Abstract：
Sex chromosomes have evolved independently in many different plant lineages. Here, we describe reference genomes for spinach (Spinacia oleracea) X and Y haplotypes by sequencing homozygous XX females and YY males. The long arm of 185-Mb chromosome 4 carries a 13-Mb X-linked region (XLR) and 24.1-Mb Y-linked region (YLR), of which 10 Mb is Y specific. We describe evidence that this reflects insertions of autosomal sequences creating a \"Y duplication region\" or \"YDR\" whose presence probably directly reduces genetic recombination in the immediately flanking regions, although both the X and Y sex-linked regions are within a large pericentromeric region of chromosome 4 that recombines rarely in meiosis of both sexes. Sequence divergence estimates using synonymous sites indicate that YDR genes started diverging from their likely autosomal progenitors about 3 MYA, around the time when the flanking YLR stopped recombining with the XLR. These flanking regions have a higher density of repetitive sequences in the YY than the XX assembly and include slightly more pseudogenes compared with the XLR, and the YLR has lost about 11% of the ancestral genes, suggesting some degeneration. Insertion of a male-determining factor would have caused Y linkage across the entire pericentromeric region, creating physically small, highly recombining, terminal pseudoautosomal regions. These findings provide a broader understanding of the origin of sex chromosomes in spinach.
摘要：
性染色体在许多不同的植物谱系中独立进化。这里,我们通过对纯合XX雌性和YY雄性进行测序来描述菠菜（Spinaciaoleracea）X和Y单倍型的参考基因组。185Mb4号染色体的长臂携带一个13MbX连锁区(XLR)和24.1MbY连锁区(YLR),其中10Mb是Y特异性的。我们描述的证据表明，这反映出常染色体序列的插入产生了一个“Y重复区域”或“YDR”，其存在可能直接减少了侧翼区域的遗传重组，尽管X和Y性别连接区都在4号染色体的一个大着丝粒区域内，该区域很少在两性的减数分裂中重组。使用同义位点的序列差异估计表明，YDR基因开始从其可能的常染色体祖细胞中发散约3MYA，大约在侧翼YLR停止与XLR重组的时候。这些侧翼区在YY中的重复序列密度高于XX组装体，并且与XLR相比，包括更多的假基因。YLR失去了大约11%的祖先基因，暗示一些退化。插入男性决定因子会导致整个着丝粒区域的Y连锁，创造物理上的小，高度重组，末端假常染色体区域。这些发现为菠菜中性染色体的起源提供了更广泛的理解。
