Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7.
Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7.
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邓氏柳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性别决定系统
DOI：
10.1111/1755-0998.13362
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发表时间：
2021-08
影响因子：
7.7
通讯作者：
Mao JF
中科院分区：
文献类型：
--
作者：
He L;Jia KH;Zhang RG;Wang Y;Shi TL;Li ZC;Zeng SW;Cai XJ;Wagner ND;Hörandl E;Muyle A;Yang K;Charlesworth D;Mao JF
植物的性别决定系统可以涉及雌性或雄性异配子（分别为ZW或XY）。在这里，我们使用Illumina短读段、Oxford Nanopore Technologies（ONT）长读段和Hi-C读段来组装雌性杨柳（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的数据库来预测基因。在29个支架中组装了总共328 Mb的最终基因组序列，并且包括31，501个预测基因。对包括雌性和雄性植物的短读段序列数据的分析表明，7号染色体上存在雄性异配子性别决定因子，这意味着与柳属中大多数物种的雌性异配子不同，柳亚属中进化出了雄性异配子。邓尼氏血吸虫性连锁区占据雌性7号染色体约3.21 Mb（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复制从其他基因组区域获得的。我们检测到纯化选择的基因是祖先存在于该地区，虽然有些已经丢失。来自雌性和雄性个体的转录组数据显示，柔荑花序和叶组织中的雄性偏向基因多于雌性偏向基因，并表明在假常染色体区域中富集了雄性偏向基因。本研究为进一步研究杨柳科植物性别决定区和性染色体进化提供了宝贵的基因组资源。
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.
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