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.
Highlights
Cerasus serrulata (Lindley) Loudon belongs to CerasusMill. in the Rosaceae family[1,2]
Genome estimation and assembly The genome size of C. serrulata was estimated by k-mer analysis to be 256.65 Mb with repeat and heterozygosity percentages of 46.55% and 1.67%, respectively (Supplementary Fig. S1)
The results of BLAST with randomly selected reads aligned to the nucleotide sequence database (Nt) were used to assess contamination
Summary
Cerasus serrulata (Lindley) Loudon belongs to CerasusMill. in the Rosaceae family[1,2]. Cerasus serrulata is widely distributed in the midwestern and eastern regions of China and possibly is present on the Korean Peninsula and in Japan[3,5]. China has the most abundant germplasm resources of C. serrulata, where various natural and artificial hybrids have been developed and selected[7,8]. We successfully assembled the genome of C. serrulata (2n = 2x = 16) and compared it with the genomes of closely related species in terms of the gene family, positive gene selection, and phylogeny. This work provides a foundation for clarifying the genetic variation, genetic diversity, and genealogical structure of C. serrulata
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