Characterization of the complete chloroplast genome of Idesia polycarpa
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TECHNICAL NOTE
Characterization of the complete chloroplast genome of Idesia polycarpa Wenlu Yang1 • Weiwei Wang1 • Lei Zhang1 • Zeyuan Chen1 • Xinyi Guo1 Tao Ma1
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Received: 17 May 2016 / Accepted: 23 May 2016 Ó Springer Science+Business Media Dordrecht 2016
Abstract The whole chloroplast (cp) genome sequence of Idesia polycarpa has been characterized from Illumina pair-end sequencing. The complete cp genome was 157,017 bp in length, containing a large single copy region (LSC) of 84,787 bp and a small single copy region (SSC) of 16,512 bp, which were separated by a pair of 27,859 bp inverted repeat regions (IRs). The genome contained 130 genes, including 86 protein-coding genes (77 PCG species), 36 tRNA genes (29 tRNA species) and 8 ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 20 gene species occur in double copies. The overall AT content of I. polycarpa cp genome is 63.3 %, while the corresponding values of the LSC, SSC and IR regions are 65.5, 69.4 and 58.1 %, respectively. Further, phylogenetic analysis suggested that I. polycarpa is closely related to the genera of Salix and Populus. Keywords Idesia polycarpa Chloroplast genome Phylogenetic analysis Idesia polycarpa Maxim. is an important woody oil plant with a good development and utilization value and an
Wenlu Yang and Weiwei Wang have contributed equally to this work.
Electronic supplementary material The online version of this article (doi:10.1007/s12686-016-0553-8) contains supplementary material, which is available to authorized users. & Tao Ma [email protected] 1
MOE Key Laboratory of Bio-Resources and EcoEnvironment, College of Life Science, Sichuan University, Chengdu, China
excellent afforestation tree species, which is mainly distributed in the provinces to the south of Qinling Mountain and Huaihe River in China. The I. polycarpa fruit oil has great potential of using as a feedstock for medicine, food as well as biodiesel production in terms of reducing the producing cost (Yang et al. 2009) owing to the abundance of unsaturated fatty acids and multiplex vitamin in its fruits, which make it good to one who have cardiovascular or hyperlipidemia disease (Shui et al. 2004). However, largely due to anthropogenic over-exploitation and natural habitat’s fragmentation of species, the wild resources of I. polycarpa have been dramatically decreased and need urgent conservation. A good knowledge of its genetics information would contribute to the formulation of protection strategy. In this study, we assembled and characterized the complete chloroplast genome sequence of I. polycarpa based on the Illumina pair-end sequencing data. The fresh leaves of a single individual of I. polycarpa were sampled from Qingchuan (Sichuan, China; 105°170 56.8500 E, 32°310 40.6200 N), and were used for the total genomic DNA extraction with the modified CTAB method (Doyle 1987). The whole-genome sequencing was conducted with 150 bp pair-end reads on the Illumina Hiseq Platform (Illumina, San Diego, CA). In total, about
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