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Genome-wide identification and functional analysis of JmjC domain-containing genes in flower development of Rosa chinensis

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We genome-wide identified 28 JmjC domain-containing genes, further spatio-temporal expression profiling and genetic analysis defined them as epigenetic regulators in flowering initiation of Rosa chinensis.

Abstract

The JmjC domain-containing histone demethylases play critical roles in maintaining homeostasis of histone methylations, thus are vital for plant growth and development. Genome-wide identification of the JmjC domain-containing genes have been reported in several species, however, no systematic study has been performed in rose plants. In this paper, we identified 28 JmjC domain-containing genes from the newly published genome database of Rosa chinensis. The JmjC domain-containing proteins in R. chinensis were divided into seven groups, KDM3 was the largest group with 13 members, and JmjC domain-only A and KDM5B were the smallest clades both with only one member. Although all the JmjC domain proteins having a conserved JmjC domain, the gene and protein structure experienced differentiation and specification during the evolution, especially in KDM3 clade, one gene (RcJMJ40) was found carrying site deletions for cofactors Fe (II) and α-KG binding which were crucial for demethylase activities, three genes (RcJMJ41, RcJMJ43 and RcJMJ44) had no intron while two of them had tandem JmjC domains. Spatial expression pattern analysis of these JmjC domain-containing genes in different tissues showed most of them were highly expressed in reproductive tissues such as floral meristem and closed flowers than vegetative tissues, demonstrating their important functions in developmental switch from vegetative to reproductive growth of roses. Temporal expression profiling indicated majority of JmjC domain-containing genes from R. chinensis fluctuated along with floral bud differentiation and development, further proving their essential roles in flower organogenesis. VIGS induced silencing of RcJMJ12 led to delayed flowering time, and decreased the expression levels of flowering integrator such as RcFT, RcSOC1, RcFUL, RcLFY and RcAP1, therefore providing the genetic evidence of RcJMJ12 in flowering initiation. Collectively, spatio-temporal expression profiling and genetic analysis defined the JmjC domain-containing genes as important epigenetic regulators in flower development of R. chinensis.

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Acknowledgements

This work was supported by the NSFC-XINJIANG joint foundation (U1803102) and NSFC (31972449) granted to Changquan Wang, and the China Postdoctoral Science Foundation (2016M600425) and the NSFC (31801890) granted to Jinyi Liu, and a Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions.

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  1. Yuwei Dong and Jun Lu have contributed equally to this paper.

Authors and Affiliations

  1. College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

    Yuwei Dong, Jun Lu, Jinyi Liu, Abdul Jalal & Changquan Wang

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  1. Yuwei Dong
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  2. Jun Lu
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  3. Jinyi Liu
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Methodology, YD; formal analysis, JL; data curation, JL; validation, JA; writing—original draft, CW.

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Correspondence to Changquan Wang.

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Fig. S1. Statistics of JmjC domain gene family in 22 species of green plants. (PDF 241 kb)

11103_2019_955_MOESM2_ESM.pdf

Fig. S2. The represented RT-PCR data of JmjC-domain containing genes in different tissues of Rosa chinensis. (PDF 513 kb)

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Fig. S3. The represented RT-PCR data of JmjC-domain containing genes across different floral organ initiation stages of Rosa chinensis. (PDF 472 kb)

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Fig. S4. Expression profile of JmjC-domain containing genes across different floral organ initiation stages from Rosa chinensis organized according to the expression pattern. (PDF 176 kb)

11103_2019_955_MOESM5_ESM.pdf

Fig. S5. The expression levels of RcJMJ11 and RcJMJ13 in RcJMJ12-silenced seedlings. Relative expression levels of RcJMJ11 (a) and RcJMJ13 (b) were determined by qRT-PCR in three independent RcJMJ12 silenced lines and mock treated seedlings of R. chinensis, RcGAPDH was used as an internal control. Three biological replicates were performed for each experiment. (PDF 68 kb)

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Dong, Y., Lu, J., Liu, J. et al. Genome-wide identification and functional analysis of JmjC domain-containing genes in flower development of Rosa chinensis. Plant Mol Biol 102, 417–430 (2020). https://doi.org/10.1007/s11103-019-00955-2

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