Pettersson ME, Rochus CM, Han F, Chen J, Hill J, Wallerman O, Fan G, Hong X, Xu Q, Zhang H, Liu S, Liu X, Haggerty L, Hunt T, Martin FJ, Flicek P, Bunikis I, Folkvord A, Andersson L.

Genome Res. 2019 Nov;29(11):1919-1928. doi:10.1101/gr.253435.119

A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.

Linkage analysis of 45,000 markers from 2 crosses with ~50 offsprings each confirmed that there are 26 linkage groups, and suggests ~1 recombination per chromosome pair at meiosis. Recombination rate is lower towards centromeres. This is in line with the known fact that 3 chromosomes are metacentric and the other are acrocentric. When comparing with other fish species, genes tend to stay on the same chromosomes, but move within (like birds and invertebrates, but unlike mammals). A 7.8-Mb region on chr12 with strange linkage desequilibrium pattern was shown to be an inversion between southern and northern individuals. It may act as a supergene. Genetic exchanges between both haplotypes is reduced by the inversion.