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Year of grant: 2014 Research Area: Náttúra og náttúrutilfeingi Project type: Ph.d.verkætlan Project title: Sekvensering av Norðhavssilda (Clupea harengus) genominum og menning av einum genetiskum stovnsumsitingaramboði. Hergen 2014 verkætlanin. Grant number: 0442 Project manager: Hans Atli Dahl Institution/company: Amplexa Genetics Other participants: Sunnvør Klettskarð í Kongsstovu Project period: 1.1.2016-31.12.2018 Total budget: 2.700.000 kr. Grant from the FRC in DKK: 500.000 kr. Project description: Original Pelagiske fisk, som makrel og sild, har som arter en stor udbredelse i nord Atlanten hvor de også migrerer over store områder. Store (og muligvis separate) bestande blandes på fourageringsområderne hvilket skaber problemer for fiskeindustrien og for fiskeriforvaltningen - det er svært at afgøre om fiskeriet foregår fra den ene eller den anden bestand og dermed også svært at vudere de enkelte bestandes tilstand. Indtil videre har det ikke lykkedes at udvikle metoder der kunne adskille disse bestande og definere deres egentlige tilhørsforhold. Den oplagte måde at beskrive en bestand og dermed differentiere denne ville være med DNA markører. Det har dog vist sig svært at finde sådanne genetiske DNA markører, som kunne skelne bestandene. Dette skyldes dels at silden er meget artsrig og blandes på fourageringsstederne hvor man mener der foregår en del opblanding mellem bestande medførende et stort “gene flow” mellem bestandene – dette fænomen modvirker en genetisk differentiering. Dernæst så har man teknisk set ikke kunne læse sildens arvemasse (DNA), også kaldet genomet, før nu – det har simpelthen været for teknisk krævende og for dyrt - man kender derfor ikke dens genetiske variation godt nok og muligheden for at vælge korrekte DNA markører har derfor været sparsom. De DNA markører man har kendt, har som regel været få markører opnået fra den “gamle” sparsommme teknologi og forsøg på at benytte disse markører til differentiering af bestande har ofte bygget på “det forhåndenværende søms princip” og man har fejlet (de har været såkaldte “neutrale” DNA markører og ikke markører påvirket af selektions tryk – derfor er de ikke forskellige fra bestand til bestand). Nye teknologier gør det nu mulig at læse hele sildens arvemasse til rimelige omkostninger. Hvis man læser hele sildens arvemasse og gør det på individer fra flere bestande, så vil man kunne identificere genetiske variationer mellem disse bestande. Grunden til at man mener man kan finde genetiske foskelle mellem disse bestande er, at de, selv om de blandes til at fouragere, skilles og har forskellige præferencer for gydningssted og tidspunkt. Dette er en fysiologisk egeneskab grupperne har tilegnet sig og da fysiologiske egenskaber styres af arvemassen (DNA’et) så vil denne præference være indkodet i bestandens DNA et eller andet sted i tid og rum – disse individer har haft et selektions tryk fra omgivelser som har gjort at de har tilpasset sig denne egenskab og overlevet. Det vil sige, der må findes en forskel i arvemassen og hvis denne findes så kan den måles. Som før nævnt så har nye teknologier nu gjort det muligt at læse et individs arvemasse til en overkommleig pris dvs. at genetiske forskelle som gør det muligt at differentiere bestande nu kan identificeres. Final In this project, 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 manual analysis of the connexin gene family in nine teleosts, including herring, indicated that the annotation of this gene family was poor, and 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. Project status: Liðug Project output: Scientific articles, books, thesis etc. Sunnvør í Kongsstovu. Sequencing the North Atlantic herring (Clupea harengus) genome and development of a genetic stock management tool. PhD thesis. Sunnvør í Kongsstovu, Svein-Ole Mikalsen, Eydna í Homrum, Jan Arge Jacobsen, Paul Flicek & Hans Atli Dahl. Using long and linked reads to improve an Atlantic herring (Clupea harengus) genome assembly. Scientific Reports 9, 17716 (2019) doi:10.1038/s41598-019-54151-9. Other results, such as unpublished articles, patents, computer systems, original models and new procedures Mikalsen, S-O., Tausen, M., í Kongsstovu, S. Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies (Submitted BMC Genomics). í Kongsstovu, S., Dahl, H.A., Gislason, H., í Homrum, E., Jacobsen, J.A., Flicek, P., Mikalsen, S-O. Identification of male heterogametic sex determining regions on the Atlantic herring (Clupea harengus) genome (In prep). í Kongsstovu, S., Mikalsen, S-O., í Homrum, E., Jacobsen, J.A., Als, T.D., Gislason, H., Flicek, P., Dahl, H.A. Atlantic herring (Clupea harengus) population structure in the Northeast Atlantic Ocean (In prep). Poster presentation at BIOINFORMATICS: FROM ALGORITHMS TO APPLICATIONS (BiATA) 2017 conference in Saint Petersburg, Russia, August 1–5, 2017. Oral and poster presentations at Gransking í Føroyum on 16th of November 2017. Oral presentation at ICES Workshop on Stock Identification and allocation of catches of herring to stocks (WKSIDAC). Monday 20 November – Friday 24 November 2017 in Galway, Ireland. Publications outside the scientific community, i.e. lectures, periodicals, articles in newspapers, television and radio 28.11.19 – Press releases and articles regarding the published article about the herring genome on the University’s, Havstovan’s and Granskingarráðið’s webpages as well as local news portals (www.vp.fo, www.nordlysid.fo, www.in.fo). 18.08.17 - Lecture during Vísindavøka á ferð 2017. Lecture was titled « Arvafrøði sum amboð í fiskivinnuni » 29.08.17 - Article about the project published in Vísindavøkublaðið 2017/Sosialurin 11.04.16 - Article about the project and Amplexa Genetics in Sosialurin (Faroese newspaper) 10.04.16 - Interview with Hans Atli Dahl about the project in Útvarpstíðindi at Kringvarp Føroya. 14.04.16 - Article about the project on various Faroese news portals (www.vp.fo, www.portal.fo, www.nordlysid.fo ) << Back |
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