Yi Xian-Gui, Yu Xia-Qing, Chen Jie, Zhang Min, Liu Shao-Wei, Zhu Hong, Li Meng, Duan Yi-Fan, Chen Lin, Wu Lei, Zhu Shun, Sun Zhong-Shuai, Liu Xin-Hong, Wang Xian-Rong
Co-Innovation Center for the Sustainable Forestry in Southern China, College of Biology and the Environment; Cerasus Research Center, Nanjing Forestry University, 210037 Nanjing, Jiangsu China.
College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, Jiangsu China.
Hortic Res. 2020 Oct 1;7:165. doi: 10.1038/s41438-020-00382-1. eCollection 2020.
is a flowering cherry germplasm resource for ornamental purposes. In this work, we present a de novo chromosome-scale genome assembly of by the use of Nanopore and Hi-C sequencing technologies. The assembled genome is 265.40 Mb across 304 contigs and 67 scaffolds, with a contig N50 of 1.56 Mb and a scaffold N50 of 31.12 Mb. It contains 29,094 coding genes, 27,611 (94.90%) of which are annotated in at least one functional database. Synteny analysis indicated that and have 333 syntenic blocks composed of 14,072 genes. Blocks on chromosome 01 of are distributed on all chromosomes of , implying that chromosome 01 is the most ancient or active of the chromosomes. The comparative genomic analysis confirmed that has 740 expanded gene families, 1031 contracted gene families, and 228 rapidly evolving gene families. By the use of 656 single-copy orthologs, a phylogenetic tree composed of 10 species was constructed. The present species diverged from ~17.34 million years ago (Mya), while the divergence of and was estimated to have occurred ∼21.44 Mya. In addition, a total of 148 MADS-box family gene members were identified in , accompanying the loss of the AGL32 subfamily and the expansion of the SVP subfamily. The MYB and WRKY gene families comprising 372 and 66 genes could be divided into seven and eight subfamilies in , respectively, based on clustering analysis. Nine hundred forty-one plant disease-resistance genes (R-genes) were detected by searching within the PRGdb. This research provides high-quality genomic information about as well as insights into the evolutionary history of species.
是一种用于观赏目的的樱花种质资源。在这项工作中，我们利用纳米孔和Hi-C测序技术对其进行了从头染色体水平的基因组组装。组装后的基因组大小为265.40 Mb，分布在304个重叠群和67个支架上，重叠群N50为1.56 Mb，支架N50为31.12 Mb。它包含29,094个编码基因，其中27,611个（94.90%）在至少一个功能数据库中得到注释。共线性分析表明，[物种名称1]和[物种名称2]有333个由14,072个基因组成的共线性块。[物种名称1] 01号染色体上的块分布在[物种名称2]的所有染色体上，这意味着01号染色体是最古老或最活跃的染色体。比较基因组分析证实，[物种名称1]有740个扩展基因家族、1031个收缩基因家族和228个快速进化基因家族。利用656个单拷贝直系同源基因构建了一个由10个物种组成的系统发育树。目前的[物种名称1]物种大约在1734万年前（百万年前）从[物种名称2]分化而来，而[物种名称1]和[物种名称3]的分化估计发生在约2144万年前。此外，在[物种名称1]中总共鉴定出148个MADS-box家族基因成员，同时AGL32亚家族缺失，SVP亚家族扩张。基于聚类分析，分别包含372个和66个基因的MYB和WRKY基因家族在[物种名称1]中可分为七个和八个亚家族。通过在PRGdb中搜索[物种名称1]，检测到941个植物抗病基因（R基因）。这项研究提供了关于[物种名称1]的高质量基因组信息以及对[物种名称1]物种进化历史的见解。
