Abstract
Dipentodon is a monotypic genus of Dipentodontaceae and the only species, Dipentodon sinicus, is scattered in southwest China as well as adjacent Myanmar, northeast India and northern Vietnam. This species was evaluated as vulnerable in ‘China Species Red List’. Here, we assembled and characterized the complete chloroplast (cp) genome of D. sinicus using Illumina sequencing data for the first time. The complete cp genome was 158,795 bp in length, consisting of a pair of inverted repeats of 26,587 bp, a large single-copy region of 87,233 bp and a small single-copy region of 18,388 bp. The genome encoded 113 unique genes, including 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenetic analysis based on 16 complete cp genome sequences indicated that D. sinicus is a member of Huerteales, consistent with its position in the latest classification of flowering plants (AGP IV).
References
Angiosperm Phylogeny Group. 2016 An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20.
Dierckxsens N., Mardulyn P. and Smits G. 2017 NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45, e18.
Doyle J. J. and Doyle J. L. 1987 A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11–15.
Fu C. N., Li H. T., Milne R., Zhang T., Ma P. F., Yang J. et al. 2017 Comparative analyses of plastid genomes from fourteen Cornales species: Inferences for phylogenetic relationships and genome evolution. BMC Genomics 18, 956.
Geng Y. F., Hu G. X., Wang S. and Xu J. C. 2018 Complete chloroplast genome of the threatened Rhoiptelea chiliantha (Juglandaceae s.l.). Conserv. Genet. Resour. (in press).
Hu G. X., Takano A., Drew B. T., Liu E. D., Soltis D. E., Soltis P. S. et al. 2018 Phylogeny and staminal evolution of Salvia (Lamiaceae, Nepetoideae) in East Asia. Ann. Bot. 122, 649–668.
Lohse M., Drechsel O., Kahlau S. and 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(Web Server issue), W575–W581.
Ma J. S. and Bartholomew B. 2008 Dipentodontaceae. In Flora of China (ed. C. Y. Wu, P. H. Raven and D. Y. Hong), p. 359. Science Press, Beijing & Missouri Botanical Garden Press, St Louis.
Miller M. A., Pfeiffer W. and Schwartz T. 2010 Creating the CIPRES science gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop (GCE), 2010. IEEE (http://www.phylo.org).
Parks M., Cronn R. and Liston A. 2009 Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol. 7, 84.
Schattner P., Brooks A. N. and Lowe T. M. 2005 The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33, 686–689.
Stamatakis A. 2014 RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313.
Wang S. and Xie Y. 2004 China species red list. Higher Education Press, Beijing.
Wyman S. K., Jansen R. K. and Boore J. L. 2004 Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20, 3252–3255.
Yuan Q. J., Zhang Z. Y., Peng. H. and Ge S. 2008 Chloroplast phylogeography of Dipentodon (Dipentodontaceae) in southwest china and northern Vietnam. Mol. Ecol. 17, 1054–1065.
Zhang M. Y., Fritsch P. W., Ma P. F., Wang H., Lu L. and Li D. Z. 2017 Plastid phylogenomics and adaptive evolution of Gaultheria series Trichophyllae (Ericaceae), a clade from sky islands of the Himalaya-Hengduan Mountains. Mol. Phylogenet. Evol. 110, 7–18.
Acknowledgements
This work was supported by the Natural Science Foundation of Guizhou Province (Qian-Ke-He [2016]1049 and [2016]1033), Application Fundamentals Major Special Projects (Qian-Ke-He JZ [2014] 2002) and the Second Investigation on National Key Protected Wild Plant Resources in Guizhou Province (Lin-Hu-Fa-No. [2012] 87 and Qian-Lin-Hu-Tong-No. [2013] 251).
Author information
Authors and Affiliations
Corresponding author
Additional information
Corresponding editor: Manoj Prasad
Rights and permissions
About this article
Cite this article
An, MT., Cui, XY., Yang, JX. et al. The complete chloroplast genome of the threatened Dipentodon sinicus (Dipentodontaceae). J Genet 98, 4 (2019). https://doi.org/10.1007/s12041-018-1051-4
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s12041-018-1051-4