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

Chen, Donghong; Qiu, Han-Lin; Huang, Yong; Zhang, Lei; Si, Jinping

doi:10.1186/s12870-020-2244-6

Cited by 31 publications

(22 citation statements)

References 123 publications

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“…Importantly, the sequences of SET-domain proteins within each subfamily formed monophyletic groups without mixing (fig. 3) as in previous phylogenetic analyses (Huang et al 2017; Chen et al 2020), and the relationships and topology of the SET-domain subfamilies were highly similar. Interestingly, the E(z) subfamily clustered in the crown of the tree without interaction with the prokaryotic sequences and shows the same topology as the eukaryotic-E(z) tree (fig.…”

Section: Resultssupporting

confidence: 73%

Phylogenetic profiling suggests early origin of the core subunits of Polycomb Repressive Complex 2 (PRC2)

Sharaf

Vijayanathan

Oborník

et al. 2021

Preprint

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Polycomb Repressive Complex 2 (PRC2) is involved in establishing transcriptionally silent chromatin states through its ability to methylate lysine 27 of histone H3 by the catalytic subunit Enhancer of zeste [E(z)]. Polycomb group (PcG) proteins play a crucial role in the maintenance of cell identity and in developmental regulation. Previously, the diversity of PRC2 subunits within some eukaryotic lineages has been reported and its presence in early eukaryotic evolution has been hypothesized. So far however, systematic survey of the presence of PRC2 subunits in species of all eukaryotic lineages is missing. Here, we report the diversity of PRC2 core subunit proteins in different eukaryotic supergroups with emphasis on the early-diverged lineages and explore the molecular evolution of PRC2 subunits by phylogenetics. In detail, we investigate the SET-domain protein sequences and their evolution across the four domains of life and particularly focus on the structural diversity of the SET-domain subfamily containing E(z), the catalytic subunit of PRC2. We show that PRC2 subunits are already present in early eukaryotic lineages, strengthening the support for PRC2 emergence prior to diversification of eukaryotes. We identify a common presence of E(z) and ESC, suggesting that Su(z)12 may have emerged later and/or may be dispensable from the evolutionarily conserved functional core of PRC2. Furthermore, our results broaden our understanding of the E(z) evolution within the SET-domain protein family, suggesting possibilities of function evolution. Through this, we shed light on a possible emerging point of the PRC2 and the evolution of its function in eukaryotes.

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Section: Resultssupporting

confidence: 73%

Phylogenetic profiling suggests early origin of the core subunits of Polycomb Repressive Complex 2 (PRC2)

Sharaf

Vijayanathan

Oborník

et al. 2021

Preprint

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“…The DcACTIN was used as the internal control gene, which was stably expressed in D. catenatum plants and not affected by treatments and genotypes. The relative expression levels were evaluated automatically by the Bio-Rad CFX Manager (version 2.3) with 2 −ΔΔCT method [ 3 ].…”

Section: Methodsmentioning

confidence: 99%

“…Dendrobium of Orchidaceae is an importantly economical genera, which comprises nearly 1,600 accepted species [ 1 , 2 ]. Among them, D. catenatum (also known as D. officinale ) is a popular tonic and traditional Chinese medicine herb with prominent commercial value, including protection against upset stomach, promotion of body fluid production, immune enhancement, nourishing Yin, as well as antioxidant and antitumor effects [ 3 ]. In the past 20 years, scientists have successfully overcome the bottleneck problems against D. catenatum industrious development, such as seedling breeding and facility cultivation [ 3 ], which makes it from an endangered medicinal plant to multi-billion dollar grade industry [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

“…Among them, D. catenatum (also known as D. officinale ) is a popular tonic and traditional Chinese medicine herb with prominent commercial value, including protection against upset stomach, promotion of body fluid production, immune enhancement, nourishing Yin, as well as antioxidant and antitumor effects [ 3 ]. In the past 20 years, scientists have successfully overcome the bottleneck problems against D. catenatum industrious development, such as seedling breeding and facility cultivation [ 3 ], which makes it from an endangered medicinal plant to multi-billion dollar grade industry [ 4 ]. However, in the process of large-scale cultivation of D. catenatum , Southern Blight disease caused by Sclerotium delphinii leads to heavy yield losses by infecting its leaves, stems, and roots [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

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JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen

et al. 2021

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Background Dendrobium catenatum belongs to the Orchidaceae, and is a precious Chinese herbal medicine. In the past 20 years, D. catenatum industry has developed from an endangered medicinal plant to multi-billion dollar grade industry. The necrotrophic pathogen Sclerotium delphinii has a devastating effection on over 500 plant species, especially resulting in widespread infection and severe yield loss in the process of large-scale cultivation of D. catenatum. It has been widely reported that Jasmonate (JA) is involved in plant immunity to pathogens, but the mechanisms of JA-induced plant resistance to S. delphinii are unclear. Results In the present study, the role of JA in enhancing D. catenatum resistance to S. delphinii was investigated. We identified 2 COI1, 13 JAZ, and 12 MYC proteins in D. catenatum genome. Subsequently, systematic analyses containing phylogenetic relationship, gene structure, protein domain, and motif architecture of core JA pathway proteins were conducted in D. catenatum and the newly characterized homologs from its closely related orchid species Phalaenopsis equestris and Apostasia shenzhenica, along with the well-investigated homologs from Arabidopsis thaliana and Oryza sativa. Public RNA-seq data were investigated to analyze the expression patterns of D. catenatum core JA pathway genes in various tissues and organs. Transcriptome analysis of MeJA and S. delphinii treatment showed exogenous MeJA changed most of the expression of the above genes, and several key members, including DcJAZ1/2/5 and DcMYC2b, are involved in enhancing defense ability to S. delphinii in D. catenatum. Conclusions The findings indicate exogenous MeJA treatment affects the expression level of DcJAZ1/2/5 and DcMYC2b, thereby enhancing D. catenatum resistance to S. delphinii. This research would be helpful for future functional identification of core JA pathway genes involved in breeding for disease resistance in D. catenatum.

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“…D. catenatum contains many medicinal components, such as polysaccharides, alkaloids, and flavonoids [15]. In the last 20 years, D. catenatum has been successfully cultivated and become an important economic crop in China [16]. As an epiphytic plant, the growth of D. catenatum usually requires a warm and humid environment.…”

Section: Introductionmentioning

confidence: 99%

Identification and Expression Profiling of Nonphosphorus Glycerolipid Synthase Genes in Response to Abiotic Stresses in Dendrobium catenatum

Zhan

Qian

Mao

2021

Plants

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Dendrobium catenatum, a valuable Chinese herb, frequently experiences abiotic stresses, such as cold and drought, under natural conditions. Nonphosphorus glycerolipid synthase (NGLS) genes are closely linked to the homeostasis of membrane lipids under abiotic stress in plants. However, there is limited information on NGLS genes in D. catenatum. In this study, a total of eight DcaNGLS genes were identified from the D. catenatum genome; these included three monogalactosyldiacylglycerol synthase (DcaMGD1, 2, 3) genes, two digalactosyldiacylglycerol synthase (DcaDGD1, 2) genes, and three sulfoquinovosyldiacylglycerol synthase (DcaSQD1, 2.1, 2.2) genes. The gene structures and conserved motifs in the DcaNGLSs showed a high conservation during their evolution. Gene expression profiling showed that the DcaNGLSs were highly expressed in specific tissues and during rapid growth stages. Furthermore, most DcaNGLSs were strongly induced by freezing and post-freezing recovery. DcaMGD1 and DcaSQDs were greatly induced by salt stress in leaves, while DcaDGDs were primarily induced by salt stress in roots. Under drought stress, most DcaNGLSs were regulated by circadian rhythms, and DcaSQD2 was closely associated with drought recovery. Transcriptome analysis also revealed that MYB might be regulated by circadian rhythm and co-expressed with DcaNGLSs under drought stress. These results provide insight for the further functional investigation of NGLS and the regulation of nonphosphorus glycerolipid biosynthesis in Dendrobium.

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

Cited by 31 publications

References 123 publications

Phylogenetic profiling suggests early origin of the core subunits of Polycomb Repressive Complex 2 (PRC2)

Phylogenetic profiling suggests early origin of the core subunits of Polycomb Repressive Complex 2 (PRC2)

JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen

Identification and Expression Profiling of Nonphosphorus Glycerolipid Synthase Genes in Response to Abiotic Stresses in Dendrobium catenatum

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