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Chang Y, Gelaye Y, Yao R, Yang P, Li J, Liu N, Huang L, Zhou X, Chen W, Yu B, Jiang H, Liao B, Lei Y, Luo H. Identification and Characterization of Histone Modification Gene Families and Their Expression Patterns During Pod and Seed Development in Peanut. Int J Mol Sci 2025; 26:2591. [PMID: 40141232 PMCID: PMC11942463 DOI: 10.3390/ijms26062591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2025] [Revised: 03/07/2025] [Accepted: 03/10/2025] [Indexed: 03/28/2025] Open
Abstract
Histone methylation and acetylation play potential roles in plant growth and development through various histone modification (HM) genes. However, studies of HM genes are still limited in peanut (Arachis hypogaea L.), a globally important oilseed crop. Here, comprehensive identification and investigation of HM genes were performed using the whole genome of peanut, and a total of 207 AhHMs encoding 108 histone methyltransferases, 51 histone demethylases, 16 histone acetylases, and 32 histone deacetylases were identified. Detailed analysis of these AhHMs, including chromosome locations, gene structures, protein motifs, and protein-protein interactions, was performed. Tandem, segmental, transposed, dispersed, and whole-genome duplications were involved in the evolution and expansion of the HM gene families in peanut. Ka/Ks analysis indicated that the AhHMs underwent purifying selection. The expression profiles of the 207 AhHMs were investigated during the pod and seed development stages on the basis of the transcriptome sequencing results. Quantitative real-time PCR confirmed that eight AhHMs were differentially expressed during pod and seed development. These results provide data support for further studying the epigenetic mechanism of peanut histones, deepen the understanding of seed development, and provide a new direction for the cultivation of more high-yield and high-quality peanut varieties.
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Affiliation(s)
- Yingying Chang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (Y.C.); (Y.G.); (R.Y.); (P.Y.); (J.L.); (N.L.); (L.H.); (X.Z.); (W.C.); (B.Y.); (H.J.); (B.L.); (Y.L.)
| | - Yohannes Gelaye
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (Y.C.); (Y.G.); (R.Y.); (P.Y.); (J.L.); (N.L.); (L.H.); (X.Z.); (W.C.); (B.Y.); (H.J.); (B.L.); (Y.L.)
- Department of Horticulture, College of Agriculture and Natural Resources, Debre Markos University, Debre Markos P.O. Box 269, Ethiopia
| | - Ruonan Yao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (Y.C.); (Y.G.); (R.Y.); (P.Y.); (J.L.); (N.L.); (L.H.); (X.Z.); (W.C.); (B.Y.); (H.J.); (B.L.); (Y.L.)
| | - Ping Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (Y.C.); (Y.G.); (R.Y.); (P.Y.); (J.L.); (N.L.); (L.H.); (X.Z.); (W.C.); (B.Y.); (H.J.); (B.L.); (Y.L.)
| | - Jihua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (Y.C.); (Y.G.); (R.Y.); (P.Y.); (J.L.); (N.L.); (L.H.); (X.Z.); (W.C.); (B.Y.); (H.J.); (B.L.); (Y.L.)
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (Y.C.); (Y.G.); (R.Y.); (P.Y.); (J.L.); (N.L.); (L.H.); (X.Z.); (W.C.); (B.Y.); (H.J.); (B.L.); (Y.L.)
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (Y.C.); (Y.G.); (R.Y.); (P.Y.); (J.L.); (N.L.); (L.H.); (X.Z.); (W.C.); (B.Y.); (H.J.); (B.L.); (Y.L.)
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (Y.C.); (Y.G.); (R.Y.); (P.Y.); (J.L.); (N.L.); (L.H.); (X.Z.); (W.C.); (B.Y.); (H.J.); (B.L.); (Y.L.)
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (Y.C.); (Y.G.); (R.Y.); (P.Y.); (J.L.); (N.L.); (L.H.); (X.Z.); (W.C.); (B.Y.); (H.J.); (B.L.); (Y.L.)
| | - Bolun Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (Y.C.); (Y.G.); (R.Y.); (P.Y.); (J.L.); (N.L.); (L.H.); (X.Z.); (W.C.); (B.Y.); (H.J.); (B.L.); (Y.L.)
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (Y.C.); (Y.G.); (R.Y.); (P.Y.); (J.L.); (N.L.); (L.H.); (X.Z.); (W.C.); (B.Y.); (H.J.); (B.L.); (Y.L.)
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (Y.C.); (Y.G.); (R.Y.); (P.Y.); (J.L.); (N.L.); (L.H.); (X.Z.); (W.C.); (B.Y.); (H.J.); (B.L.); (Y.L.)
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (Y.C.); (Y.G.); (R.Y.); (P.Y.); (J.L.); (N.L.); (L.H.); (X.Z.); (W.C.); (B.Y.); (H.J.); (B.L.); (Y.L.)
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (Y.C.); (Y.G.); (R.Y.); (P.Y.); (J.L.); (N.L.); (L.H.); (X.Z.); (W.C.); (B.Y.); (H.J.); (B.L.); (Y.L.)
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Revalska M, Radkova M, Zhiponova M, Vassileva V, Iantcheva A. Functional Genomics of Legumes in Bulgaria-Advances and Future Perspectives. Genes (Basel) 2025; 16:296. [PMID: 40149448 PMCID: PMC11941780 DOI: 10.3390/genes16030296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Revised: 02/23/2025] [Accepted: 02/27/2025] [Indexed: 03/29/2025] Open
Abstract
Members of the Leguminosae family are important crops that provide food, animal feed and vegetable oils. Legumes make a substantial contribution to sustainable agriculture and the nitrogen cycle through their unique ability to fix atmospheric nitrogen in agricultural ecosystems. Over the past three decades, Medicago truncatula and Lotus japonicus have emerged as model plants for genomic and physiological research in legumes. The advancement of innovative molecular and genetic tools, particularly insertional mutagenesis using the retrotransposon Tnt1, has facilitated the development of extensive mutant collections and enabled precise gene tagging in plants for the identification of key symbiotic and developmental genes. Building on these resources, twelve years ago, our research team initiated the establishment of a platform for functional genomic studies of legumes in Bulgaria. In the framework of this initiative, we conducted systematic sequencing of selected mutant lines and identified genes involved in plant growth and development for detailed functional characterization. This review summarizes our findings on the functions of selected genes involved in the growth and development of the model species, discusses the molecular mechanisms underlying important developmental processes and examines the potential for the translation of this fundamental knowledge to improve commercially important legume crops in Bulgaria and globally.
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Affiliation(s)
- Miglena Revalska
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164 Sofia, Bulgaria; (M.R.); (M.R.)
| | - Mariana Radkova
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164 Sofia, Bulgaria; (M.R.); (M.R.)
| | - Miroslava Zhiponova
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tsankov blvd., 1164 Sofia, Bulgaria;
| | - Valya Vassileva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria;
| | - Anelia Iantcheva
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164 Sofia, Bulgaria; (M.R.); (M.R.)
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Mali S, Zinta G. Genome-wide identification and expression analysis reveal the role of histone methyltransferase and demethylase genes in heat stress response in potato (Solanum tuberosum L.). Biochim Biophys Acta Gen Subj 2024; 1868:130507. [PMID: 37925032 DOI: 10.1016/j.bbagen.2023.130507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/05/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Potato (Solanum tuberosum L.), the third most important non-cereal crop, is sensitive to high temperature. Histone modifications have been known to regulate various abiotic stress responses. However, the role of histone methyltransferases and demethylases remain unexplored in potato under heat stress. METHODS Potato genome database was used for genome-wide analysis of StPRMT and StHDMA gene families, which were further characterized by analyzing gene structure, conserved motif, domain organization, sub-cellular localization, promoter region and phylogenetic relationships. Additionally, expression profiling under high-temperature stress in leaf and stolon tissue of heat contrasting potato genotypes was done to study their role in response to high temperature stress. RESULTS The genome-wide analysis led to identification of nine StPRMT and eleven StHDMA genes. Structural analysis, including conserved motifs, exon/intron structure and phylogenetic relationships classified StPRMT and StHDMA gene families into two classes viz. Class I and Class II. A variety of cis-regulatory elements were explored in the promoter region associated with light, developmental, hormonal and stress responses. Prediction of sub-cellular localization of StPRMT proteins revealed their occurrence in nucleus and cytoplasm, whereas StHDMA proteins were observed in different sub-cellular compartments. Furthermore, expression profiling of StPRMT and StHDMA gene family members revealed genes responding to heat stress. Heat-inducible expression of StPRMT1, StPRMT3, StPRMT4 and StPRMT5 in leaf and stolon tissues of HS and HT cultivar indicated them as probable candidates for enhancing thermotolerance in potato. However, StHDMAs responded dynamically in leaf and stolon tissue of heat contrasting genotypes under high temperature. CONCLUSION The current study presents a detailed analysis of histone modifiers in potato and indicates their role as an important epigenetic regulators modulating heat tolerance. GENERAL SIGNIFICANCE Understanding epigenetic mechanisms underlying heat tolerance in potato will contribute towards breeding of thermotolerant potato varieties.
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Affiliation(s)
- Surbhi Mali
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Gaurav Zinta
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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An B, Cai H, Li B, Zhang S, He Y, Wang R, Jiao C, Guo Y, Xu L, Xu Y. Molecular Evolution of Histone Methylation Modification Families in the Plant Kingdom and Their Genome-Wide Analysis in Barley. Int J Mol Sci 2023; 24:ijms24098043. [PMID: 37175750 PMCID: PMC10178440 DOI: 10.3390/ijms24098043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
In this study, based on the OneKP database and through comparative genetic analysis, we found that HMT and HDM may originate from Chromista and are highly conserved in green plants, and that during the evolution from algae to land plants, histone methylation modifications gradually became complex and diverse, which is more conducive to the adaptation of plants to complex and variable environments. We also characterized the number of members, genetic similarity, and phylogeny of HMT and HDM families in barley using the barley pangenome and the Tibetan Lasa Goumang genome. The results showed that HMT and HDM were highly conserved in the domestication of barley, but there were some differences in the Lasa Goumang SDG subfamily. Expression analysis showed that HvHMTs and HvHDMs were highly expressed in specific tissues and had complex expression patterns under multiple stress treatments. In summary, the amplification and variation of HMT and HDM facilitate plant adaptation to complex terrestrial environments, while they are highly conserved in barley and play an important role in barley growth and development with abiotic stresses. In brief, our findings provide a novel perspective on the origin and evolutionary history of plant HvHMTs and HvHDMs, and lay a foundation for further investigation of their functions in barley.
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Affiliation(s)
- Bingzhuang An
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Haiya Cai
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Bo Li
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Shuo Zhang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Yonggang He
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Rong Wang
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Chunhai Jiao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Ying Guo
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Le Xu
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Yanhao Xu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Scientific Observation and Experiment Station for Crop Gene Resources and Germplasm Enhancement in Hubei, Ministry of Agriculture and Rural Affairs, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
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Genome-Wide Identification and Spatial Expression Analysis of Histone Modification Gene Families in the Rubber Dandelion Taraxacum kok-saghyz. PLANTS 2022; 11:plants11162077. [PMID: 36015381 PMCID: PMC9415798 DOI: 10.3390/plants11162077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/29/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022]
Abstract
Taraxacum kok-saghyz (Tks), also known as the Russian dandelion, is a recognized alternative source of natural rubber quite comparable, for quality and use, to the one obtained from the so-called rubber tree, Hevea brasiliensis. In addition to that, Tks roots produce several other compounds, including inulin, whose use in pharmaceutical and dietary products is quite extensive. Histone-modifying genes (HMGs) catalyze a series of post-translational modifications that affect chromatin organization and conformation, which, in turn, regulate many downstream processes, including gene expression. In this study, we present the first analysis of HMGs in Tks. Altogether, we identified 154 putative Tks homologs: 60 HMTs, 34 HDMs, 42 HATs, and 18 HDACs. Interestingly, whilst most of the classes showed similar numbers in other plant species, including M. truncatula and A. thaliana, HATs and HMT-PRMTs were indeed more abundant in Tks. Composition and structure analysis of Tks HMG proteins showed, for some classes, the presence of novel domains, suggesting a divergence from the canonical HMG model. The analysis of publicly available transcriptome datasets, combined with spatial expression of different developmental tissues, allowed us to identify several HMGs with a putative role in metabolite biosynthesis. Overall, our work describes HMG genomic organization and sets the premises for the functional characterization of epigenetic modifications in rubber-producing plants.
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