The complete chloroplast genome of a staple food of the giant panda, Fargesia denudata (Poaceae)
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TECHNICAL NOTE
The complete chloroplast genome of a staple food of the giant panda, Fargesia denudata (Poaceae) Yue Zhang1 · Jinyuan Su1 · Junqing Li1 · Fang K. Du1
Received: 26 February 2017 / Accepted: 10 March 2017 © Springer Science+Business Media Dordrecht 2017
Abstract Fargesia denudata: T. P. Yi (Poaceae), endemic to China, is the most important food for the giant panda. Here we reported the complete chloroplast (cp) genome sequence for the F. denudate using Illumina high-throughput sequencing technology. The F. denudata cp genome is 133,784 bp long, and the overall GC content is 39.69%. The F. denudata cp genome encodes 129 unique genes, including 82 protein-coding genes (PCG), 39 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The majority of the genes occur as single-copy sequences, and 19 genes are duplicated in the inverted repeats (IRs). Further, phylogenetic analysis suggests that F. denudata is close to Fargesia nitida. Keywords Fargesia denudate · Staple food of the giant panda · Conservation · Chloroplast genome The chloroplast (cp) is the organelle of photosynthesis, which provides the essential energy for plants and algae (Dyall et al. 2004). The cp genomes of most angiosperms plants are typically circular DNA, containing a pair of inverted repeats (IRs), one large single copy region (LSC) and one small single copy region (SSC). Since the first report of the complete cp genome sequences of the tobacco (Shinozaki et al. 1986), the number of completely sequenced cp genomes has increased significantly. Until 2015, more than 300 complete chloroplast genome * Fang K. Du [email protected] 1
Key Laboratory for Forest Resources and Ecosystem Processes of Beijing, College of Forestry, Beijing Forestry University, Beijing 100083, People’s Republic of China
sequences from angiosperm species have been deposited at NCBI, and the information is publicly available (http:// www.ncbi.nlm.nih.gov/genome). F. denudata is a variety of the Fargesia genus (Poaceae) in Southern Gansu Province and Northern Sichuan Province of China at elevations of 2100–3100 m (Huang and Yang. 1990). It is one of the most important staple food bamboos for the giant panda (Ailuropoda melanoleuca). However, F. denudata died across a large area after flowering in the 1970s, seriously threatening the giant panda’s survival (Qin 1985). There are many studies on its physiology and ecology of the species, such as on its photosynthetic characteristics (Yang 2011), however, is still little research on heredity (Lv et al. 2016). Here we reported the complete cp genome sequence of F. denudate, which will provide a genetic resource for Fargesia species and can play an important role in bamboo phylogenetic research due to its maternal inheritance and highly conserved characteristics. Fresh leaves of F. denudata were collected from a northern part of Wanglang National Nature Reserve of Pingwu County, Sichuan Province, China (32°49′–33°02′N, 103°50′–104°58′E) (Li and Shen 2012), and vouchers were deposited at Beijing
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