Mapping and assembly of the Midas cichlid male-specific region supports molecular parallelism in the evolution of a master sex-determining role for amhr2

The evolution of sex chromosomes and their differentiation from autosomes
is a major event during genome evolution that happened many times in
several lineages. The repeated evolution and lability of sex-determination
mechanisms in fishes makes this a well-suited system to test for general
and predictable patterns in evolution. According to current theory,
differentiation is triggered by the suppression of recombination following
the evolution of a new master-sex determining gene. However, the molecular
mechanisms that establish recombination suppression are known from few
examples, owing to the intrinsic difficulties of assembling sex
determining regions (SDRs). Forward-genetics data and the development of
long-read sequencing have generated a wealth of data questioning central
aspects of the current theory. Here, we demonstrate that sex in Midas
cichlids is determined by an XY system, identify and assemble the SDR by
combining forward-genetics, long-read sequencing and optical mapping. We
show how long-reads aid in the detection of artifacts in
genotype-phenotype mapping that arise from incomplete genome assemblies.
The male-specific region is restricted to a 100 kb segment on chromosome 4
that harbors transposable elements and a Y-specific duplicate of the
anti-Mullerian receptor 2 locus, a known sex-determining gene. Our data
suggests that amhr2Y originated by an interchromosomal
translocation from chromosome 20 to 4 predating the split of Midas and
Flier cichlids. In the later, it is pseudogenized and translocated to
another chromosome. Duplication of anti-Mullerian genes is a common route
to establishing new sex determiners, highlighting the role of molecular
parallelism in the evolution of sex determination.