Genomic analysis and a consensus chloroplast genome sequence of Prunus yedoensis for DNA marker development
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Genomic analysis and a consensus chloroplast genome sequence of Prunus yedoensis for DNA marker development Neha Samir Roy1 · Ukhan Jeong2 · Minho Na2 · Ik‑Young Choi1 · Eun Ju Cheong2 Received: 31 October 2019 / Revised: 19 May 2020 / Accepted: 17 June 2020 © Korean Society for Horticultural Science 2020
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. Keywords Chloroplast DNA assembly · Genetic diversity · Illumina · Prunus yedoensis · Standard reference
1 Introduction The genus Prunus belongs to the subfamily Amygdaloideae and family Rosaceae and comprises approximately 250 species (Lee and Wen 2001; Potter et al. 2007). P. yedoensis (so-called ‘Somei-yoshino’) is the most widespread and common of these species, and is distributed throughout East Asia (Cheng et al. 1999; Cho et al. 2014) and the United Communicated by Tae-Ho Han, Ph.D. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13580-020-00265-3) contains supplementary material, which is available to authorized users. * Eun Ju Cheong [email protected] 1
Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, South Korea
Division of Forest Science, Kangwon National University, Chuncheon 24341, South Korea
2
States (Bailey 1976). There has been confusion over the name, origin, and delimitation of the wild and cultivated taxa of this species (Baek et al. 2018). Recently, wild P. yedoensis was reporte
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