Phased genome sequence of an interspecific hybrid flowering cherry, 'Somei-Yoshino' (Cerasus × yedoensis)

• Published in: DNA research Vol. 26; no. 5; pp. 379 - 389
• Main Authors: Shirasawa, Kenta, Esumi, Tomoya, Hirakawa, Hideki, Tanaka, Hideyuki, Itai, Akihiro, Ghelfi, Andrea, Nagasaki, Hideki, Isobe, Sachiko
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-10-2019
• Subjects: Base Sequence; DNA, Plant; Genome, Plant; Phylogeny; Prunus - genetics; Sequence Analysis, DNA; Sequence Analysis, RNA; Transcriptome; phased genome sequence; flowering cherry; interspecific hybrid; transcriptome; floral bud
• ISSN: 1340-2838; 1756-1663
• DOI: 10.1093/dnares/dsz016

We report the phased genome sequence of an interspecific hybrid, the flowering cherry 'Somei-Yoshino' (Cerasus × yedoensis). The sequence data were obtained by single-molecule real-time sequencing technology, split into two subsets based on genome information of the two probable ancestors, and assembled to obtain two haplotype phased genome sequences of the interspecific hybrid. The resultant genome assembly consisting of the two haplotype sequences spanned 690.1 Mb with 4,552 contigs and an N50 length of 1.0 Mb. We predicted 95,076 high-confidence genes, including 94.9% of the core eukaryotic genes. Based on a high-density genetic map, we established a pair of eight pseudomolecule sequences, with highly conserved structures between the two haplotype sequences with 2.4 million sequence variants. A whole genome resequencing analysis of flowering cherries suggested that 'Somei-Yoshino' might be derived from a cross between C. spachiana and either C. speciosa or its relatives. A time-course transcriptome analysis of floral buds and flowers suggested comprehensive changes in gene expression in floral bud development towards flowering. These genome and transcriptome data are expected to provide insights into the evolution and cultivation of flowering cherry and the molecular mechanism underlying flowering.