The complete chloroplast genome of Daphne kiusiana , an evergreen broad-leaved shrub on Jeju Island
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TECHNICAL NOTE
The complete chloroplast genome of Daphne kiusiana, an evergreen broad-leaved shrub on Jeju Island Won‑Bum Cho1 · Eun‑Kyeong Han1 · Goya Choi2 · Jung‑Hyun Lee1
Received: 15 May 2017 / Accepted: 19 May 2017 © Springer Science+Business Media Dordrecht 2017
Abstract Plants of Daphne kiusiana on Jeju Island exhibit morphologically and genetically unique traits. Its taxonomic entity is still unclear and populations are decreasing in size because of human activity. Taxonomic delimitation and conservation efforts are required at the genomic level. We determined the complete chloroplast (cp) genome of this endangered species on Jeju Island, South Korea. Its sequence is 171,491 bp long, and comprises a pair of 41,891 bp inverted repeats, a large-singlecopy (LSC) region (85,028 bp), and a diminished smallsingle-copy region (2681 bp). The cp genome has 135 genes, including 89 that encode proteins, plus 38 tRNAs, and eight rRNAs. Five genes (rpl32, ndhF, accD, clpP, and ndhK) are pseudogenized or lost in its cpDNA. When compared with that of a related species, Aquilaria sinensis, its LSC region contains a large inversion event between rbcL and rps12 that caused pseudogenization of clpP and accD. Keywords Chloroplast genome · Conservation · Daphne kiusiana · Jeju Island
* Jung‑Hyun Lee [email protected] Won‑Bum Cho [email protected] Eun‑Kyeong Han [email protected] Goya Choi [email protected] 1
Department of Biology Education, Chonnam National University, Gwangju 61186, Republic of Korea
2
K‑herb Research Center, Korea Institute of Oriental Medicine, Daejeon 34054, Republic of Korea
Jeju Island, created by volcanic eruptions 2 million years ago (Jo et al. 2012), was designated as a UNESCO Biosphere Reserve in 2002, based on its high endemism, unique elevational zonation of vegetation, and untouched environments (Choi et al. 2014). Its basal zone is dominated by species of evergreen broad-leaved trees that are also disjunctively located along the north-central margin of climatically equivalent vegetation zones in eastern China and on southwestern main islands of Japan. Because of its geographical and evolutionary significance in East Asia with the Quaternary oscillations, plants on Jeju Island are of interest to many scientists who conduct phylogeographic, systematic, and conservation research (Chung et al. 2010; Choi et al. 2013; Lee et al. 2014). Daphne kiusiana Miq. var. kiusiana is an evergreen broad-leaved shrub endemic to Korea (mostly on Jeju Island) and Japan. However, populations on Jeju Island are extremely restricted to only a few areas, where plants are being managed as endangered organisms (Korea National Arboretum 2008). They also exhibit morphologically and genetically unique traits when compared with populations found elsewhere (Lee et al. 2013, 2017). Such features (not negligible and may be treated as another species) are associated with only this shrub, which occurs among many evergreen trees distributed on the Jeju Island. Despite its importance, its population size is c
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