Advertisement

Molecular Breeding

, 38:112 | Cite as

Complete chloroplast genome of cultivated flowering cherry, Prunus ×yedoensis ‘Somei-yoshino’ in comparison with wild Prunus yedoensis Matsum. (Rosaceae)

  • Myong-Suk Cho
  • Hwan Su Yoon
  • Seung-Chul Kim
Short Communication
  • 201 Downloads

Abstract

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.

Keywords

Phylogenetic relationship Artificial hybrid origin Characterization of cp genomes The genetic structure Genome-wide comparative analysis Highly resolute cp markers 

Notes

Funding information

This study was supported by the Grants from the National Research Foundation of Korea (numbers 2017R1A6A3A01075954 and 2017R1A2B3001923).

Supplementary material

11032_2018_871_MOESM1_ESM.xlsx (18 kb)
Table S1 (XLSX 17 kb)
11032_2018_871_MOESM2_ESM.xlsx (11 kb)
Table S2 (XLSX 11 kb)
11032_2018_871_MOESM3_ESM.xlsx (11 kb)
Table S3 (XLSX 11 kb)
11032_2018_871_MOESM4_ESM.xlsx (11 kb)
Table S4 (XLSX 11 kb)
11032_2018_871_MOESM5_ESM.xlsx (12 kb)
Table S5 (XLSX 11 kb)

References

  1. Bafeel SO, Arif IA, Bakir MA, Al Homaidan AA, Al Farhan AH, Khan HA (2012) DNA barcoding of arid wild plants using rbcL gene sequences. Genet Mol Res 11(3):1934–1941CrossRefPubMedGoogle Scholar
  2. Bailey LH, Bailey EZ (1976) A concise dictionary of plants cultivated in the United States and Canada. Macmillan, New YorkGoogle Scholar
  3. Brettin TS, Karle R, Crowe EL, Iezzoni AF (2000) Chloroplast inheritance and DNA variation in sweet, sour, and ground cherry. J Hered 91:75–79CrossRefPubMedGoogle Scholar
  4. Cheng S, Mcbride JR, Fukunari K (2000) The urban forest of Tokyo. Arboric J 23:379–392CrossRefGoogle Scholar
  5. Cho MS, Kim CS, Kim SH, Kim TO, Heo KI, Jun J, Kim SC (2014) Molecular and morphological data reveal hybrid origin of wild Prunus yedoensis (Rosaceae) from Jeju Island, Korea: implications for the origin of the flowering cherry. Am J Bot 101:1976–1986CrossRefPubMedGoogle Scholar
  6. Daniell H, Lin CS, Yu M, Chang WJ (2016) Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Boil 17(1):134CrossRefGoogle Scholar
  7. Flower Association of Japan (compilers) (1982) Manual of Japanese flowering cherries. Flower Association of Japan, TokyoGoogle Scholar
  8. 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
  9. Iketani H, Ohta S, Kawahara T, Katsuki T, Mase N, Sato Y, Yamamoto T (2007) Analyses of clonal status in ‘Somei-yoshino’ and confirmation of genealogical record in other cultivars of Prunus × yedoensis by microsatellite markers. Breed Sci 57:1–6CrossRefGoogle Scholar
  10. Innan H, Terauchi R, Miyashita NT, Tsunewaki K (1995) DNA fingerprinting study on the intraspecific variation and the origin of Prunus yedoensis (Someiyoshino). Jpn J Genet 70:185–196CrossRefPubMedGoogle Scholar
  11. Kaneko T, Terachi T, Tsunewaki K (1986) Studies on the origin of crop species by restriction endonuclease analysis of organellar DNA. II. Restriction analysis of cpDNA of 11 Prunus species. Jpn J Genet 61:157–168CrossRefGoogle Scholar
  12. 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
  13. Kuitert W (1999) Japanese flowering cherries. Timber, PortlandGoogle Scholar
  14. Lagesen K, Hallin PF, Rødland E, Stærfeldt HH, Rognes T, Ussery D (2007) RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res 35(9):3100–3108CrossRefPubMedPubMedCentralGoogle Scholar
  15. Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16CrossRefPubMedPubMedCentralGoogle Scholar
  16. Lohse M, Drechsel O, Kahlau S, Bock R (2007) OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52(5–6):267–274CrossRefPubMedGoogle Scholar
  17. 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
  18. Matsumoto S, Wakita H, Soejima J (1997) Chloroplast DNA probes as an aid in the molecular classification of Malus species. Sci Hortic 70:81–86CrossRefGoogle Scholar
  19. Matsumura J (1901) Cerasi Japanicae duae species novae. Bot Mag Tokyo 15:99–101CrossRefGoogle Scholar
  20. 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
  21. Ohta S, Osumi S, Katsuki T, Nakamura I, Yamamoto T, Sato YI (2006) Genetic characterization of flowering cherries (Prunus subgenus Cerasus) using rpl16-rpl14 spacer sequences of chloroplast DNA. J Jpn Soc Hortic Sci 75:72–78CrossRefGoogle Scholar
  22. Parks M, Cronn R, Liston A (2009) Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Boil 7(1):84CrossRefGoogle Scholar
  23. Raspé O (2001) Inheritance of the chloroplast genome in Sorbus aucuparia L. (Rosaceae). J Hered 92:507–509CrossRefPubMedGoogle Scholar
  24. 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
  25. Roh MS, Cheong EJ, Choi IY, Joung YH (2007) Characterization of wild Prunus yedoensis analyzed by inter-simple sequence repeat and chloroplast DNA. Sci Hortic 114:121–128CrossRefGoogle Scholar
  26. Thiel T, Michalek W, Varshney R, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106(3):411–422CrossRefPubMedGoogle Scholar
  27. 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
  28. Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255CrossRefPubMedGoogle Scholar

Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.Department of Biological SciencesSungkyunkwan UniversitySuwonRepublic of Korea

Personalised recommendations