Complete chloroplast genome of Cercidiphyllum japonicum (Cercidiphyllaceae), a tertiary relic endangered tree
- PDF / 2,000,084 Bytes
- 3 Pages / 595.276 x 790.866 pts Page_size
- 7 Downloads / 186 Views
TECHNICAL NOTE
Complete chloroplast genome of Cercidiphyllum japonicum (Cercidiphyllaceae), a tertiary relic endangered tree Hao Qin1 · Na Duan1 · Meng‑ben Wang1 · Bing‑bing Liu1 Received: 7 December 2017 / Accepted: 30 December 2017 © Springer Science+Business Media B.V., part of Springer Nature 2018
Abstract The dioecious relic Cercidiphyllum japonicum is one of two species of the sole genus Cercidiphyllum (Cercidiphyllaceae). Using an Illumina platform, we sequenced its complete chloroplast genome. Our study reveals that C. japonicum have a typical cp genome of 159,854 bp in length, comprised of a large single-copy region of 88,035 bp, a small single-copy region of 30,535 bp, and two inverted repeat regions of 20,642 bp, respectively. A total of 131 genes, 84 of which are protein coding genes, 37 tRNA genes, eight rRNA genes and one pseudogenes were identified. Phylogenetic analysis indicate that C. japonicum is closely related to the species of Sinowilsonia henryi. Keywords Cercidiphyllum japonicum · Chloroplast genome · Phylogenetic analysis Cercidiphyllum japonicum Sieb.Et Zucc. (Cercidiphyllaceae) is a tertiary relic tall canopy tree and only occurs as a species of east Asian flora (Siebold and Zuccarini 1846). As a cretaceous relic, it is an important species in the evolutionary study of the origin of flora in the Tertiary Period (Sun 1980). In addition, its fruits, leaves and bark can be used as medicines, has important economic value. However, because of the small number of populations, C. japonicum is treated as “endangered” in China (Fu 1992) and it has been registered on the China Species Red List (Wang and Xie 2004). It is thus urgent to take effective measures to conserve this endangered and rare species. In plants, chloroplast DNA (cpDNA) provided valuable phylogenetic signals for all kinds of lineages, owing to its conserved genome structures and comparatively high substitution rates (Wu and Ge 2012). Hence, a good knowledge of its genomic information would have made it easy to investigate genetic variations and contribute to the preservation and stabilization of local ecosystems. Herein, we first report the complete chloroplast genome of C. japonicum. It will aid in in-depth evolutionary study of the origin of flora in the Tertiary Period. The genetic sequence information will also have valuable applications for chloroplast genetic engineering. * Bing‑bing Liu [email protected] 1
Institute of Loess Plateau, Shanxi University, Taiyuan 030006, Shanxi, China
The fresh leaves of a single individual of C. japonicum were sampled from Lishan National Nature Reserve (Shanxi, China; 111.55 E, 35.18 N), and were used for the total genomic DNA extraction with a DNeasy Plant Mini Kit (QIAGEN, Valencia, California, USA). The whole-genome sequencing was conducted with 150 bp pair-end reads on the Illumina Hiseq Platform (Illumina, San Diego, CA). In total, about 649 million high quality clean reads were obtained and used for the cp genome de novo assembly by the program NOVOPlasty (Dierckxsens et al. 2
Data Loading...
