Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 May 18;7(1):2073.
doi: 10.1038/s41598-017-02252-8.

Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots

Niu Zhitao  1 , Zhu Shuying  1 , Pan Jiajia  1 , Li Ludan  1 , Sun Jing  1 , Ding Xiaoyu  2
Affiliations

Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots

Niu Zhitao et al. Sci Rep. .

Abstract

Dendrobium is one of the largest genera in Orchidaceae, comprising about 800-1500 species mainly distributed in tropical Asia, Australasia, and Australia. There are 74 species and two varieties of this genus in China. Because of their ornamental and commercial value, Dendrobium orchids have been studied at low taxonomic levels. However, structural changes and effective mutational hotspots of Dendrobium plastomes have rarely been documented. Here, 30 Dendrobium plastomes were compared, comprising 25 newly sequenced in this study and five previously published. Except for their differences in NDH genes, these plastomes shared identical gene content and order. Comparative analyses revealed that the variation in size of Dendroubium plastomes was associated with dramatically changed length of InDels. Furthermore, ten loci were identified as the top-ten mutational hotspots, whose sequence variability was almost unchanged with more than 10 plastomes sampled, suggesting that they may be powerful markers for Dendrobium species. In addition, primer pairs of 47 polymorphic microsatellites were developed. After assessing the mean BS values of all combinations derived from the top-ten hotspots, we recommend that the combination of five hotspots-trnT-trnL, rpl32-trnL, clpP-psbB, trnL intron, and rps16-trnQ-should be used in the phylogenetic and identification studies of Dendrobium.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1
InDel distribution among different Dendrobium plastomes. The InDel mutations were determined based on the comparison between plastoms of each tested Dendrobium species and D. officinale. Histograms with different colors indicate the numbers of InDels in LSC, SSC, and IR regions.
Figure 2
Figure 2
The sequence variability (%) and GC content among the 92 syntenic intergenic and intronic loci from Dendrobium plastomes. The red and green lines represent the sequence variability (%) and GC content of each locus, respectively. These syntenic loci are oriented according to their locations in the plastome. The top-ten syntenic intergenic and intronic loci with the highest sequence variability (%) in the tested Dendrobium plastomes were indicated with blue box.
Figure 3
Figure 3
Relation between the number of combined hotspots and the mean value of bootstrap (BS). The mean (±SD) BS values were calculated based on different numbers of combined hotspots. Regression analysis: R2 = 0.904, y = 3.64x + 49.38. The plateau of the mean BS value reached 71% when five hotspots were combined.
Figure 4
Figure 4
Maximum likelihood trees based on different plastid DNA data.
See this image and copyright information in PMC

References

    1. Wood, H. P. The Dendrobiums (Timber Press, 2006).
    1. Adams P. Systematics of Dendrobiinae (Orchidaceae), with special reference to Australian taxa. Botanical Journal of the Linnean Society. 2011;166:105–126. doi: 10.1111/j.1095-8339.2011.01141.x. - DOI
    1. Xiang XG, et al. Molecular systematics of Dendrobium (Orchidaceae, Dendrobieae) from mainland Asia based on plastid and nuclear sequences. Molecular Phylogenetics and Evolution. 2013;69:950–960. doi: 10.1016/j.ympev.2013.06.009. - DOI - PubMed
    1. The State Pharmacopoeia Commission of P. R. China. Pharmacopoeia of the People’s Republic of China 2010, Set of 3 (China Medical Science and Technology Press, 2010).
    1. Feng S, et al. Molecular identification of Dendrobium species (Orchidaceae) based on the DNA barcode ITS2 region and its application for phylogenetic study. International Journal of Molecular Sciences. 2014;16:21975–21988. doi: 10.3390/ijms160921975. - DOI - PMC - PubMed

Publication types

LinkOut - more resources