Genome-Wide Identification and Characterization of the <i>Salvia miltiorrhiza</i> Histone Deacetylase (HDAC) Family in Response to Multiple Abiotic Stresses
<i>Salvia miltiorrhiza</i> is a plant commonly used in traditional Chinese medicine. Its material bases for treating diseases are tanshinones and phenolic acids, including salvianolic acids. Histone deacetylase proteins (HDACs) are a class of specific functional enzymes that interact wit...
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MDPI AG
2024-02-01
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| Series: | Plants |
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| author | Junyu Chen Yuxin Ying Lingtiao Yao Zhangting Xu Zhenming Yu Guoyin Kai |
| author_facet | Junyu Chen Yuxin Ying Lingtiao Yao Zhangting Xu Zhenming Yu Guoyin Kai |
| author_sort | Junyu Chen |
| collection | DOAJ |
| description | <i>Salvia miltiorrhiza</i> is a plant commonly used in traditional Chinese medicine. Its material bases for treating diseases are tanshinones and phenolic acids, including salvianolic acids. Histone deacetylase proteins (HDACs) are a class of specific functional enzymes that interact with acetylation groups on the N-terminal lysine of histone proteins further regulate gene transcription through structural changes at the chromatin level. HDACs involved in the growth and development of various plants, and induced by plant hormones to regulate the internal environment of plants to resist stress, at the same time affect the accumulation of some secondary metabolites. However, the role of SmHDACs on the accumulation of salvianolic acid in <i>S. miltiorrhiza</i> remains unclear. In this study, 16 SmHDACs genes were identified from the high-quality <i>S. miltiorrhiza</i> genome, their physicochemical properties were predicted. In phylogenetic trees co-constructed with HDACs proteins from other plants, SmHDACs was divided into three subfamilies, each with similar motif and conserved domain composition. The distribution of the three subfamilies is similar to that of dicotyledonous plants. Chromosome localization analysis showed that SmHDACs genes were randomly located. Cis-acting element analysis predicted that SmHDACs gene expression may be related to and induced by various phytohormones, such as MeJA and ABA. By combining the expression pattern and co-expression network induced by phytohormones, we speculate that SmHDACs may further influence the synthesis of salvianolic acid, and identified SmHDA5, a potential functional gene, then speculate its downstream target based on the co-expression network. In summary, we analyzed the SmHDACs gene family of <i>S. miltiorrhiza</i> and screened out the potential functional gene <i>SmHDA5</i>. From the perspective of epigenetics, we proposed the molecular mechanism of plant hormone promoting salvianolic acid synthesis, which filled the gap in the subdivision of histone deacetylase in <i>S. miltiorrhiza</i> research, provided a theoretical basis for the culture and transformation of <i>S. miltiorrhiza</i> germplasm resources. |
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| last_indexed | 2024-04-25T00:22:49Z |
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| spelling | doaj.art-e81a30e2f5064827938eacdea64932d92024-03-12T16:52:32ZengMDPI AGPlants2223-77472024-02-0113558010.3390/plants13050580Genome-Wide Identification and Characterization of the <i>Salvia miltiorrhiza</i> Histone Deacetylase (HDAC) Family in Response to Multiple Abiotic StressesJunyu Chen0Yuxin Ying1Lingtiao Yao2Zhangting Xu3Zhenming Yu4Guoyin Kai5School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, ChinaCollege of Food and Health, Zhejiang A & F University, Hangzhou 311300, ChinaSchool of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, ChinaSchool of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, ChinaSchool of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, ChinaSchool of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China<i>Salvia miltiorrhiza</i> is a plant commonly used in traditional Chinese medicine. Its material bases for treating diseases are tanshinones and phenolic acids, including salvianolic acids. Histone deacetylase proteins (HDACs) are a class of specific functional enzymes that interact with acetylation groups on the N-terminal lysine of histone proteins further regulate gene transcription through structural changes at the chromatin level. HDACs involved in the growth and development of various plants, and induced by plant hormones to regulate the internal environment of plants to resist stress, at the same time affect the accumulation of some secondary metabolites. However, the role of SmHDACs on the accumulation of salvianolic acid in <i>S. miltiorrhiza</i> remains unclear. In this study, 16 SmHDACs genes were identified from the high-quality <i>S. miltiorrhiza</i> genome, their physicochemical properties were predicted. In phylogenetic trees co-constructed with HDACs proteins from other plants, SmHDACs was divided into three subfamilies, each with similar motif and conserved domain composition. The distribution of the three subfamilies is similar to that of dicotyledonous plants. Chromosome localization analysis showed that SmHDACs genes were randomly located. Cis-acting element analysis predicted that SmHDACs gene expression may be related to and induced by various phytohormones, such as MeJA and ABA. By combining the expression pattern and co-expression network induced by phytohormones, we speculate that SmHDACs may further influence the synthesis of salvianolic acid, and identified SmHDA5, a potential functional gene, then speculate its downstream target based on the co-expression network. In summary, we analyzed the SmHDACs gene family of <i>S. miltiorrhiza</i> and screened out the potential functional gene <i>SmHDA5</i>. From the perspective of epigenetics, we proposed the molecular mechanism of plant hormone promoting salvianolic acid synthesis, which filled the gap in the subdivision of histone deacetylase in <i>S. miltiorrhiza</i> research, provided a theoretical basis for the culture and transformation of <i>S. miltiorrhiza</i> germplasm resources.https://www.mdpi.com/2223-7747/13/5/580phytohormonehistone deacetylase (HDAC)expression profilesgenome-wide identificationphenolic acids<i>Salvia miltiorrhiza</i> |
| spellingShingle | Junyu Chen Yuxin Ying Lingtiao Yao Zhangting Xu Zhenming Yu Guoyin Kai Genome-Wide Identification and Characterization of the <i>Salvia miltiorrhiza</i> Histone Deacetylase (HDAC) Family in Response to Multiple Abiotic Stresses Plants phytohormone histone deacetylase (HDAC) expression profiles genome-wide identification phenolic acids <i>Salvia miltiorrhiza</i> |
| title | Genome-Wide Identification and Characterization of the <i>Salvia miltiorrhiza</i> Histone Deacetylase (HDAC) Family in Response to Multiple Abiotic Stresses |
| title_full | Genome-Wide Identification and Characterization of the <i>Salvia miltiorrhiza</i> Histone Deacetylase (HDAC) Family in Response to Multiple Abiotic Stresses |
| title_fullStr | Genome-Wide Identification and Characterization of the <i>Salvia miltiorrhiza</i> Histone Deacetylase (HDAC) Family in Response to Multiple Abiotic Stresses |
| title_full_unstemmed | Genome-Wide Identification and Characterization of the <i>Salvia miltiorrhiza</i> Histone Deacetylase (HDAC) Family in Response to Multiple Abiotic Stresses |
| title_short | Genome-Wide Identification and Characterization of the <i>Salvia miltiorrhiza</i> Histone Deacetylase (HDAC) Family in Response to Multiple Abiotic Stresses |
| title_sort | genome wide identification and characterization of the i salvia miltiorrhiza i histone deacetylase hdac family in response to multiple abiotic stresses |
| topic | phytohormone histone deacetylase (HDAC) expression profiles genome-wide identification phenolic acids <i>Salvia miltiorrhiza</i> |
| url | https://www.mdpi.com/2223-7747/13/5/580 |
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