Characterization of the complete chloroplast genome of Fraxinus chiisanensis (Oleaceae), an endemic to Korea
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TECHNICAL NOTE
Characterization of the complete chloroplast genome of Fraxinus chiisanensis (Oleaceae), an endemic to Korea Changkyun Kim1 · Hyuk‑Jin Kim2 · Hoang Dang Khoa Do1 · Joonhyung Jung1 · Joo‑Hwan Kim1 Received: 30 November 2017 / Accepted: 30 December 2017 © Springer Science+Business Media B.V., part of Springer Nature 2018
Abstract Fraxinus chiisanensis (Oleaceae), endemic to South Korea, is a deciduous tree and its natural populations are facing extinction due to habitat deterioration and low germination rates. Here, we characterized the complete chloroplast (cp) genome of F. chiisanensis using next-generation sequencing to provide an effective approach for achieving phylogenetic resolution and a fundamental conservation strategy. The F. chiisanensis cp genome was 155,541 bp in length with a typical quadripartite structure, including the large (86,386 bp) and small (17,767 bp) single-copy regions, separated by a pair of identical inverted repeats (25,694 bp). The genome encoded 132 genes, of which 113 were unique, including 80 protein coding genes, 29 tRNA genes, and 4 rRNA genes. The overall GC content of the cp genome was 37.9%. The Bayesian inference phylogram showed that F. chiisanensis is sister to the rest of the tribe Oleeae within Oleaceae. Keywords Chloroplast genome · Endemic species · Fraxinus chiisanensis · Oleaceae · Oleeae · Phylogenetic relationship Fraxinus chiisanensis Nakai (Oleaceae) is an endemic and deciduous tree found in stream valleys and lower slopes of mountains of South Korea (Chang 2007). This species is characterized by the presence of panicle from leafless lateral bud of previous year, apetalous flower, persistent calyx, and brownish naked bud (Chang et al. 2002). The phylogenetic relationships of F. chiisanensis are contentious. F. chiisanensis was proposed as a putative hybrid between F. chinensis Roxb. and F. mandshurica Rupr. on the basis of its intermediate morphological characteristics (Lee 1980; Song et al. 1988). More recently, Hinsinger et al. (2013) suggested that this species was most closely related to East Asian F. platypoda Oliv. using nuclear and chloroplast (cp) DNA sequences. To solve the problems, use of such molecular analysis as DNA sequence data and microsatellite markers Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12686-017-0969-9) contains supplementary material, which is available to authorized users. * Joo‑Hwan Kim [email protected] 1
Department of Life Science, Gachon University, Seongnam 13120, Republic of Korea
Forest Biodiversity Division, Korea National Arboretum, Pocheon 11186, Republic of Korea
2
has been critical for clarifying the taxonomic identities of species and for understanding the origins of the hybrids (Kim et al. 2012; Park et al. 2016). Natural populations of F. chiisanensis are facing extinction because of destruction of their habitats resulting either directly or indirectly from human activities, low germination rates, and geographically restricted range and p
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