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Article|01 Oct 2020|OPEN
The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species
Xian-Gui Yi1, Xia-Qing Yu2, Jie Chen1, Min Zhang1, Shao-Wei Liu3, Hong Zhu1, Meng Li1, Yi-Fan Duan1, Lin Chen1, Lei Wu4, Shun Zhu4, Zhong-Shuai Sun5, Xin-Hong Liu6 & Xian-Rong Wang1,
1Co-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
2College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, Jiangsu, China
3College of Food Science and Technology, Nanjing Agricultural University, 210095 Nanjing, Jiangsu, China
4Biomarker Technologies Corporation, 101300 Beijing, China
5Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, 318000 Taizhou, Zhejiang, China
6Zhejiang Academy of Forestry, 310023 Hangzhou, Zhejiang, China

Horticulture Research 7,
Article number: 20165 (2020)
doi: 10.1038/hortres.2020.165
Views: 151

Received: 16 Mar 2020
Revised: 22 Jun 2020
Accepted: 03 Jul 2020
Published online: 01 Oct 2020

Abstract

Cerasus serrulata is a flowering cherry germplasm resource for ornamental purposes. 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. 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. 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. The comparative genomic analysis confirmed that C. serrulata 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 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. 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. This research provides high-quality genomic information about C. serrulata as well as insights into the evolutionary history of Cerasus species.