Abstract
Eleutherococcus brachypus: (Harms) Nakai (Araliaceae) is an endangered shrub that it is endemic to western China. In this study, we characterized the complete nucleotide sequence of the chloroplast (cp) genome in E. brachypus. The total length of the cp genome was 156,981 bp, including a large single copy (LSC) region of 86,921 bp, a small single copy (SSC) region of 18,184 bp, and a pair of inverted repeats (IRs) comprising 25,938 bp. The cp genome of E. brachypus contained 114 genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. In total, 15 genes comprising tRNA-Lys (UUU), tRNA-Gly (UCC), tRNA-Leu (UAA), tRNA-Val (UAC), tRNA-Ile (GAU), tRNA-Ala (UGC), rps16, atpF, rpoC1, petB, petD, rps16, rpl2, ndhB, and ndhA contained a single intron, and three genes contained two introns, i.e., ycf3, clpP, and rps12. The GC contents of the whole cp genome, LSC region, SSC region, and IR region were 38.0, 36.2, 32.0, and 43.0% respectively, which are similar to those in other Araliaceae plants. Phylogenetic analysis suggested that E. brachypus has a close relationship with congeneric E. gracilistylus.
This is a preview of subscription content, log in via an institution to check access.
References
Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WE, Wetter T, Suhai S (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14:1147–1159
Doyle JJ (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Hahn C, Bachmann L, Chevreux B (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads-a baiting and iterative mapping approach. Nucl Acids Res 41:e129
He J, Zeng CJ (1978) Flora of China, vol 54. Science Press, Beijing, p 104–106
Hu HB, Fan J (2009) Studies on chemical constituents of Acanthopanax brachypus (II). Chin Pharm J 44:1137–1140
Hu HB, Fan J (2012) Chemical constituents from Acanthopanax brachypus. Biochem Syst Ecol 43:67–72
Hu HB, Zhang XW, Wu Y (2014) Antitumor activity of stilbenoids and flavonoids isolated from Acanthopanax brachypus. Russ J Gen Chem 84:1434–1441
Lohse M, Drechsel O, Kahlau S, Bock R (2013) OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucl Acids Res 41:W575-W581
Patel RK, Jain M (2012) NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One 7:e30619
Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818
Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analysis with thousands of taxa and mixed models. Bioinformatics 22:2688–2690
Wang ZL, Liu LD, Tian GW, Shen JH (1997) Flowering and pollination biology of Eleutherococcus brachypus. Biodiv Sci 5:251–256
Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255
Yue CL, Jiang H, Wei W, Chai ZL (2003) Analysis of endangering process and factors of Eleutherococcus brachypus population. Chin J Appl Environ Biol 9:24–27
Acknowledgements
This study was funded by the project of the fourth national Chinese medicine resources census in Min County and Tanchang County, and the Scientific Research Project of the Higher Education Institutions of Gansu Province (2017A-085).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Zhang, YJ., Gao, H., Chen, Y. et al. Characterization of the complete plastid genome sequence of eleutherococcus brachypus (araliaceae), an endangered shrub in China. Conservation Genet Resour 11, 295–297 (2019). https://doi.org/10.1007/s12686-018-1012-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12686-018-1012-5