Evolutionary genomics of Atlantic cod

Project facts

Project promoter
University of A Coruña
Project Number:
ES07-0037
Target groups
Researchers or scientists
Status:
Completed
Initial project cost:
€16,000
Final project cost:
€15,547
From EEA Grants:
€ 15,547
The project is carried out in:
Spain

Description

The main goal of the Genomics of Atlantic cod (Gadus morhua) study is finding the genomic basis for the small size caused by harvesting pressure in this species. Knowledge of the techniques and experimental design used in this project will prove invaluable to properly address evolutionary questions in other non-model organisms. The partnership will achieve the description of the genetic basis of the adaptive phenotype (earlier maturation and smaller size) caused by fishery-induced evolution and how much does it depend on environmental conditions and knowledge about the special case of the Atlantic cod immune system. Contribute to the development of more efficient vaccines for aquaculture should give healthier fish and less use of drugs. This would have a positive environmental impact, which is beneficial to society. The applicant will acquire new technical knowledge and analytical skills, benefiting of the position of the donor partner as a leading research institution using Next-Generation Sequencing technologies. The host institution will benefit from the work of a highly qualified molecular ecologist.

Summary of project results

The main goal of the project was the study of the immune system of Atlantic cod /Gadus morhua), the first species reported that has lost the major histocompatibility complex (MCH) II. Given that the use of historical samples from museums can add a temporal perspective to genetic studies, a large number of individuals from historical populations adapted to different environments were sampled to investigate this unusual phenomenon. However, contamination is a serious problem in ancient DNA studies, as the data collected may content not only DNA from the organism of interest, but also DNA from other sources, mainly derived from microbial contamination during the handling of the samples or ancestrally present microbes. The project has processed each genomic dataset as a metagenomics sample to investigate the impact of different preservation conditions on the microbial community composition of museum samples of Atlantic cod. For this purpose, a collection of forty-two aDNA genomic datasets was explored in a custom metagenomics pipeline for stating their microbial constitution. The genomic dataset used was generated from samples preserved at the Natural History Museum of Oslo. The adapters were trimmed and the sequences were collapsed before the analysis of the metagenomics content. Some results are: microbies such as Leishmania sp or Eimeria tenella or Arthroderma behamiae were found, which are common sources of human infections, with different presence in samples from Canada, Iceland and Norway; bacteria such as P. haloplanktis were also found, typically found in the biofilm of marine eukaryotic organisms. Also, ancient DNA damage patterns were studied, suggesting that microbial DNA sequenced from Canadian samples may reflect a recent colonization from the environment or during the handling process, whereas all the marine bacteria are ancient and were present before sampling in the Atlantic cod.

Summary of bilateral results

The involved researchers had never cooperated before but now expect to establish a further cooperation. The co-authored manuscript under preparation at the end of this project may be the basis for a future relationship among both institutions and researchers, with the application of the methods here used to future studies. A genome-wide scanning or even a population genomics project could be started since the finding of high coverage in one of the marine bacteria species. This fellowship has opened an opportunity for the beneficiary to apply for a postdoctoral position to work with the research group at the host institution. During the stay, beneficiary developed bioinformatics tools to analyse the vast amount of data produce by next-generation-sequencing technologies applied to evolutionary questions. At the same time, methods learnt during the stay have added a new genomic dimension to beneficiary’s future research projects. The beneficiary presented his previous research in two different talks at the host institution, and results of the work performed at the end of this period. Once back to Spain, he was asked by the University of A Coruña to give a talk on his work and experience at Oslo. The knowledge of the techniques and experimental design used in this project may be used for properly address evolutionary questions in other non-model organisms. Partners expect to apply next-generation-sequencing techniques to many questions about genetic-environmental interactions (and adaptation) in the Spanish region of Galicia. The production volumes of the Spanish aquaculture are dominated by far by mussels (Mytilus galloprovincialis), which are most concentrated in the North Western region of Galicia, also leading producer of several fish species such as the turbot Psetta maxima.