The mammalian sex chromosome system (XX female/XY male) is ancient and highly conserved. The sex chromosome karyotype of the creeping vole (Microtus oregoni) represents a long-standing anomaly, with an X chromosome that is unpaired in females (X0) and exclusively maternally transmitted. We produced a highly contiguous male genome assembly, together with short-read genomes and transcriptomes for both sexes. We show that M. oregoni has lost an independently segregating Y chromosome and that the male-specific sex chromosome is a second X chromosome that is largely homologous to the maternally transmitted X. Both maternally inherited and male-specific sex chromosomes carry fragments of the ancestral Y chromosome. Consequences of this recently transformed sex chromosome system include Y-like degeneration and gene amplification on the male-specific X, expression of ancestral Y-linked genes in females, and X inactivation of the male-specific chromosome in male somatic cells. The genome of M. oregoni elucidates the processes that shape the gene content and dosage of mammalian sex chromosomes and exemplifies a rare case of plasticity in an ancient sex chromosome system.

哺乳动物的性染色体系统（XX 女性/XY 男性）是古老且高度保守的。匍匐田鼠 ( Microtus oregoni )的性染色体核型代表了一种长期存在的异常，其 X 染色体在雌性 (X0) 中未配对并且完全由母系传播。我们制作了一个高度连续的男性基因组组装，以及两性的短读基因组和转录组。我们证明了M. oregoni已经失去了独立分离的 Y 染色体，男性特异性性染色体是第二条 X 染色体，与母系传播的 X 很大程度上同源。母系遗传和男性特异性性染色体都携带祖先 Y 染色体的片段。这种最近转变的性染色体系统的后果包括男性特异性 X 上的 Y 样变性和基因扩增，女性祖先 Y 连锁基因的表达，以及男性体细胞中男性特异性染色体的 X 失活。M. oregoni的基因组阐明了塑造哺乳动物性染色体基因含量和剂量的过程，并举例说明了古代性染色体系统中罕见的可塑性。