Characterization of the complete chloroplast genome of black cherry ( Prunus serotina Ehrh.)
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TECHNICAL NOTE
Characterization of the complete chloroplast genome of black cherry (Prunus serotina Ehrh.) Aiping Luan1,2 · Aiping Gao2 · Junhu He2 · Guiqi Bi3 · Yehua He1
Received: 12 July 2017 / Accepted: 8 August 2017 © Springer Science+Business Media B.V. 2017
Abstract Prunus serotina, with high wildlife value, is a tree with edible fruits that is native to North America. In this study, the complete chloroplast (cp) genome of Prunus serotina (Amygdaleae) was determined through Illumina sequencing method. The complete chloroplast genome of P. serotina was 158,788 bp in length and contained a pair of IR regions (26,294 bp) separated by a small single copy region (18,911 bp) and a large single copy region (82,048 bp). The cp genome of P. serotina encoded 130 genes including 84 protein-coding genes, 37 tRNA genes and eight ribosomal RNA genes. The overall GC content of P. serotina cp genome is 36.6%. By phylogenetic analysis using Bayesian method, P. serotina showed the closest relationship with Sohing (Prunus nepalensis). This complete chloroplast genomes can be subsequently used for population genomic studies of P. serotina and provide valuable insight into its in situ and ex situ conservation. Keywords Prunus serotina · Chloroplast genome · Illumina sequencing · Phylogenetic analysis Prunus serotina, the largest native cherries and the only one of commercial value, is found throughout the Eastern United States. It is a species with rapid growth, persistence * Yehua He [email protected] 1
College of Horticulture, South China Agricultural University, Guangzhou, China
2
Institute of Tropical Crop Germplasm, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
3
College of Marine Life Sciences, Ocean University of China, Qingdao, China
in shaded sites, a hermaphrodite reproductive system, high seed production. It is also an important source of mast for various birds, squirrel, deer, turkey, mice, moles and other wildlife. The leaves, twigs, and bark of black cherry contain cyanide in bound form as the cyanogenic glycoside, prunasin (Horsley 1981). Their bark has medicinal properties. In the southern Appalachians, bark is stripped from young black cherries for use in cough medicines, tonics, and sedatives (Fowells 1965; Krochmal et al. 1969). The wild variation is valuable, but vulnerable. Becasue it is threatened by the increasing introduction of preferred germplasm. Moreover, agricultural land division is severely disturbing the environment of the species being developed (Fresnedo-Ramírez et al. 2011). Thus, both in situ and ex situ conservation are urgently needed and recommended for the wild populations. Here, we assembled and analyzed the chloroplast genome of P. serotina based on the next-generation sequencing method. Our aim was to retrieve valuable cp molecular markers, indels and SSRs by comparative analyses with other recently published Prunus cp genomes. The raw reads sequenced by Illumina Hiseq 2000 platform were retrieved from NCBI Sequence Read Archive database under
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