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
. 2022 Aug 9;11(16):2077.
doi: 10.3390/plants11162077.

Genome-Wide Identification and Spatial Expression Analysis of Histone Modification Gene Families in the Rubber Dandelion Taraxacum kok-saghyz

Francesco Panara  1 , Carlo Fasano  1 , Loredana Lopez  1 , Andrea Porceddu  2 , Paolo Facella  1 , Elio Fantini  1 , Loretta Daddiego  1 , Giorgio Perrella  3
Affiliations

Genome-Wide Identification and Spatial Expression Analysis of Histone Modification Gene Families in the Rubber Dandelion Taraxacum kok-saghyz

Francesco Panara et al. Plants (Basel). .

Abstract

Taraxacum kok-saghyz (Tks), also known as the Russian dandelion, is a recognized alternative source of natural rubber quite comparable, for quality and use, to the one obtained from the so-called rubber tree, Hevea brasiliensis. In addition to that, Tks roots produce several other compounds, including inulin, whose use in pharmaceutical and dietary products is quite extensive. Histone-modifying genes (HMGs) catalyze a series of post-translational modifications that affect chromatin organization and conformation, which, in turn, regulate many downstream processes, including gene expression. In this study, we present the first analysis of HMGs in Tks. Altogether, we identified 154 putative Tks homologs: 60 HMTs, 34 HDMs, 42 HATs, and 18 HDACs. Interestingly, whilst most of the classes showed similar numbers in other plant species, including M. truncatula and A. thaliana, HATs and HMT-PRMTs were indeed more abundant in Tks. Composition and structure analysis of Tks HMG proteins showed, for some classes, the presence of novel domains, suggesting a divergence from the canonical HMG model. The analysis of publicly available transcriptome datasets, combined with spatial expression of different developmental tissues, allowed us to identify several HMGs with a putative role in metabolite biosynthesis. Overall, our work describes HMG genomic organization and sets the premises for the functional characterization of epigenetic modifications in rubber-producing plants.

Keywords: Taraxacum kok-saghyz; gene expression; histone modification; natural rubber.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic tree of SDG (A) and JMJ (B) proteins of Taraxacum kok-saghyz and Arabidopsis thaliana (in colour according to their respective classes). The numbers near the tree branches represent bootstrap values.
Figure 2
Figure 2
Domain composition and intron-exon structure of Taraxacum kok-saghyz HMTs and HDMs.
Figure 3
Figure 3
Phylogenetic tree of HAG (A) and HDA (B) proteins of Taraxacum kok-saghyz and Arabidopsis thaliana (in colour according to their respective classes). The numbers near the tree branches represent bootstrap values.
Figure 4
Figure 4
Domain composition and intron–exon structure of Taraxacum kok-saghyz HAGs.
Figure 5
Figure 5
Heat map of TksHMTs and TksHDMs in different organs and developmental stages. The main clusters are indicated by square brackets. Genes with higher expression are indicated in bold. Asterisks indicate the genes analyzed by qPCR.
Figure 6
Figure 6
Heat map of TksHATs and TksHDACs in different organs and developmental stages. The main clusters are indicated by square brackets. Genes with a higher expression are indicated in bold. Asterisks indicate the genes analysed by qPCR.
Figure 7
Figure 7
qPCR expression analysis of 13 HM genes in Taraxacum kok-saghyz developing leaves (DL), fully developed leaves (FL), root tips (RT), and mature roots (R). (a) Absolute quantification (mean ± SD fg/μL) of HM genes with an average expression above 1 fg/μL; (b) Absolute quantification (mean ± SD ag/μL) of HMG genes with an average expression below 1 fg/μL.
See this image and copyright information in PMC

References

    1. Sharifi-Rad M., Roberts T.H., Matthews K.R., Bezerra C.F., Morais-Braga M.F.B., Coutinho H.D.M., Sharopov F., Salehi B., Yousaf Z., Sharifi-Rad M., et al. Ethnobotany of the Genus Taraxacum—Phytochemicals and Antimicrobial Activity. Phytother. Res. 2018;32:2131–2145. doi: 10.1002/ptr.6157. - DOI - PubMed
    1. Schütz K., Carle R., Schieber A. Taraxacum-A Review on Its Phytochemical and Pharmacological Profile. J. Ethnopharmacol. 2006;107:313–323. doi: 10.1016/j.jep.2006.07.021. - DOI - PubMed
    1. Van Beilen J.B., Poirier Y. Establishment of New Crops for the Production of Natural Rubber. Trends Biotechnol. 2007;25:522–529. doi: 10.1016/j.tibtech.2007.08.009. - DOI - PubMed
    1. Kirschner J., Štěpánek J., Černý T., De Heer P., van Dijk P.J. Available Ex Situ Germplasm of the Potential Rubber Crop Taraxacum Koksaghyz Belongs to a Poor Rubber Producer, T. Brevicorniculatum (Compositae-Crepidinae) Genet. Resour. Crop Evol. 2013;60:455–471. doi: 10.1007/s10722-012-9848-0. - DOI
    1. Mooibroek H., Cornish K. Alternative Sources of Natural Rubber. Appl. Microbiol. Biotechnol. 2000;53:355–365. doi: 10.1007/s002530051627. - DOI - PubMed