1
|
Wang WX, Yang C, Xiong W, Chen CY, Li N. Transcriptome-wide identification of ARF gene family in medicinal plant Polygonatum kingianum and expression analysis of PkARF members in different tissues. Mol Biol Rep 2024; 51:648. [PMID: 38727802 DOI: 10.1007/s11033-024-09608-0] [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: 02/22/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Polygonatum kingianum holds significant importance in Traditional Chinese Medicine due to its medicinal properties, characterized by its diverse chemical constituents including polysaccharides, terpenoids, flavonoids, phenols, and phenylpropanoids. The Auxin Response Factor (ARF) is a pivotal transcription factor known for its regulatory role in both primary and secondary metabolite synthesis. However, our understanding of the ARF gene family in P. kingianum remains limited. METHODS AND RESULTS We employed RNA-Seq to sequence three distinct tissues (leaf, root, and stem) of P. kingianum. The analysis revealed a total of 31,558 differentially expressed genes (DEGs), with 43 species of transcription factors annotated among them. Analyses via gene ontology and the Kyoto Encyclopedia of Genes and Genomes demonstrated that these DEGs were predominantly enriched in metabolic pathways and secondary metabolite biosynthesis. The proposed temporal expression analysis categorized the DEGs into nine clusters, suggesting the same expression trends that may be coordinated in multiple biological processes across the three tissues. Additionally, we conducted screening and expression pattern analysis of the ARF gene family, identifying 12 significantly expressed PkARF genes in P. kingianum roots. This discovery lays the groundwork for investigations into the role of PkARF genes in root growth, development, and secondary metabolism regulation. CONCLUSION The obtained data and insights serve as a focal point for further research studies, centred on genetic manipulation of growth and secondary metabolism in P. kingianum. Furthermore, these findings contribute to the understanding of functional genomics in P. kingianum, offering valuable genetic resources.
Collapse
Affiliation(s)
- Wen-Xiang Wang
- School of Pharmacy, Chongqing Three Gorges Medical College, Chongqing, 404120, China
| | - Ce Yang
- School of Pharmacy, Chongqing Three Gorges Medical College, Chongqing, 404120, China
| | - Wei Xiong
- Faculty of Basic Medical Sciences, Chongqing Three Gorges Medical College, Chongqing, 404120, China
| | - Chun-Yu Chen
- School of Pharmacy, Chongqing Three Gorges Medical College, Chongqing, 404120, China.
| | - Ning Li
- School of Pharmacy, Chongqing Three Gorges Medical College, Chongqing, 404120, China.
| |
Collapse
|
2
|
Zhang J, Li S, Gao X, Liu Y, Fu B. Genome-wide identification and expression pattern analysis of the Aux/IAA (auxin/indole-3-acetic acid) gene family in alfalfa (Medicago sativa) and the potential functions under drought stress. BMC Genomics 2024; 25:382. [PMID: 38637768 PMCID: PMC11025244 DOI: 10.1186/s12864-024-10313-2] [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: 01/15/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Auxin/induced-3-acetic acid (Aux/IAA) is an important plant hormone that affects plant growth and resistance to abiotic stresses. Drought stress is a vital factor in reducing plant biomass yield and production quality. Alfalfa (Medicago sativa L.) is the most widely planted leguminous forage and one of the most economically valuable crops in the world. Aux/IAA is one of the early responsive gene families of auxin, playing a crucial role in response to drought stress. However, the characteristics of the Aux/IAA gene family in alfalfa and its potential function in response to drought stress are still unknown. RESULT A total of 41 Aux/IAA gene members were identified in alfalfa genome. The physicochemical, peptide structure, secondary and tertiary structure analysis of proteins encoded by these genes revealed functional diversity of the MsIAA gene. A phylogenetic analysis classified the MsIAA genes into I-X classes in two subgroups. And according to the gene domain structure, these genes were classified into typical MsIAA and atypical MsIAA. Gene structure analysis showed that the MsIAA genes contained 1-4 related motifs, and except for the third chromosome without MsIAAs, they were all located on 7 chromosomes. The gene duplication analysis revealed that segmental duplication and tandem duplication greatly affected the amplification of the MsIAA genes. Analysis of the Ka/Ks ratio of duplicated MsAux/IAA genes suggested purification selection pressure was high and functional differences were limited. In addition, identification and classification of promoter cis-elements elucidated that MsIAA genes contained numerous elements associated to phytohormone response and abiotic stress response. The prediction protein-protein interaction network showed that there was a complex interaction between the MsAux/IAA genes. Gene expression profiles were tissue-specific, and MsAux/IAA had a broad response to both common abiotic stress (ABA, salt, drought and cold) and heavy metal stress (Al and Pb). Furthermore, the expression patterns analysis of 41 Aux/IAA genes by the quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that Aux/IAA genes can act as positive or negative factors to regulate the drought resistance in alfalfa. CONCLUSION This study provides useful information for the alfalfa auxin signaling gene families and candidate evidence for further investigation on the role of Aux/IAA under drought stress. Future studies could further elucidate the functional mechanism of the MsIAA genes response to drought stress.
Collapse
Affiliation(s)
- Jinqing Zhang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, 750021, China
| | - Shuxia Li
- College of Forestry and Prataculture, Ningxia University, Yinchuan, 750021, China
- Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Xixia District, Yinchuan, Ningxia Hui Autonomous Region, Yinchuan, 750021, China
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Yinchuan, 750021, China
| | - Xueqin Gao
- College of Forestry and Prataculture, Ningxia University, Yinchuan, 750021, China
- Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Xixia District, Yinchuan, Ningxia Hui Autonomous Region, Yinchuan, 750021, China
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Yinchuan, 750021, China
| | - Yaling Liu
- Inner Mongolia Pratacultural Technology Innovation Center Co, Ltd, Hohhot, 010000, China
| | - BingZhe Fu
- College of Forestry and Prataculture, Ningxia University, Yinchuan, 750021, China.
- Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Xixia District, Yinchuan, Ningxia Hui Autonomous Region, Yinchuan, 750021, China.
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Yinchuan, 750021, China.
| |
Collapse
|
3
|
Yang L, Kang Y, Li N, Wang Y, Mou H, Sun H, Ao T, Chen L, Chen W. Unlocking hormesis and toxic effects induced by cadmium in Polygonatum cyrtonema Hua based on morphology, physiology and metabolomics. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133447. [PMID: 38219579 DOI: 10.1016/j.jhazmat.2024.133447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/16/2024]
Abstract
Traditional Chinese medicine materials (TCMMs) are widely planted and used, while cadmium (Cd) is a widespread pollutant that poses a potential risk to plant growth and human health. However, studies on the influences of Cd on TCMMs have been limited. Our study aims to reveal the antioxidation-related detoxification mechanism of Polygonatum cyrtonema Hua under Cd stress based on physiology and metabolomics. The results showed that Cd0.5 (total Cd: 0.91 mg/kg; effective Cd: 0.45 mg/kg) induced hormesis on the biomass of roots, tubers and aboveground parts with increases of 22.88%, 27.12% and 17.02%, respectively, and significantly increased the flavonoids content by 57.45%. Additionally, the metabolism of caffeine, glutamine, arginine and purine was upregulated to induce hormesis in Cd0.5, which enhanced the synthesis of resistant substances such as spermidine, choline, IAA and saponins. Under Cd2 stress, choline and IAA decreased, and fatty acid metabolites (such as peanut acid and linoleic acid) and 8-hydroxyguanosine increased in response to oxidative damage, resulting in a significant biomass decrease. Our findings further reveal the metabolic process of detoxification by antioxidants and excessive Cd damage in TCMMs, deepen the understanding of detoxification mechanisms related to antioxidation, and enrich the relevant theories of hormesis induced by Cd.
Collapse
Affiliation(s)
- Li Yang
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources, Ministry of Education, Sichuan Normal University, Chengdu 610068, China; College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Yuchen Kang
- Institute for Disaster Management and Reconstruction, Sichuan University-The Hong Kong Polytechnic University, Chengdu 610207, China; College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Na Li
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Yuhao Wang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Haiyan Mou
- Institute for Disaster Management and Reconstruction, Sichuan University-The Hong Kong Polytechnic University, Chengdu 610207, China
| | - Hui Sun
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Tianqi Ao
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Li Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China.
| | - Wenqing Chen
- Institute for Disaster Management and Reconstruction, Sichuan University-The Hong Kong Polytechnic University, Chengdu 610207, China; College of Architecture and Environment, Sichuan University, Chengdu 610065, China; State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China.
| |
Collapse
|
4
|
Lian C, Lan J, Ma R, Li J, Zhang F, Zhang B, Liu X, Chen S. Genome-Wide Analysis of Aux/IAA Gene Family in Artemisia argyi: Identification, Phylogenetic Analysis, and Determination of Response to Various Phytohormones. PLANTS (BASEL, SWITZERLAND) 2024; 13:564. [PMID: 38475411 DOI: 10.3390/plants13050564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 03/14/2024]
Abstract
Artemisia argyi is a traditional herbal medicine plant, and its folium artemisia argyi is widely in demand due to moxibustion applications globally. The Auxin/indole-3-acetic acid (Aux/IAA, or IAA) gene family has critical roles in the primary auxin-response process, with extensive involvement in plant development and stresses, controlling various essential traits of plants. However, the systematic investigation of the Aux/IAA gene family in A. argyi remains limited. In this study, a total of 61 Aux/IAA genes were comprehensively identified and characterized. Gene structural analysis indicated that 46 Aux/IAA proteins contain the four typical domains, and 15 Aux/IAA proteins belong to non-canonical IAA proteins. Collinear prediction and phylogenetic relationship analyses suggested that Aux/IAA proteins were grouped into 13 distinct categories, and most Aux/IAA genes might experience gene loss during the tandem duplication process. Promoter cis-element investigation indicated that Aux/IAA promoters contain a variety of plant hormone response and stress response cis-elements. Protein interaction prediction analysis demonstrated that AaIAA26/29/7/34 proteins are possibly core members of the Aux/IAA family interaction. Expression analysis in roots and leaves via RNA-seq data indicated that the expression of some AaIAAs exhibited tissue-specific expression patterns, and some AaIAAs were involved in the regulation of salt and saline-alkali stresses. In addition, RT-qPCR results indicated that AaIAA genes have differential responses to auxin, with complex response patterns in response to other hormones, indicating that Aux/IAA may play a role in connecting auxin and other hormone signaling pathways. Overall, these findings shed more light on AaIAA genes and offer critical foundational knowledge toward the elucidation of their function during plant growth, stress response, and hormone networking of Aux/IAA family genes in A. argyi.
Collapse
Affiliation(s)
- Conglong Lian
- School of Pharmacy, Henan University of Chinese Medicine, 156 East Jin-shui Rd., Zhengzhou 450046, China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 East Jin-shui Rd., Zhengzhou 450046, China
| | - Jinxu Lan
- School of Pharmacy, Henan University of Chinese Medicine, 156 East Jin-shui Rd., Zhengzhou 450046, China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 East Jin-shui Rd., Zhengzhou 450046, China
| | - Rui Ma
- School of Pharmacy, Henan University of Chinese Medicine, 156 East Jin-shui Rd., Zhengzhou 450046, China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 East Jin-shui Rd., Zhengzhou 450046, China
| | - Jingjing Li
- School of Pharmacy, Henan University of Chinese Medicine, 156 East Jin-shui Rd., Zhengzhou 450046, China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 East Jin-shui Rd., Zhengzhou 450046, China
| | - Fei Zhang
- School of Pharmacy, Henan University of Chinese Medicine, 156 East Jin-shui Rd., Zhengzhou 450046, China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 East Jin-shui Rd., Zhengzhou 450046, China
| | - Bao Zhang
- School of Pharmacy, Henan University of Chinese Medicine, 156 East Jin-shui Rd., Zhengzhou 450046, China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 East Jin-shui Rd., Zhengzhou 450046, China
| | - Xiuyu Liu
- School of Pharmacy, Henan University of Chinese Medicine, 156 East Jin-shui Rd., Zhengzhou 450046, China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 East Jin-shui Rd., Zhengzhou 450046, China
| | - Suiqing Chen
- School of Pharmacy, Henan University of Chinese Medicine, 156 East Jin-shui Rd., Zhengzhou 450046, China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 East Jin-shui Rd., Zhengzhou 450046, China
| |
Collapse
|
5
|
Cai K, Zhao Q, Zhang J, Yuan H, Li H, Han L, Li X, Li K, Jiang T, Zhao X. Unraveling the Guardians of Growth: A Comprehensive Analysis of the Aux/ IAA and ARF Gene Families in Populus simonii. PLANTS (BASEL, SWITZERLAND) 2023; 12:3566. [PMID: 37896029 PMCID: PMC10610179 DOI: 10.3390/plants12203566] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/27/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023]
Abstract
The auxin/indole-3-acetic acid (Aux/IAA) and auxin response factor (ARF) genes are two crucial gene families in the plant auxin signaling pathway. Nonetheless, there is limited knowledge regarding the Aux/IAA and ARF gene families in Populus simonii. In this study, we first identified 33 putative PsIAAs and 35 PsARFs in the Populus simonii genome. Analysis of chromosomal location showed that the PsIAAs and PsARFs were distributed unevenly across 17 chromosomes, with the greatest abundance observed on chromosomes 2. Furthermore, based on the homology of PsIAAs and PsARFs, two phylogenetic trees were constructed, classifying 33 PsIAAs and 35 PsARFs into three subgroups each. Five pairs of PsIAA genes were identified as the outcome of tandem duplication, but no tandem repeat gene pairs were found in the PsARF family. The expression profiling of PsIAAs and PsARFs revealed that several genes exhibited upregulation in different tissues and under various stress conditions, indicating their potential key roles in plant development and stress responses. The variance in expression patterns of specific PsIAAs and PsARFs was corroborated through RT-qPCR analysis. Most importantly, we instituted that the PsIAA7 gene, functioning as a central hub, exhibits interactions with numerous Aux/IAA and ARF proteins. Furthermore, subcellular localization findings indicate that PsIAA7 functions as a protein localized within the nucleus. To conclude, the in-depth analysis provided in this study will contribute significantly to advancing our knowledge of the roles played by PsIAA and PsARF families in both the development of P. simonii tissue and its responses to stress. The insights gained will serve as a valuable asset for further inquiries into the biological functions of these gene families.
Collapse
Affiliation(s)
- Kewei Cai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (K.C.); (Q.Z.); (H.L.); (K.L.); (T.J.)
| | - Qiushuang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (K.C.); (Q.Z.); (H.L.); (K.L.); (T.J.)
| | - Jinwang Zhang
- Tongliao Forestry and Grassland Science Research Institute, Tongliao 028000, China; (J.Z.); (H.Y.)
| | - Hongtao Yuan
- Tongliao Forestry and Grassland Science Research Institute, Tongliao 028000, China; (J.Z.); (H.Y.)
| | - Hanxi Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (K.C.); (Q.Z.); (H.L.); (K.L.); (T.J.)
| | - Lu Han
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China;
| | - Xuebo Li
- Changling County Front Seven State-Owned Forest Protection Center, Changling 131500, China
| | - Kailong Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (K.C.); (Q.Z.); (H.L.); (K.L.); (T.J.)
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (K.C.); (Q.Z.); (H.L.); (K.L.); (T.J.)
| | - Xiyang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (K.C.); (Q.Z.); (H.L.); (K.L.); (T.J.)
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China;
| |
Collapse
|