Abstract
Rhoiptelea chiliantha is the only species of traditionally defined family Rhoipteleaceae which is confined to S Guizhou, SE Yunnan, N and W Guangxi of China as well as N Vietnam, and is evaluated as vulnerable (VU) in “The IUCN Red List Threatened Species” and “Chinese Species Red List”. Here, we de novo assembled the complete chloroplast (cp) genome of R. chiliantha using Illumina sequencing data for the first time. The whole cp genome was 161,692 bp in length consisting of a pair of inverted repeat (IRa and IRb) regions of respectively 25,335 bp, a small single-copy region of 23,659 bp and a large single-copy region of 89,039 bp. The genome encoded 116 unique genes including 85 protein-coding genes, 27 tRNA genes and four rRNA genes. Phylogenetic analysis based on 21 complete cp genome sequences indicates that R. chiliantha is sister to the traditionally defined walnut family (Juglandaceae s.s.) and supports to merge Rhoipteleaceae into Juglandaceae s.l.
References
Angiosperm Phylogeny Group (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc 161:105–121
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
Chen ZD, Wang XQ, Sun HY, Han Y, Zhang ZX, Zou YP, Lu AM (1998) Systematic position of the Rhoipteleaceae: evidence from nucleotide sequences of rbcL gene. Acta Phytotaxonomica Sin 36:1–7
Dierckxsens N, Mardulyn P, Smits G (2017) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res 45:e18
Fu LG, Xin YQ, Bruce B (2003) Rhoipteleaceae. In: Wu CY, Raven PH, Hong DY (eds) Flora of China, vol 5. Science Press, Beijing & Missouri Botanical Garden Press, St. Louis, p. 20
Kuang KZ (1960) De familia monotypica Rhoipteleaceae. Acta Bot Sin 9:43–47
Manos PS, Stone DE (2001) Evolution, phylogeny, and systematics of the Juglandaceae. Ann Mo Bot Gard 88:231–269
Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop (GCE), 2010, IEEE
Shi C, Hu N, Huang H, Gao J, Zhao YJ et al (2012) An improved chloroplast DNA extraction procedure for whole plastid genome sequencing. PLoS ONE 7:e31468
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313
Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S (2017) GeSeq-versatile and accurate annotation of organelle genomes. Nucleic Acids Res 45:6–11
Wang S, Xie Y (2004) Chinese species red list. Higher Education Press, Beijing
World Conservation Monitoring Centre (1998). Rhoiptelea chiliantha. IUCN Red List Threatened Species 1998:e.T32371A9701413
Acknowledgements
This work was supported by the Natural Science Foundation of Guizhou Province [(2016)1049].
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare no conflicts of interest.
Rights and permissions
About this article
Cite this article
Geng, YF., Hu, GX., Wang, S. et al. Complete chloroplast genome of the threatened Rhoiptelea chiliantha (Juglandaceae s.l.). Conservation Genet Resour 11, 317–319 (2019). https://doi.org/10.1007/s12686-018-1021-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12686-018-1021-4