Abstract
Prunus yedoensis (P. yedoensis) is a popular flowering species that is appreciated worldwide. While there are very few genetic variations among the planted populations of this species that are considered cultivated, diverse variations have been found in natural wild cherry populations on Jeju Island. In this study, we assembled a consensus reference chloroplast DNA (cpDNA) sequence with an aim to build a standard reference sequence of cpDNA to study genetic diversity and to characterize individual lines with the DNA barcoding technique in P. yedoensis. Full cpDNA was sequenced using the Illumina high-throughput DNA sequencing platform (HiSeq2500). Standard cpDNA sequences of P. yedoensis were obtained based on the four collected samples and two previously reported cp genome sequences from the NCBI. The sequenced cp genome consisted of 131 genes, of which 37 encoded tRNAs, 8 encoded rRNAs and 86 encoded proteins. There were 17 duplicated genes, including 4 rRNA genes, 7 tRNA genes and 6 protein-coding genes, with an overall GC content of 36%. When compared with the reference genome, 66 SSRs, 168 SNPs and 531 INDELs were identified within the 4 individual samples. These divergences comprising SSR, SNP and INDEL markers will be useful for testing the maternal inheritance of the chloroplast genome, for detecting species differentiation and even for breeding programs. Standard whole cp sequences were successfully assembled, resulting in a good resource to develop DNA barcodes, which will facilitate studies on genetic diversity, evolution, origins and cultivar-specific marker development.
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The datasets generated during and/or analysed during the current study are available from the corresponding author upon reasonable request.
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Acknowledgements
This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2017R1D1A3B03032994).
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IKC and EJC conceptualised the manuscript. UJ and MN provided the plant samples and performed the experiment. NSR analysed the data and wrote the manuscript. IKC and EJC revised the manuscript.
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Communicated by Tae-Ho Han, Ph.D.
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Roy, N.S., Jeong, U., Na, M. et al. Genomic analysis and a consensus chloroplast genome sequence of Prunus yedoensis for DNA marker development. Hortic. Environ. Biotechnol. 61, 859–867 (2020). https://doi.org/10.1007/s13580-020-00265-3
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DOI: https://doi.org/10.1007/s13580-020-00265-3