The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species

第一作者：Xian-Gui Yi

第一单位：南京林业大学

通讯作者：Xian-Rong Wang

 Abstract 

背景回顾：Cerasus serrulata is a flowering cherrygermplasm resource for ornamental purposes.

主要研究：In this work, we present a de novo chromosome-scale genome assembly of C. serrulata by the use of Nanopore and Hi-C sequencing technologies.

结果1-组装+注释：The assembled C. serrulata 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.

结果2-共线性分析：Synteny analysis indicated that C. serrulata and C. avium have 333 syntenic blocks composed of 14,072 genes. Blocks on chromosome 01 of C. serrulata are distributed on all chromosomes of C. avium, implying that chromosome 01 is the most ancient or active of the chromosomes.

结果3-基因家族扩张与收缩：The comparative genomic analysis confirmed that C. serrulata has 740 expanded gene families, 1031 contracted gene families, and 228 rapidly evolving gene families.

结果4-进化树与分化时间估计：By the use of 656 single-copy orthologs, a phylogenetic tree composed of 10 species was constructed. The present C. serrulata species diverged from Prunus yedoensis ~17.34 million years ago (Mya), while the divergence of C. serrulata and C. avium was estimated to have occurred ～21.44 Mya.

结果5-基因家族鉴定：In addition, a total of 148 MADS-box family gene members were identified in C. serrulata, 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 C. serrulata, respectively, based on clustering analysis. Nine hundred forty-one plant disease-resistance genes (R-genes) were detected by searching C. serrulata within the PRGdb.

结论：This research provides high-quality genomic information about C. serrulata as well as insights into the evolutionary history of Cerasus species.

 摘  要 

山樱花（Cerasus serrulata）是用于观赏的开花樱桃种质资源。本文中，作者基于Nanopore和Hi-C测序技术，报道了从头组装的山樱花染色体级别参考基因组。山樱花的基因组大小约为265.40Mb，共获得304个contigs（contig N50长1.56Mb），67个scaffolds（scaffold N50长31.12Mb）。山樱花基因组中包含29094个编码基因，其中94.90%的基因至少能够在一个功能数据库中获得同源注释条目。山樱花与欧洲甜樱桃（Cerasus avium）基因组之间的共线性分析共鉴定了333个共线性块，包含14072个基因。山樱花1号染色体上的共线性块对应的区域散落在欧洲甜樱桃的各个染色体上，说明1号染色体是最古老或者最活跃的染色体。比较基因组显示山樱花有740个基因家族发生扩张，1031个基因家族发生收缩，228个基因家族发生了快速的演化。通过656个单拷贝同源基因，作者构建了一个包含10个物种的系统发育树。现如今的山樱花与日本樱花约在一千七百三十四万年前分化，而山樱花与欧洲甜樱桃的分化时间约在两千一百四十四万年前。另外，作者共鉴定了148个MADS-box基因，其中AGL32亚家族在山樱花中丢失，而SVP亚家族发生了扩张。此外，作者还鉴定了MYB和WRKY基因家族，分别包含372和66个基因，可以分成7个和8个亚家族。作者通过PRGdb数据库的同源搜索，在山樱花基因组中共鉴定到了541个植物抗性基因（R genes）。本文的研究结果为山樱花提供了一个可供参考的高质量基因组，同时也为樱属植物的演化提供了新的视野。

 通讯作者 

doi: 10.1038/s41438-020-00382-1

Journal: Horticultural Research

Published date: Oct 01, 2020