaching

You will be supervised by Torsten Struck and Lutz Bachmann (both NHM Oslo). You will be provided with a broad training in different aspects of biology, which includes, among others, metazoan evolution, comparative genomics, sequencing techniques, phylogenetic reconstruction and bioinformatics. All of these techniques are state-of-the-art techniques, which are not only relevant for molecular taxonomy, but also for a variety of other academic and non-academic positions. As methods, which were developed for cancer research, are employed this also includes positions in the medical field.

 

For further inquiries feel free to contact Torsten Struck.

Torsten Struck – t.h.struck@nhm.uio.no

Lutz Bachmann – bachmann@nhm.uio.no  

 

 

Publisert 12. apr. 2018 07:22 - Sist endret 12. apr. 2018 07:22

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