Complete chloroplast genome of cultivated flowering cherry, Prunus ×yedoensis ‘Somei-yoshino’ in comparison with wild Prunus yedoensis Matsum. (Rosaceae)
- 201 Downloads
Prunus ×yedoensis Matsum. ‘Somei-yoshino’ is the most common and widespread cultivar of the ornamental flowering cherries. We hereby report its complete chloroplast (cp) genome sequences generated by whole-genome next-generation sequencing approach. The cp genome size was 157,792 bp in length consisting of four regions; large single-copy region (85,914 bp), small single-copy region (19,120 bp), and a pair of inverted repeat regions (26,379 bp). The genome contained a total of 131 genes, including 86 coding genes, 8 rRNA genes, and 37 tRNA genes. A total of 92 simple sequence repeats (SSRs) were detected within the cp genome. Its molecular features were compared with the complete cp genome of wild P. yedoensis, which occurs rarely in natural habitats of Mt. Halla in Jeju Island, Korea, displaying nearly indistinguishable morphology as P. ×yedoensis ‘Somei-yoshino’. Although both cp genomes were structured highly alike, the sequence variations between them were revealed in several single-nucleotide polymorphisms (SNPs). Using additional individuals of wild and cultivated flowering cherries, PCR amplification confirmed that those SNPs were phylogenetically informative, providing distinction between wild and cultivated flowering cherries. In future study, the SNPs and SSRs reported in this study could be used to identify wild individuals from morphologically identical cultivars of flowering cherries and also to conserve the genetic diversity of wild flowering cherries in Jeju Island.
KeywordsPhylogenetic relationship Artificial hybrid origin Characterization of cp genomes The genetic structure Genome-wide comparative analysis Highly resolute cp markers
This study was supported by the Grants from the National Research Foundation of Korea (numbers 2017R1A6A3A01075954 and 2017R1A2B3001923).
- Bailey LH, Bailey EZ (1976) A concise dictionary of plants cultivated in the United States and Canada. Macmillan, New YorkGoogle Scholar
- Flower Association of Japan (compilers) (1982) Manual of Japanese flowering cherries. Flower Association of Japan, TokyoGoogle Scholar
- Iketani H, Katsuki T, Kawahara T (2006) Prunus ×yedoensis ‘Somei-yoshino’, a correct cultivar name for Yoshino cherry. J Jpn Bot 81:123–124Google Scholar
- Kato S, Matsumoto A, Yoshimura K, Katsuki T, Iwamoto K, Kawahara T, Mukai Y, Tsuda Y, Ishio S, Nakamura K, Moriwaki K, Shiroishi T, Gojobori T, Yoshimaru H (2014) Origins of Japanese flowering cherry (Prunus subgenus Cerasus) cultivars revealed using nuclear SSR markers. Tree Genet Genomes 10:477–487CrossRefGoogle Scholar
- Kuitert W (1999) Japanese flowering cherries. Timber, PortlandGoogle Scholar
- Ma H, Olsen R, Pooler M (2009) Evaluation of flowering cherry species, hybrids, and cultivars using simple sequence repeat markers. J Am Soc Hortic Sci 134:435–444Google Scholar
- Nakamura I, Takahashi H, Ohta S, Moriizumi T, Hanashiro Y, Sato YI, Mii M (2015) Origin of Prunus x yedoensis ‘Somei-yoshino’ based on sequence analysis of PolAI gene. Adv Hortic Sci 29:17–23Google Scholar
- Rehder A (1940) A manual of cultivated trees and shrubs hardy in North America exclusive of the subtropical and warmer temperate regions, 2nd edn. Macmillan, New YorkGoogle Scholar
- U.S. Department of Agriculture (2001) 1998 Census of horticultural specialties. http://www.nass.usda.gov/census/census97/horticulture/table13.pdf. Accessed 14 May 2009