Genome-wide identification and expression profiling of SET DOMAIN GROUP family in Dendrobium catenatum

Abstract

Background: Dendrobium catenatum, as a precious Chinese herbal medicine, is an epiphytic orchid plant, which grows on the trunks and cliffs and often faces up to diverse environmental stresses. SET DOMAIN GROUP (SDG) proteins act as histone lysine methyltransferases, which are involved in pleiotropic developmental events and stress responses through modifying chromatin structure and regulating gene transcription, but their roles in D. catenatum are unknown.

Results: In this study, we identified 44 SDG proteins from D. catenatum genome. Subsequently, comprehensive analyses related to gene structure, protein domain organization, and phylogenetic relationship were performed to evaluate these D. catenatum SDG (DcSDG) proteins, along with the well-investigated homologs from the model plants Arabidopsis thaliana and Oryza sativa as well as the newly characterized 42 SDG proteins from a closely related orchid plant Phalaenopsis equestris. We showed DcSDG proteins can be grouped into eight distinct classes (I~VII and M), mostly consistent with the previous description. Based on the catalytic substrates of the reported SDG members mainly in Arabidopsis, Class I (E(z)-Like) is predicted to account for the deposition of H3K27me2/3, Class II (Ash-like) for H3K36me, Class III (Trx/ATX-like) for H3K4me2/3, Class M (ATXR3/7) for H3K4me, Class IV (Su (var)-like) for H3K27me1, Class V (Suv-like) for H3K9me, as well as class VI (S-ET) and class VII (RBCMT) for methylation of both histone and non-histone proteins. RNA-seq derived expression profiling showed that DcSDG proteins usually displayed wide but distinguished expressions in different tissues and organs. Finally, environmental stresses examination showed the expressions of DcASHR3, DcSUVR3, DcATXR4, DcATXR5b, and DcSDG49 are closely associated with drought-recovery treatment, the expression of DcSUVH5a, DcATXR5a and DcSUVR14a are significantly influenced by low temperature, and even 61% DcSDG genes are in response to heat shock.

Conclusions: This study systematically identifies and classifies SDG genes in orchid plant D. catenatum, indicates their functional divergence during the evolution, and discovers their broad roles in the developmental programs and stress responses. These results provide constructive clues for further functional investigation and epigenetic mechanism dissection of SET-containing proteins in orchids.

Keywords: Environmental stress; Expression profiling; Histone lysine methylation; SDG; SET domain.

Fig. 1

Phylogenetic analysis of SDGs in D. catenatum, P. equestris, Arabidopsis and rice. This tree includes 44 SET domain-containing proteins from D. catenatum, 42 from P. equestris, 49 from A. thaliana and 46 from O. sativa. The 181 SET domain-containing proteins were divided into eight classes combined with the further phylogenetic analysis in Fig. 4. SDGs amino acid sequences were aligned using Clustalx, and the phylogenetic tree was constructed using MEGA7 with the following settings: Tree Inference as Neighbor-Joining (NJ); Include Sites as Pairwise deletion option for total sequence analyses; Substitution Model: p-distance; and Bootstrap test of 1000 replicates for internal branch reliability. Bootstrap values > 50% are shown. Dc, D. catenatum; Pe, P. equestris; At, A. thaliana; Os, O. sativa

Fig. 2

Domain organization and gene structure of the Class I DcSDGs. The NJ tree was generated using MEGA7 with parameter settings as Fig. 1 based on full-length amino acid sequences of Class I SDG proteins in D. catenatum, P. equestris, Arabidopsis and rice. The number along the tree branch indicates bootstrap value. Different conserved protein domains (SANT, CXC, and SET) are colored as indicated. Gene structures of SDGs in each species were indicated in distinct colors. The solid boxes represent exons and black lines represent introns

Fig. 3

Domain organization and gene structure of the Class II SDGs. The NJ tree was generated using MEGA7 with parameter settings as Fig. 1 based on full-length amino acid sequences of Class II SDG proteins in D. catenatum, P. equestris, Arabidopsis and rice. The number along the tree branch indicates bootstrap value. Different conserved protein domains (AWS, PHD, zf-CW, SET and PostSET) are colored as indicated. Gene structures of SDGs in each species were indicated in distinct colors. The solid boxes represent exons and black lines represent introns

Fig. 4

Domain organization and gene structure of the DcSDGs in Classes III, M and IV. The NJ tree was generated using MEGA7 with parameter settings as Fig. 1 based on full-length amino acid sequences of Class III/M/IV SDGs in D. catenatum, P. equestris, Arabidopsis and rice. The number along the tree branch indicates bootstrap value. Different conserved protein domains are colored as indicated. Gene structures of SDGs in each species were indicated in distinct colors. The solid boxes represent exons and black lines represent introns

Fig. 5

Domain organization and gene structure of the class V DcSDGs. The NJ tree was generated using MEGA7 with parameter settings as Fig. 1 based on full-length amino acid sequences of Class-V SDGs in D. catenatum, P. equestris, Arabidopsis and rice. The number along the tree branch indicates bootstrap value. Different conserved protein domains are colored as indicated. Gene structures of SDGs in each species were indicated in distinct colors. The solid boxes represent exons and black lines represent introns

Fig. 6

Tissue and organ expression profiles of DcSDGs across different tissues and organs. Hierarchical clustering of expression profiles of DcSDGs across different tissues and organs. Heat map generated using the software MultiExperiment Viewer (MeV) shows relative organ expression profiles of DcSDG genes in D. catenatum. Color scale at the top represents log 2 expression values, green and red represent low and high levels of transcript abundances, respectively. Lf: leaf, Ro: root, Gr: green root tip, Wr: white part of root, St: stem, Fb: flower bud, Se: sepal, Lb: labellum (lip), Po: pollinia, and Gs, gynostemium (column)

Fig. 7

Expression of DcSDGs in response to drought stress. Heat map showing expression pattern of DcSDG genes in leaves under different drought treatments. The seedlings were watered on the 1st day, dried from the 2nd to the 7th day, and re-watered on the 8th day. Leaves were collected at different times; DR5/ DR8, DR6/DR10, and DR7/DR15 indicate sampling at 06:30 and 18:30 on the 2nd, 7th, and 9th days, respectively, and DR11 indicates sampling at 18:30 on the 8th day. The Y-axis represents the value of the relative expression level [log 2 (FPKM + 1)]

Fig. 8

Expression of DcSDGs in response to cold stress. Heat map showing expression pattern of DcSDG genes in leaves under cold stress for 20 h. The Y-axis represents the value of the relative expression level [log 2 (FPKM + 1)]

Fig. 9

Expression of DcSDGs in response to high temperature stress through RT-qPCR assay. The actin gene of D. catenatum was used as an internal reference. The data are representative of three independent experiments. The error bars indicate SD and the asterisk shows the corresponding gene between the heat shock (35 °C) and the control (20 °C) significantly affected by Student′s t test (*, P < 0.05; **, P < 0.01)