TY  - JOUR
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
Y1  - 2019/11/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1919 
EP  - 1928 
DO  - 10.1101/gr.253435.119 
VL  - 29 
IS  - 11 
UR  - http://genome.cshlp.org/content/29/11/1919.abstract 
N2  - 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. 
ER  -