Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 scaffolds, and includes 31,501 predicted genes. Analyses of short-read sequence data that included female and male plants suggested a male heterogametic sex-determining factor on chromosome 7, implying that, unlike the female heterogamety of most species in the genus Salix, male heterogamety evolved in the subgenus Salix. The S. dunnii sex-linked region occupies about 3.21 Mb of chromosome 7 in females (representing its position in the X chromosome), probably within a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one-third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purifying selection on the genes that were ancestrally present in the region, though some have been lost. Transcriptome data from female and male individuals show more male- than female-biased genes in catkin and leaf tissues, and indicate enrichment for male-biased genes in the pseudo-autosomal regions. Our study provides valuable genomic resources for further studies of sex-determining regions in the family Salicaceae, and sex chromosome evolution.

中文翻译：

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Salix dunnii 基因组的染色体规模组装揭示了 7 号染色体上的雄性异配子性别决定系统

植物中的性别决定系统可能涉及雌性或雄性异配性（分别为 ZW 或 XY）。在这里，我们使用 Illumina 短读长、牛津纳米孔技术 (ONT) 长读长和 Hi-C 读长来组装雌性柳树 ( Salix dunnii )的第一个染色体规模的基因组，并使用转录组序列和可用数据库来预测基因。最终的 328 Mb 基因组序列在 29 个支架中组装，包括 31,501 个预测基因。对包括雌性和雄性植物在内的短读序列数据的分析表明，第 7 号染色体上存在雄性异配性决定因素，这意味着与柳属中大多数物种的雌性异配性不同，雄性异配性在柳属亚属中进化。该S. dunnii性连锁区域在雌性中占据约 3.21 Mb 的 7 号染色体（代表其在 X 染色体中的位置），可能位于着丝粒周围区域内。我们的数据表明，该区域富含转座因子插入，其 124 个蛋白质编码基因中约有三分之一是通过从其他基因组区域复制获得的。我们检测到该地区祖先存在的基因的纯化选择，尽管有些已经丢失。来自雌性和雄性个体的转录组数据显示，柳絮和叶组织中的雄性偏向基因多于雌性，并表明假常染色体区域中雄性偏向基因的富集。我们的研究为进一步研究杨柳科的性别决定区域和性染色体进化提供了宝贵的基因组资源。