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

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.

Bioaccumulation and cycling of polybrominated diphenyl ethers (PBDEs) and dechlorane plus (DP) in three natural mangrove ecosystems of South China.

Polybrominated diphenyl ethers (PBDEs) and dechlorane plus (DP) in mangrove sediments and tissues of nine species from three Mangrove Reserves of Hainan Island were studied. The average concentrations of PBDEs and DP in mangrove leaves, branches, roots and fruits were 1048, 498, 546 and 364 pg g-1 dw, and 294, 181, 108 and 165 pg g-1 dw, respectively. The elevated PBDEs and DP concentrations in mangrove leaves may be caused by atmospheric sedimentation. The predominant PBDE congeners in sediments were BDE-209 and those in mangrove tissues were BDE-28. The average fanti (ratio of [anti-DP]/[DP]) of DP in sediments and tissues were 0.47 and 0.32, respectively. Sonneratia hainanensis, a fast growing mangrove plant, has a relatively high tolerance and absorptive capacity to PBDEs and DP in sediments, suggesting that it could be used as an effective plant for phytoremediation. The biota sediment accumulation factors (BSAFs) of PBDEs in mangrove branches were positively correlated with log KOW (R2 = 0.43, p < 0.05). The standing accumulation, annual absorption, annual net retention, annual return, and turnover period of PBDEs and DP in mangrove tissues of the ecosystems were estimated, and the results indicated that mangroves are playing an important role in retaining PBDEs and DP.

Bioaccumulation and cycling of organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) in three mangrove reserves of south China.

Total 22 organochlorine pesticides (OCPs) compounds and 31 polychlorinated biphenyls (PCBs) congeners in mangrove sediments and tissues (leaf, branch, root and fruit) of nine species from three Mangrove Reserves of China were studied. The mean concentrations of total DDTs, HCHs, OCPs and PCBs in sediments were 2.84, 0.06, 3.84 and 0.17 ng g-1 dw, while those in tissues were 1.85, 0.22, 9.43 and 1.61 ng g-1 dw, respectively. The elevated OCPs and PCBs levels in mangrove leaves may be caused by atmospheric sedimentation. The biota sediment accumulation factor (BSAF) values of both OCPs (mean: 3.4) and PCBs (mean: 9.9) are generally larger than one, implying mangroves' bioaccumulation and their ability to intercept pollutants. The BSAFs of PCBs in mangrove tissues were negatively correlated with the PCB congener's octanol-water partition coefficients (KOW, R = 0.58, n = 31, p < 0.001), suggesting that lower chlorinated CB congeners are more bioaccumulative in mangroves. In order to better understanding the fate of these organochlorine compounds, the cycling (including the standing accumulation, the annual absorption, the annual net retention, the annual return, and the turnover period) of OCPs and PCBs in the Mangrove Reserves were estimated, and the results indicated that mangroves are playing important roles in retaining OCPs and PCBs.

Bioaccumulation and Cycling of Polycyclic Aromatic Hydrocarbons (PAHs) in Typical Mangrove Wetlands of Hainan Island, South China.

Mangrove wetlands are important coastal ecosystems in tropical and subtropical regions, and mangrove sediments and tissues often are the pollutant sinks due to their high organic matter contents. Polycyclic aromatic hydrocarbons (PAHs) in the mangrove sediments and tissues of nine species from three typical mangrove wetlands of Hainan Island were studied. The average concentration of PAHs in all mangrove tissues was 403 ng g-1 dw, with PAHs concentrations in leaf, branch, root, and fruit of 566, 335, 314, and 353 ng g-1 dw, respectively. PAHs levels were much higher in leaf than in other mangrove tissues, which may be caused partly by atmospheric deposition of PAHs. The dominant individual PAH compounds in mangrove tissues were phenanthrene (41.3%), fluoranthene (14.7%), and pyrene (11.4%), while in sediments were naphthalene (73.4%), phenanthrene (3.9%), and pyrene (3.6%), respectively. The biota-sediment accumulation factors of PAH congeners in the mangrove wetlands showed different patterns, with the most predominant of phenanthrene. The cycling of PAHs in the mangrove wetlands of Hainan Island also were estimated, and the results showed that the standing accumulation, the annual absorption, the annual net retention, the annual return, and the turnover period in all mangrove tissues of the community were 2228 µg m-2, 869 µg m-2 a-1, 206 µg m-2 a-1, 663 µg m-2 a-1, and 3.4 a, respectively. These results indicated that mangroves are playing an important role in retaining PAHs.

Phylogeny-dominant classification of J-proteins in Arabidopsis thaliana and Brassica oleracea.

Hsp40s or DnaJ/J-proteins are evolutionarily conserved in all organisms as co-chaperones of molecular chaperone HSP70s that mainly participate in maintaining cellular protein homeostasis, such as protein folding, assembly, stabilization, and translocation under normal conditions as well as refolding and degradation under environmental stresses. It has been reported that Arabidopsis J-proteins are classified into four classes (types A-D) according to domain organization, but their phylogenetic relationships are unknown. Here, we identified 129 J-proteins in the world-wide popular vegetable Brassica oleracea, a close relative of the model plant Arabidopsis, and also revised the information of Arabidopsis J-proteins based on the latest online bioresources. According to phylogenetic analysis with domain organization and gene structure as references, the J-proteins from Arabidopsis and B. oleracea were classified into 15 main clades (I-XV) separated by a number of undefined small branches with remote relationship. Based on the number of members, they respectively belong to multigene clades, oligo-gene clades, and mono-gene clades. The J-protein genes from different clades may function together or separately to constitute a complicated regulatory network. This study provides a constructive viewpoint for J-protein classification and an informative platform for further functional dissection and resistant genes discovery related to genetic improvement of crop plants.