A chromosome-level assembly of the Atlantic herring genome—detection of a supergene and other signals of selection
- Mats E. Pettersson1,
- Christina M. Rochus1,13,
- Fan Han1,13,
- Junfeng Chen1,
- Jason Hill1,
- Ola Wallerman1,
- Guangyi Fan2,3,
- Xiaoning Hong2,4,
- Qiwu Xu2,
- He Zhang2,
- Shanshan Liu2,
- Xin Liu2,5,6,
- Leanne Haggerty7,
- Toby Hunt7,
- Fergal J. Martin7,
- Paul Flicek7,
- Ignas Bunikis8,
- Arild Folkvord9,10 and
- Leif Andersson1,11,12
- 1Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden;
- 2BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China;
- 3State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China;
- 4BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China;
- 5BGI-Shenzhen, Shenzhen 518083, China;
- 6China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China;
- 7European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom;
- 8Science for Life Laboratory Uppsala, Department of Immunology, Genetics and Pathology, Uppsala University, SE-75123 Uppsala, Sweden;
- 9Department of Biological Sciences, University of Bergen, 5020 Bergen, Norway;
- 10Institute of Marine Research, 5018 Bergen, Norway;
- 11Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden;
- 12Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA
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↵13 These authors contributed equally to this work.
Abstract
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.253435.119.
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Freely available online through the Genome Research Open Access option.
- Received June 11, 2019.
- Accepted September 27, 2019.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
