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Luo M, Liu X, Su H, Li M, Li M, Wei J. Regulatory Networks of Flowering Genes in Angelica sinensis during Vernalization. PLANTS 2022; 11:plants11101355. [PMID: 35631780 PMCID: PMC9144295 DOI: 10.3390/plants11101355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 11/29/2022]
Abstract
Angelica sinensis is a low-temperature and long-day perennial herb that has been widely used for cardio-cerebrovascular diseases in recent years. In commercial cultivation, up to 40% of flowering decreases the officinal yield of roots and accumulation of bioactive compounds. Although the regulatory mechanism of flowering genes during the photoperiod has been revealed, the networks during vernalization have not been mapped. Here, transcriptomics profiles of A. sinensis with uncompleted (T1), completed (T2) and avoided vernalization (T3) were performed using RNA-seq, and genes expression was validated with qRT-PCR. A total of 61,241 isoforms were annotated on KEGG, KOG, Nr and Swiss-Prot databases; 4212 and 5301 differentially expressed genes (DEGs) were observed; and 151 and 155 genes involved in flowering were dug out at T2 vs. T1 and T3 vs. T1, respectively. According to functional annotation, 104 co-expressed genes were classified into six categories: FLC expression (22; e.g., VILs, FCA and FLK), sucrose metabolism (12; e.g., TPSs, SUS3 and SPSs), hormone response (18; e.g., GID1B, RAP2s and IAAs), circadian clock (2; i.e., ELF3 and COR27), downstream floral integrators and meristem identity (15; e.g., SOC1, AGL65 and SPLs) and cold response (35; e.g., PYLs, ERFs and CORs). The expression levels of candidate genes were almost consistent with FPKM values and changes in sugar and hormone contents. Based on their functions, four pathways that regulate flowering during vernalization were mapped, including the vernalization pathway, the autonomic pathway, the age pathway and the GA (hormone) pathway. This transcriptomic analysis provides new insights into the gene-regulatory networks of flowering in A. sinensis.
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Affiliation(s)
- Mimi Luo
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.L.); (X.L.); (H.S.); (M.L.)
| | - Xiaoxia Liu
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.L.); (X.L.); (H.S.); (M.L.)
| | - Hongyan Su
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.L.); (X.L.); (H.S.); (M.L.)
| | - Meiling Li
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.L.); (X.L.); (H.S.); (M.L.)
| | - Mengfei Li
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.L.); (X.L.); (H.S.); (M.L.)
- Correspondence: (M.L.); (J.W.)
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Correspondence: (M.L.); (J.W.)
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Gao G, Lv Z, Zhang G, Li J, Zhang J, He C. An ABA-flavonoid relationship contributes to the differences in drought resistance between different sea buckthorn subspecies. TREE PHYSIOLOGY 2021; 41:744-755. [PMID: 33184668 DOI: 10.1093/treephys/tpaa155] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 11/08/2020] [Indexed: 06/11/2023]
Abstract
Drought is the most severe abiotic stress and hinders the normal growth and development of plants. Sea buckthorn (Hippophae rhamnoides Linn.) is a typical drought-resistant tree species. In this study, the leaves of the H. rhamnoides ssp. sinensis ('FN') and H. rhamnoides ssp. mongolica ('XY') were selected during drought-recovery cycles for RNA sequencing, and physiological and biochemical analyses. The results revealed that drought stress significantly decreased leaf water potential, net photosynthetic rate and stomatal conductance in both sea buckthorn subspecies. Similarly, the contents of flavone, flavonol, isoflavone and flavanone significantly decreased under drought stress in 'XY'. Conversely, in 'FN', the flavone and abscisic acid (ABA) contents were significantly higher under drought stress and recovered after rehydration. Meanwhile, 4618 and 6100 differentially expressed genes (DEGs) were identified under drought stress in 'FN' and 'XY', respectively. In total, 5164 DEGs were observed in the comparison between 'FN' and 'XY' under drought stress. This was more than the 3821 and 3387 DEGs found when comparing the subspecies under control and rehydration conditions, respectively. These DEGs were mainly associated with carotenoid biosynthesis, flavonoid biosynthesis, photosynthesis and plant hormone signal transduction. Six hub DEGs (ABCG5, ABCG22, ABCG32, ABCG36, ABF2 and PYL4) were identified to respond to drought stress based on weighted gene co-expression network analysis and Basic Local Alignment Search Tool (BLAST) analysis using DroughtDB. These six DEGs were annotated to play roles in the ABA-dependent signaling pathway. Sixteen RNA sequencing results involving eight genes and similar expression patterns (12/16) were validated using quantitative real-time Polymerase Chain Reaction (PCR). The biochemical and molecular mechanisms underlying the regulation of drought responses by ABA and flavonoids in sea buckthorn were clarified. In this study, gene co-expression networks were constructed, and the results suggested that the mutual regulation of ABA and flavonoid signaling contributed to the difference in drought resistance between the different sea buckthorn subspecies.
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Affiliation(s)
- Guori Gao
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan road, Haidian District, Beijing 100091, China
| | - Zhongrui Lv
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan road, Haidian District, Beijing 100091, China
| | - Guoyun Zhang
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan road, Haidian District, Beijing 100091, China
| | - Jiayi Li
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan road, Haidian District, Beijing 100091, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan road, Haidian District, Beijing 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, No.159, Longpan Road, Xuanwu district, Nanjing 210037, China
| | - Caiyun He
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan road, Haidian District, Beijing 100091, China
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Rashid M, Guangyuan H, Guangxiao Y, Hussain J, Xu Y. AP2/ERF Transcription Factor in Rice: Genome-Wide Canvas and Syntenic Relationships between Monocots and Eudicots. Evol Bioinform Online 2012; 8:321-55. [PMID: 22807623 PMCID: PMC3396566 DOI: 10.4137/ebo.s9369] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The transcription factor family intimately regulates gene expression in response to hormones, biotic and abiotic factors, symbiotic interactions, cell differentiation, and stress signalling pathways in plants. In this study, 170 AP2/ERF family genes are identified by phylogenetic analysis of the rice genome (Oryza sativa l. japonica) and they are divided into a total of 11 groups, including four major groups (AP2, ERF, DREB, and RAV), 10 subgroups, and two soloists. Gene structure analysis revealed that, at position-6, the amino acid threonine (Thr-6) is conserved in the double domain AP2 proteins compared to the amino acid arginine (Arg-6), which is preserved in the single domain of ERF proteins. In addition, the histidine (His) amino acid is found in both domains of the double domain AP2 protein, which is missing in single domain ERF proteins. Motif analysis indicates that most of the conserved motifs, apart from the AP2/ERF domain, are exclusively distributed among the specific clades in the phylogenetic tree and regulate plausible functions. Expression analysis reveals a widespread distribution of the rice AP2/ERF family genes within plant tissues. In the vegetative organs, the transcripts of these genes are found most abundant in the roots followed by the leaf and stem; whereas, in reproductive tissues, the gene expression of this family is observed high in the embryo and lemma. From chromosomal localization, it appears that repetition and tandem-duplication may contribute to the evolution of new genes in the rice genome. In this study, interspecies comparisons between rice and wheat reveal 34 rice loci and unveil the extent of collinearity between the two genomes. It was subsequently ascertained that chromosome-9 has more orthologous loci for CRT/DRE genes whereas chromosome-2 exhibits orthologs for ERF subfamily members. Maximum conserved synteny is found in chromosome-3 for AP2 double domain subfamily genes. Macrosynteny between rice and Arabidopsis, a distant, related genome, uncovered 11 homologs/orthologs loci in both genomes. The distribution of AP2/ERF family gene paralogs in Arabidopsis was most frequent in chromosome-1 followed by chromosome-5. In Arabidopsis, ERF subfamily gene orthologs are found on chromosome-1, chromosome-3, and chromosome-5, whereas DRE subfamily genes are found on chromosome-2 and chromosome-5. Orthologs for RAV and AP2 with double domains in Arabidopsis are located on chromosome-1 and chromosome-3, respectively. In conclusion, the data generated in this survey will be useful for conducting genomic research to determine the precise role of the AP2/ERF gene during stress responses with the ultimate goal of improving crops.
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Affiliation(s)
- Muhammad Rashid
- China-UK HUST-RRes Genetic Engineering and Genomics Joint Laboratory, International Science and Technology Cooperation Base (Genetic Engineering) of Chinese Ministry of Science and Technology, The key laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan 430074, China
| | - He Guangyuan
- China-UK HUST-RRes Genetic Engineering and Genomics Joint Laboratory, International Science and Technology Cooperation Base (Genetic Engineering) of Chinese Ministry of Science and Technology, The key laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan 430074, China
| | - Yang Guangxiao
- China-UK HUST-RRes Genetic Engineering and Genomics Joint Laboratory, International Science and Technology Cooperation Base (Genetic Engineering) of Chinese Ministry of Science and Technology, The key laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan 430074, China
| | - Javeed Hussain
- China-UK HUST-RRes Genetic Engineering and Genomics Joint Laboratory, International Science and Technology Cooperation Base (Genetic Engineering) of Chinese Ministry of Science and Technology, The key laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan 430074, China
| | - Yan Xu
- China-UK HUST-RRes Genetic Engineering and Genomics Joint Laboratory, International Science and Technology Cooperation Base (Genetic Engineering) of Chinese Ministry of Science and Technology, The key laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan 430074, China
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Ashida Y, Nishimoto M, Matsushima A, Watanabe J, Hirata T. Molecular cloning and mRNA expression of geraniol-inducible genes in cultured shoot primordia of Matricaria chamomilla. Biosci Biotechnol Biochem 2002; 66:2511-4. [PMID: 12506999 DOI: 10.1271/bbb.66.2511] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genes for two geraniol-responsive factors, designated McEREBP1 and McWRKY1, from cultured shoot primordia of Matricaria chamomilla were cloned. The deduced amino acid sequences of these genes were highly similar to those of the family of ethylene-responsive element binding proteins and elicitor-induced DNA-binding proteins containing a WRKY domain, respectively. The levels of McEREBP1 and McWRKY1 mRNAs were maximum when measured 1 h after treatment of the cultured cells with geraniol.
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MESH Headings
- Acyclic Monoterpenes
- Amino Acid Sequence
- Cloning, Molecular
- Culture Techniques/methods
- DNA-Binding Proteins/genetics
- Gene Expression Regulation, Plant/drug effects
- Genes, Plant/drug effects
- Genes, Plant/genetics
- Matricaria/genetics
- Matricaria/metabolism
- Molecular Sequence Data
- Plant Shoots/cytology
- Plant Shoots/genetics
- Plants, Genetically Modified/drug effects
- Plants, Genetically Modified/genetics
- Protein Structure, Tertiary
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Sequence Alignment
- Sequence Homology, Amino Acid
- Terpenes/pharmacology
- Time Factors
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Affiliation(s)
- Yoshiyuki Ashida
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
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