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A chromosome-level assembly of the Atlantic herring: detection of a supergene and other signals of selection
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.ORCID iD: 0000-0002-7570-6847
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
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2019 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 29, no 11, p. 1919-1928Article in journal (Refereed) Published
Abstract [en]

The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo Pacific Biosciences (PacBio) assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb, which has been corroborated by a high-resolution linkage map. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few inter-chromosomal but frequent intra-chromosomal rearrangements. The improved assembly facilitates analysis of previously intractable large-scale structural variation, allowing, for example, the detection of a 7.8-Mb inversion on Chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation.

Place, publisher, year, edition, pages
Cold Spring Harbor Laboratory Press (CSHL), 2019. Vol. 29, no 11, p. 1919-1928
Keywords [en]
Atlantic herring, assembly, ecological adaptation, supergene
National Category
Genetics Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-396775DOI: 10.1101/gr.253435.119ISI: 000493952800015PubMedID: 31649060OAI: oai:DiVA.org:uu-396775DiVA, id: diva2:1368969
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilThe Research Council of Norway, 254774Wellcome trust, WT108749/Z/15/ZAvailable from: 2019-11-09 Created: 2019-11-09 Last updated: 2019-11-28Bibliographically approved
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Pettersson, MatsRochus, Christina MarieHan, FanHill, JasonWallerman, OlaBunikis, IgnasAndersson, Leif
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