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Status即將出版Forthcoming
A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection
Pettersson, Mats E.1; Rochus, Christina M.1; Han, Fan1; Chen, Junfeng1; Hill, Jason1; Wallerman, Ola1; Fan, Guangyi2,3; Hong, Xiaoning2,4; Xu, Qiwu2; Zhang, He2; Liu, Shanshan2; Liu, Xin2,5,6; Haggerty, Leanne7; Hunt, Toby7; Martin, Fergal J.7; Flicek, Paul7; Bunikis, Ignas8; Folkvord, Arild9,10; Andersson, Leif1,11,12
2019
Source PublicationGenome Research
ISSN1088-9051
Volume29Issue:11Pages:1919-1928
AbstractThe 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.
DOI10.1101/gr.253435.119
URLView the original
Language英語English
Scopus ID2-s2.0-85074446026
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Citation statistics
Cited Times [WOS]:40   [WOS Record]     [Related Records in WOS]
Document TypeJournal article
CollectionUniversity of Macau
Affiliation1.Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-75123, Sweden
2.BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
3.State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, Macao
4.BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
5.BGI-Shenzhen, Shenzhen, 518083, China
6.China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
7.European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
8.Science for Life Laboratory Uppsala, Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, SE-75123, Sweden
9.Department of Biological Sciences, University of Bergen, Bergen, 5020, Norway
10.Institute of Marine Research, Bergen, 5018, Norway
11.Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
12.Department of Veterinary Integrative Biosciences, Texas AandM University, College Station, 77843, United States
Recommended Citation
GB/T 7714
Pettersson, Mats E.,Rochus, Christina M.,Han, Fan,et al. A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection[J]. Genome Research,2019,29(11):1919-1928.
APA Pettersson, Mats E.,Rochus, Christina M.,Han, Fan,Chen, Junfeng,Hill, Jason,Wallerman, Ola,Fan, Guangyi,Hong, Xiaoning,Xu, Qiwu,Zhang, He,Liu, Shanshan,Liu, Xin,Haggerty, Leanne,Hunt, Toby,Martin, Fergal J.,Flicek, Paul,Bunikis, Ignas,Folkvord, Arild,&Andersson, Leif.(2019).A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.Genome Research,29(11),1919-1928.
MLA Pettersson, Mats E.,et al."A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection".Genome Research 29.11(2019):1919-1928.
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