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.

性染色体（sex chromosomes）从常染色体（autosomes）分化并演化的过程，是基因组进化历程中的重大事件，曾在多个演化支中多次独立发生。鱼类中性别决定机制（sex-determination mechanisms）的反复演化与不稳定性，使其成为检验演化中通用且可预测模式的理想研究体系。根据现有理论，性染色体的分化由新的主性别决定基因（master-sex determining gene）演化后引发的重组抑制（recombination suppression）所触发。然而，由于组装性别决定区域（sex determining regions, SDRs）存在固有难度，目前仅在少数案例中阐明了建立重组抑制的分子机制（molecular mechanisms）。正向遗传学（forward-genetics）数据与长读长测序（long-read sequencing）技术的发展，催生了大量质疑现有理论核心观点的研究数据。本研究证实，迈达斯丽鱼（Midas cichlids）的性别由XY性别决定系统调控，并通过整合正向遗传学、长读长测序与光学图谱（optical mapping）技术，完成了对SDR的鉴定与组装。本研究揭示了长读长测序技术如何帮助检测因基因组组装（genome assemblies）不完整而导致的基因型-表型图谱（genotype-phenotype mapping）伪影。雄性特异性区域（male-specific region）被限定在4号染色体上一段长100 kb的区段内，该区域包含转座因子（transposable elements）以及已知性别决定基因抗缪勒管受体2基因座（anti-Mullerian receptor 2 locus）的Y染色体特异性重复拷贝。本研究数据显示，amhr2Y起源于一次染色体间易位（interchromosomal translocation）：将20号染色体上的相关序列易位至4号染色体，该事件发生于迈达斯丽鱼与弗利尔丽鱼（Flier cichlids）分化之前。在弗利尔丽鱼中，该拷贝已发生假基因化（pseudogenized）并易位至其他染色体。抗缪勒管基因的重复是形成新性别决定因子的常见途径，这凸显了分子平行演化（molecular parallelism）在性别决定演化过程中的重要作用。