Sequencing the North Atlantic herring (Clupea harengus) genome and development of a genetic stock management tool

Student thesis: Doctoral Thesis


In Faroese waters, quantities of several pelagic fish species have increased over the past few years. One example is the Atlantic herring (Clupea harengus L.). Its increase has affected both the fishing industry and economy of the Faroe Islands, as well as increased interest in herring biology. Furthermore, the costs of genomic methods such as genome sequencing have reduced drastically the past few years, resulting in increased use of large-scale sequencing in research. In this study, we have investigated aspects of herring biology and genomics using large-scale genomics and bioinformatical methods. This project has paved the way for the use of sequencing and bioinformatics in research in the Faroe Islands, and its results are summarised below.
The herring genome was sequenced and assembled and then compared with the existing herring assembly, which was published after the initiation of this project. The results indicated that we were able to reproduce the herring assembly, and through merging the two assemblies we generated an improved herring genome assembly. A unified nomenclature and better gene predictions would improve future annotations and would make interspecies comparisons easier.
A manual analysis of the connexin gene family in nine teleosts, including herring, indicated that the annotation of this gene family was poor in teleosts. There were wrongly predicted connexins, nonpredicted connexins, and truncated genes, and furthermore, the naming of the genes was highly inconsistent. Our analysis showed that the genes follow a similar pattern in teleosts and mammals, and by following the rules set by naming committees we suggested new naming for the connexins in teleosts.
Furthermore, we sequenced individual herring at low coverage and identified genetic variations in putative populations. These variations were used in a genome-wide association analysis, where we identified regions on the herring genome that were associated with sex. These regions indicated that herring have a male heterogametic sex determination system. This was the first time a specific sex determination system has been suggested for herring. However, we could not identify a specific sex regulatory gene.
We further used the individual variation to investigate the herring population structure in the Northeast Atlantic Ocean. We investigated four herring stocks that spawn in Faroese, Icelandic, Norwegian, and Shetland waters. These stocks were the Faroese autumn-spawning, Icelandic summer-spawning, Norwegian spring-spawning, and North Sea autumn-spawning herring. The results indicated that these stocks were genetically distinct populations with the exception of the Faroese stock, which could not be clearly distinguished from the Icelandic population. In addition, a genetic panel was developed to assign individual herring to one of these four stocks. The panel was tested but exhibited somewhat mixed results. The Norwegian and North Sea stocks could be distinguished from the other stocks with high accuracy (> 90%). However, the distinction between the Faroese and Icelandic herring was problematic. When the Icelandic and Faroese stocks were combined, we were able to assign the test individuals with an accuracy of 89%. Although further validation of the panel is still required, the panel could be useful in stock management, herring fishery monitoring, and keeping the herring fishery sustainable.
In conclusion, this study produced more knowledge about herring genetics and evolution, and could be useful for keeping herring fisheries sustainable.
Date of Award14 May 2020
Original languageEnglish
Awarding Institution
  • University of the Faroe Islands
SupervisorSvein-Ole Mikalsen (Supervisor)

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