RT Journal
A1 Pettersson, Mats E.
A1 Rochus, Christina M.
A1 Han, Fan
A1 Chen, Junfeng
A1 Hill, Jason
A1 Wallerman, Ola
A1 Fan, Guangyi
A1 Hong, Xiaoning
A1 Xu, Qiwu
A1 Zhang, He
A1 Liu, Shanshan
A1 Liu, Xin
A1 Haggerty, Leanne
A1 Hunt, Toby
A1 Martin, Fergal J.
A1 Flicek, Paul
A1 Bunikis, Ignas
A1 Folkvord, Arild
A1 Andersson, Leif
T1 A chromosome-level assembly of the Atlantic herring genome—detection of a supergene and other signals of selection
JF Genome Research 
JO Genome Research 
YR 2019 
FD November 01 
VO 29 
IS 11 
SP 1919 
OP 1928 
DO 10.1101/gr.253435.119 
UL http://genome.cshlp.org/content/29/11/1919.abstract 
AB 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.