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Wang J, Ye H, Li X, Lv X, Lou J, Chen Y, Yu S, Zhang L. Genome-Wide Analysis of the MADS-Box Gene Family in Hibiscus syriacus and Their Role in Floral Organ Development. Int J Mol Sci 2023; 25:406. [PMID: 38203576 PMCID: PMC10779063 DOI: 10.3390/ijms25010406] [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: 10/31/2023] [Revised: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Hibiscus syriacus belongs to the Malvaceae family, and is a plant with medicinal, edible, and greening values. MADS-box transcription factor is a large family of regulatory factors involved in a variety of biological processes in plants. Here, we performed a genome-wide characterization of MADS-box proteins in H. syriacus and investigated gene structure, phylogenetics, cis-acting elements, three-dimensional structure, gene expression, and protein interaction to identify candidate MADS-box genes that mediate petal developmental regulation in H. syriacus. A total of 163 candidate MADS-box genes were found and classified into type I (Mα, Mβ, and Mγ) and type II (MIKC and Mδ). Analysis of cis-acting elements in the promoter region showed that most elements were correlated to plant hormones. The analysis of nine HsMADS expressions of two different H. syriacus cultivars showed that they were differentially expressed between two type flowers. The analysis of protein interaction networks also indicated that MADS proteins played a crucial role in floral organ identification, inflorescence and fruit development, and flowering time. This research is the first to analyze the MADS-box family of H. syriacus and provides an important reference for further study of the biological functions of the MADS-box, especially in flower organ development.
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Affiliation(s)
- Jie Wang
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China; (J.W.); (H.Y.); (X.L.); (J.L.); (Y.C.)
| | - Heng Ye
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China; (J.W.); (H.Y.); (X.L.); (J.L.); (Y.C.)
| | - Xiaolong Li
- College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China;
| | - Xue Lv
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China; (J.W.); (H.Y.); (X.L.); (J.L.); (Y.C.)
| | - Jiaqi Lou
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China; (J.W.); (H.Y.); (X.L.); (J.L.); (Y.C.)
| | - Yulu Chen
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China; (J.W.); (H.Y.); (X.L.); (J.L.); (Y.C.)
| | - Shuhan Yu
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China; (J.W.); (H.Y.); (X.L.); (J.L.); (Y.C.)
| | - Lu Zhang
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China; (J.W.); (H.Y.); (X.L.); (J.L.); (Y.C.)
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Yin Y, Yang T, Li S, Li X, Wang W, Fan S. Transcriptomic analysis reveals that methyl jasmonate confers salt tolerance in alfalfa by regulating antioxidant activity and ion homeostasis. FRONTIERS IN PLANT SCIENCE 2023; 14:1258498. [PMID: 37780521 PMCID: PMC10536279 DOI: 10.3389/fpls.2023.1258498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Introduction Alfalfa, a globally cultivated forage crop, faces significant challenges due to its vulnerability to salt stress. Jasmonates (JAs) play a pivotal role in modulating both plant growth and response to stressors. Methods In this study, alfalfa plants were subjected to 150 mM NaCl with or without methyl jasmonate (MeJA). The physiological parameters were detected and a transcriptomic analysis was performed to elucidate the mechanisms underlying MeJA-mediated salt tolerance in alfalfa. Results Results showed that exogenous MeJA regulated alfalfa seed germination and primary root growth in a dose-dependent manner, with 5µM MeJA exerting the most efficient in enhancing salt tolerance. MeJA at this concentration elavated the salt tolerance of young alfalfa seedlings by refining plant growth, enhancing antioxidant capacity and ameliorating Na+ overaccumulation. Subsequent transcriptomic analysis identified genes differentially regulated by MeJA+NaCl treatment and NaCl alone. PageMan analysis revealed several significantly enriched categories altered by MeJA+NaCl treatment, compared with NaCl treatment alone, including genes involved in secondary metabolism, glutathione-based redox regulation, cell cycle, transcription factors (TFs), and other signal transductions (such as calcium and ROS). Further weighted gene co-expression network analysis (WGCNA) uncovered that turquoise and yellow gene modules were tightly linked to antioxidant enzymes activity and ion content, respectively. Pyruvate decar-boxylase (PDC) and RNA demethylase (ALKBH10B) were identified as the most central hub genes in these two modules. Also, some TFs-hub genes were identified by WGCNA in these two modules highly positive-related to antioxidant enzymes activity and ion content. Discussion MeJA triggered a large-scale transcriptomic remodeling, which might be mediated by transcriptional regulation through TFs or post-transcriptional regulation through demethylation. Our findings contributed new perspectives for understanding the underneath mechanisms by which JA-mediated salt tolerance in alfalfa.
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Affiliation(s)
- YanLing Yin
- School of Resources and Environmental Engineering, Ludong University, Yantai, Shandong, China
| | - TianHui Yang
- School of Resources and Environmental Engineering, Ludong University, Yantai, Shandong, China
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Shuang Li
- School of Resources and Environmental Engineering, Ludong University, Yantai, Shandong, China
| | - Xiaoning Li
- School of Resources and Environmental Engineering, Ludong University, Yantai, Shandong, China
| | - Wei Wang
- School of Resources and Environmental Engineering, Ludong University, Yantai, Shandong, China
| | - ShuGao Fan
- School of Resources and Environmental Engineering, Ludong University, Yantai, Shandong, China
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Zhou B, Gao X, Zhao F. Integration of mRNA and miRNA Analysis Reveals the Post-Transcriptional Regulation of Salt Stress Response in Hemerocallis fulva. Int J Mol Sci 2023; 24:ijms24087290. [PMID: 37108448 PMCID: PMC10139057 DOI: 10.3390/ijms24087290] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 04/09/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
MicroRNAs (miRNAs) belong to non-coding small RNAs which have been shown to take a regulatory function at the posttranscriptional level in plant growth development and response to abiotic stress. Hemerocallis fulva is an herbaceous perennial plant with fleshy roots, wide distribution, and strong adaptability. However, salt stress is one of the most serious abiotic stresses to limit the growth and production of Hemerocallis fulva. To identify the miRNAs and their targets involved in the salt stress resistance, the salt-tolerant H. fulva with and without NaCl treatment were used as materials, and the expression differences of miRNAs-mRNAs related to salt-tolerance were explored and the cleavage sites between miRNAs and targets were also identified by using degradome sequencing technology. In this study, twenty and three significantly differential expression miRNAs (p-value < 0.05) were identified in the roots and leaves of H. fulva separately. Additionally, 12,691 and 1538 differentially expressed genes (DEGs) were also obtained, respectively, in roots and leaves. Moreover, 222 target genes of 61 family miRNAs were validated by degradome sequencing. Among the DE miRNAs, 29 pairs of miRNA targets displayed negatively correlated expression profiles. The qRT-PCR results also showed that the trends of miRNA and DEG expression were consistent with those of RNA-seq. A gene ontology (GO) enrichment analysis of these targets revealed that the calcium ion pathway, oxidative defense response, microtubule cytoskeleton organization, and DNA binding transcription factor responded to NaCl stress. Five miRNAs, miR156, miR160, miR393, miR166, and miR396, and several hub genes, squamosa promoter-binding-like protein (SPL), auxin response factor 12 (ARF), transport inhibitor response 1-like protein (TIR1), calmodulin-like proteins (CML), and growth-regulating factor 4 (GRF4), might play central roles in the regulation of NaCl-responsive genes. These results indicate that non-coding small RNAs and their target genes that are related to phytohormone signaling, Ca2+ signaling, and oxidative defense signaling pathways are involved in H. fulva's response to NaCl stress.
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Affiliation(s)
- Bo Zhou
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Northeast Forestry University, Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
| | - Fei Zhao
- Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
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Yang M, Chen J, Liu T, Xiang L, Zhou BF. Genome-Wide Identification and Expression Analysis of Calmodulin-Like Gene Family in Paspalums vaginatium Revealed Their Role in Response to Salt and Cold Stress. Curr Issues Mol Biol 2023; 45:1693-1711. [PMID: 36826054 PMCID: PMC9954852 DOI: 10.3390/cimb45020109] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/05/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
The calmodulin-like (CML) family is an important calcium (Ca2+) sensor in plants and plays a pivotal role in the response to abiotic and biotic stresses. As one of the most salt-tolerant grass species, Paspalums vaginatum is resistant to multiple abiotic stresses, such as salt, cold, and drought. However, investigations of PvCML proteins in P. vaginatum have been limited. Based on the recently published P. vaginatum genome, we identified forty-nine PvCMLs and performed a comprehensive bioinformatics analysis of PvCMLs. The main results showed that the PvCMLs were unevenly distributed on all chromosomes and that the expansion of PvCMLs was shaped by tandem and segmental duplications. In addition, cis-acting element analysis, expression profiles, and qRT-PCR analysis revealed that PvCMLs were involved in the response to salt and cold stress. Most interestingly, we found evidence of a tandem gene cluster that independently evolved in P. vaginatum and may participate in cold resistance. In summary, our work provides important insight into how grass species are resistant to abiotic stresses such as salt and cold and could be the basis of further gene function research on CMLs in P. vaginatum.
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Affiliation(s)
- Meizhen Yang
- Guangdong Engineering Research Center for Grassland Science, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jingjin Chen
- Guangdong Engineering Research Center for Grassland Science, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Tingting Liu
- Guangdong Engineering Research Center for Grassland Science, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Leilei Xiang
- Guangdong Engineering Research Center for Grassland Science, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Biao-Feng Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Correspondence: ; Tel.: +86-17665141041
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Bei X, Wang S, Huang X, Zhang X, Zhou J, Zhang H, Li G, Cheng C. Characterization of three tandem-duplicated calcium binding protein (CaBP) genes and promoters reveals their roles in the phytohormone and wounding responses in citrus. Int J Biol Macromol 2023; 227:1162-1173. [PMID: 36473528 DOI: 10.1016/j.ijbiomac.2022.11.297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/07/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022]
Abstract
Accumulated evidences have revealed the critical roles of calcium binding protein (CaBP) in growth and stress responses of plants. However, its function in woody plants is poorly understood. In this study, we cloned the CDS, gDNA and promoter sequences of three tandem-duplicated CaBPs (CsCaBP1, CsCaBP2 and CsCaBP3) from Citrus sinensis, analyzed their sequence characteristics, and investigated their gene expression patterns and promoter activities under treatments of CaCl2, several phytohormones and wounding. Results showed that the three CsCaBPs have high sequence similarity. Their expression was strongly induced by CaCl2, ethylene, jasmonic acid, salicylic acid and wounding, and the promoting effect of wounding on their expression was found to be partially ethylene-dependent. Consistently, we identified many phytohormone-related cis-acting elements in their promoters, and their promoter activity could be induced significantly by ethylene, jasmonic acid, salicylic acid and wounding. All the three CsCaBPs can interact with WRKY40, whose encoding gene showed a similar expression pattern to CsCaBPs under phytohormone and wounding treatments. In addition, CsERF14, CsERF21, CsERF3 and CsERF2 could bind to their promoters. The results obtained in this study indicated that the three duplicated CsCaBPs were functionally redundant and played similar roles in the phytohormone and wounding responses of C. sinensis.
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Affiliation(s)
- Xuejun Bei
- Key Laboratory for Conservation and Utilization of Subtropical Bio-Resources, Education Department of Guangxi Zhuang Autonomous Region, Yulin Normal University, Yulin 537000, China.
| | - Shaohua Wang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China
| | - Xia Huang
- Key Laboratory for Conservation and Utilization of Subtropical Bio-Resources, Education Department of Guangxi Zhuang Autonomous Region, Yulin Normal University, Yulin 537000, China
| | - Xiuli Zhang
- Key Laboratory for Conservation and Utilization of Subtropical Bio-Resources, Education Department of Guangxi Zhuang Autonomous Region, Yulin Normal University, Yulin 537000, China
| | - Jiayi Zhou
- Key Laboratory for Conservation and Utilization of Subtropical Bio-Resources, Education Department of Guangxi Zhuang Autonomous Region, Yulin Normal University, Yulin 537000, China
| | - Huiting Zhang
- Key Laboratory for Conservation and Utilization of Subtropical Bio-Resources, Education Department of Guangxi Zhuang Autonomous Region, Yulin Normal University, Yulin 537000, China
| | - Guoguo Li
- Horticultural Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Chunzhen Cheng
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China.
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Zhao H, Gao Y, Du Y, Du J, Han Y. Genome-wide analysis of the CML gene family and its response to melatonin in common bean (Phaseolus vulgaris L.). Sci Rep 2023; 13:1196. [PMID: 36681714 PMCID: PMC9867747 DOI: 10.1038/s41598-023-28445-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Calmodulin-like proteins (CML) are important calcium signal transduction proteins in plants. CML genes have been analyzed in several plants. However, little information on CML in Phaseolus vulgare is available. In this study, we identified 111 PvCMLs distributed on eleven chromosomes. Phylogenetic analysis classified them into seven subfamilies. Cis-acting element prediction showed that PvCML contained elements related to growth and development, response to abiotic stress and hormones. Moreover, the majority of PvCMLs showed different expression patterns in most of the nine tissues and developmental stages which indicated the role of PvCML in the growth and development of common bean. Additionally, the common bean was treated with melatonin by seed soaking, and root transcriptome at the 5th day and qRT-PCR of different tissue at several stages were performed to reveal the response of PvCML to the hormone. Interestingly, 9 PvCML genes of subfamily VI were detected responsive to exogenous melatonin, and the expression dynamics of nine melatonin response PvCML genes after seed soaking with melatonin were revealed. Finally, the protein interaction network analysis of nine melatonin responsive PvCMLs was constructed. The systematic analysis of the PvCML gene family provides theoretical support for the further elucidation of their functions, and melatonin response molecular mechanism of the CML family in P. vulgaris.
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Affiliation(s)
- Hongyan Zhao
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
- National Coarse Cereals Engineering Research Center, Daqing, 163319, Heilongjiang, People's Republic of China
| | - Yamei Gao
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in the Cold Region, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Yanli Du
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
| | - Jidao Du
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
| | - Yiqiang Han
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China.
- National Coarse Cereals Engineering Research Center, Daqing, 163319, Heilongjiang, People's Republic of China.
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Liu Y, Yin F, Liao L, Shuai L. Genome-wide identification and expression analysis of calmodulin-like proteins in cucumber. PeerJ 2023; 11:e14637. [PMID: 36655051 PMCID: PMC9841910 DOI: 10.7717/peerj.14637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/05/2022] [Indexed: 01/15/2023] Open
Abstract
Background The calmodulin-like (CML) protein is a crucial Ca2+-binding protein that can sense and conduct the Ca2+ signal in response to extracellular stimuli. The CML protein families have been identified and characterized in many species. Nevertheless, scarce information on cucumber CML is retrievable. Methods In this study, bioinformatic analyses, including gene structure, conserved domain, phylogenetic relationship, chromosome distribution, and gene synteny, were comprehensively performed to identify and characterize CsCML gene members. Spatiotemporal expression analysis in different organs and environment conditions were assayed with real-time quantitative polymerase chain reaction (qRT-PCR). Results Forty-four CsCMLs family members were well characterized, and the results showed that the 44 CsCML proteins contained one to four EF-hand domains without other functional domains. Most of the CsCML proteins were intron-less and unevenly distributed on seven chromosomes; two tandemly duplicated gene pairs and three segmentally duplicated gene pairs were identified in the cucumber genome. Cis-acting element analysis showed that the hormone, stress, and plant growth and development-related elements were in the promotor regions. In addition, spatiotemporal expression analysis revealed distinctive expression patterns for CsCML genes in different tissues and environmental conditions, and a putative protein interaction network also confirmed their potential role in responding to various stimuli. These results provide a foundation for understanding CsCMLs and provide a theoretical basis for further study of the physiological functions of CsCMLs.
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Affiliation(s)
- Yunfen Liu
- College of Food and Biological Engineering/Institute of Food Science and Engineering Techology, Hezhou University, Hezhou, Guangxi, China,Guangxi Key Laboratory of Health Care Food Science and Technology, Hezhou University, Hezhou, Guangxi, China
| | - Feilong Yin
- College of Food and Biological Engineering/Institute of Food Science and Engineering Techology, Hezhou University, Hezhou, Guangxi, China
| | - Lingyan Liao
- College of Food and Biological Engineering/Institute of Food Science and Engineering Techology, Hezhou University, Hezhou, Guangxi, China
| | - Liang Shuai
- College of Food and Biological Engineering/Institute of Food Science and Engineering Techology, Hezhou University, Hezhou, Guangxi, China,Guangxi Key Laboratory of Health Care Food Science and Technology, Hezhou University, Hezhou, Guangxi, China
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Ma W, Yang J, Ding J, Zhao W, Peng YL, Bhadauria V. Gapless reference genome assembly of Didymella glomerata, a new fungal pathogen of maize causing Didymella leaf blight. FRONTIERS IN PLANT SCIENCE 2022; 13:1022819. [PMID: 36388559 PMCID: PMC9643772 DOI: 10.3389/fpls.2022.1022819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Didymella leaf blight (DLB) caused by Didymella glomerata is a new fungal disease of maize (Zea mays), first detected in 2021 in Panjin, Liaoning province of China. Here we report the reference genome assembly of D. glomerata to unravel how the fungal pathogen controls its virulence on maize at the molecular level. A maize-infecting strain Pj-2 of the pathogen was sequenced on the Illumina NovaSeq 6000 and PacBio Sequel II platforms at a 575-fold genomic coverage. The 33.17 Mb gapless genome assembly comprises 32 scaffolds with L/N50 of 11/1.36 Mb, four of which represent full-length chromosomes. The Pj-2 genome is predicted to contain 10,334 protein-coding genes, of which 211, 12 and 134 encode effector candidates, secondary metabolite backbone-forming enzymes and CAZymes, respectively. Some of these genes are potentially implicated in niche adaptation and expansion, such as colonizing new hosts like maize. Phylogenomic analysis of eight strains of six Didymella spp., including three sequenced strains of D. glomerata, reveals that the maize (Pj-2)- and Chrysanthemum (CBS 528.66)-infecting strains of D. glomerata are genetically similar (sharing 92.37% genome with 98.89% identity), whereas Pj-2 shows truncated collinearity with extensive chromosomal rearrangements with the Malus-infecting strain M27-16 of D. glomerata (sharing only 55.01% genome with 88.20% identity). Pj-2 and CBS 528.66 carry four major reciprocal translocations in their genomes, which may enable them to colonize the different hosts. Furthermore, germplasm screening against Pj-2 led to the identification of three sources of DLB resistance in maize, including a tropical inbred line CML496. DLB resistance in the line is attributed to the accumulation of ROS H2O2 in the apoplastic space of the infected cells, which likely restricts the fungal growth and proliferation.
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Affiliation(s)
- Wendi Ma
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jun Yang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- Ministry of Agriculture and Rural Affairs, Key Laboratory for Crop Pest Monitoring and Green Control, China Agricultural University, Beijing, China
| | - Junqiang Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Wensheng Zhao
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- Ministry of Agriculture and Rural Affairs, Key Laboratory for Crop Pest Monitoring and Green Control, China Agricultural University, Beijing, China
| | - You-Liang Peng
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- Ministry of Agriculture and Rural Affairs, Key Laboratory for Crop Pest Monitoring and Green Control, China Agricultural University, Beijing, China
| | - Vijai Bhadauria
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- Ministry of Agriculture and Rural Affairs, Key Laboratory for Crop Pest Monitoring and Green Control, China Agricultural University, Beijing, China
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Yu S, Wu J, Sun Y, Zhu H, Sun Q, Zhao P, Huang R, Guo Z. A calmodulin-like protein (CML10) interacts with cytosolic enzymes GSTU8 and FBA6 to regulate cold tolerance. PLANT PHYSIOLOGY 2022; 190:1321-1333. [PMID: 35751606 PMCID: PMC9516781 DOI: 10.1093/plphys/kiac311] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 06/04/2022] [Indexed: 05/23/2023]
Abstract
Calmodulin-like proteins (CMLs) are calcium (Ca2+) sensors involved in plant growth and development as well as adaptation to environmental stresses; however, their roles in plant responses to cold are not well understood. To reveal the role of MsCML10 from alfalfa (Medicago sativa) in regulating cold tolerance, we examined transgenic alfalfa and Medicago truncatula overexpressing MsCML10, MsCML10-RNAi alfalfa, and a M. truncatula cml10-1 mutant and identified MsCML10-interacting proteins. MsCML10 and MtCML10 transcripts were induced by cold treatment. Upregulation or downregulation of MsCML10 resulted in increased or decreased cold tolerance, respectively, while cml10-1 showed decreased cold tolerance that was complemented by expressing MsCML10, suggesting that MsCML10 regulates cold tolerance. MsCML10 interacted with glutathione S-transferase (MsGSTU8) and fructose 1,6-biphosphate aldolase (MsFBA6), and the interaction depended on the presence of Ca2+. The altered activities of Glutathione S-transferase and FBA and levels of ROS and sugars were associated with MsCML10 transcript levels. We propose that MsCML10 decodes the cold-induced Ca2+ signal and regulates cold tolerance through activating MsGSTU8 and MsFBA6, leading to improved maintenance of ROS homeostasis and increased accumulation of sugars for osmoregulation, respectively.
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Affiliation(s)
- Shuhan Yu
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaxuan Wu
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanmei Sun
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Haifeng Zhu
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiguo Sun
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengcheng Zhao
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Risheng Huang
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
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Fu M, Wu C, Li X, Ding X, Guo F. Genome-Wide Identification and Expression Analysis of CsCaM/CML Gene Family in Response to Low-Temperature and Salt Stresses in Chrysanthemum seticuspe. PLANTS 2022; 11:plants11131760. [PMID: 35807712 PMCID: PMC9268918 DOI: 10.3390/plants11131760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 11/29/2022]
Abstract
Calmodulin (CaM) and calmodulin-like proteins (CML) act as significant Ca2+ sensors binding Ca2+ with EF-hand motifs and have been reported to be involved in various environmental stresses in plants. In this study, calmodulin CsCaM/CML gene family members were identified based on the genome of Chrysanthemum seticuspe published recently; a phylogenetic tree was constructed; gene structures and chromosomal locations of CsCaM/CML were depicted; cis-acting regulatory elements were predicted; collinearity and duplicate events of CaM/CML were analyzed using MCScanX software; and the expression levels of CsCaM/CML in response to abiotic stress were analyzed, based on the published RNA-seq data. We identified 86 CsCaM/CML (4 CsCaMs and 82 CsCMLs) genes in total. Promoter sequences of CsCaM/CML contained elements related to abiotic stresses (including low-temperature and anaerobic stresses) and plant hormones (including abscisic acid (ABA), MeJA, and salicylic acid). CsCaM/CML genes were distributed on nine chromosomes unevenly. Collinearity analysis indicated that recent segmental duplications significantly enlarged the scale of the CML family in C. seticuspe. Four CsCMLs (CsCML14, CsCML50, CsCML65, and CsCML79) were statistically differentially regulated under low-temperature and salt stress compared with those in the normal condition. These results indicate diverse roles of CsCaM/CML in plant development and in response to environmental stimuli in C. seticuspe.
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Affiliation(s)
| | | | | | | | - Fangqi Guo
- Correspondence: Correspondence: ; Tel.: +86-0571-8640-4013
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Sun Q, Huang R, Zhu H, Sun Y, Guo Z. A novel Medicago truncatula calmodulin-like protein (MtCML42) regulates cold tolerance and flowering time. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1069-1082. [PMID: 34528312 DOI: 10.1111/tpj.15494] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 05/20/2023]
Abstract
Calmodulin-like proteins (CMLs) are one of the Ca2+ sensors in plants, but the functions of most CMLs remain unknown. The regulation of cold tolerance and flowering time by MtCML42 in Medicago truncatula and the underlying mechanisms were investigated using MtCML42-overexpressing plants and cml42 Medicago mutants with a Tnt1 retrotransposon insertion. Compared with the wild type (WT), MtCML42-overexpressing lines had increased cold tolerance, whereas cml42 mutants showed decreased cold tolerance. The impaired cold tolerance in cml42 could b complemented by MtCML42 expression. The transcript levels of MtCBF1, MtCBF4, MtCOR413, MtCAS15, MtLTI6A, MtGolS1 and MtGolS2 and the concentrations of raffinose and sucrose were increased in response to cold treatment, whereas higher levels were observed in MtCML42-overexpressing lines and lower levels were observed in cml42 mutants. In addition, early flowering with upregulated MtFTa1 and downregulated MtABI5 transcripts was observed in MtCML42-overexpressing lines, whereas delayed flowering with downregulated MtFTa1 and upregulated MtABI5 was observed in cml42. MtABI5 expression could complement the flowering phenotype in the Arabidopsis mutant abi5. Our results suggest that MtCML42 positively regulates MtCBF1 and MtCBF4 expression, which in turn upregulates the expression of some COR genes, MtGolS1 and MtGolS2, which leads to raffinose accumulation and increased cold tolerance. MtCML42 regulates flowering time through sequentially downregulating MtABI5 and upregulating MtFTa1 expression.
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Affiliation(s)
- Qiguo Sun
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Risheng Huang
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haifeng Zhu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanmei Sun
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhenfei Guo
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
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12
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Yu S, Sun Q, Wu J, Zhao P, Sun Y, Guo Z. Genome-Wide Identification and Characterization of Short-Chain Dehydrogenase/Reductase (SDR) Gene Family in Medicago truncatula. Int J Mol Sci 2021; 22:9498. [PMID: 34502406 PMCID: PMC8430790 DOI: 10.3390/ijms22179498] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 11/25/2022] Open
Abstract
Short-chain dehydrogenase/reductase (SDR) belongs to the NAD(P)(H)-dependent oxidoreductase superfamily. Limited investigations reveal that SDRs participate in diverse metabolisms. A genome-wide identification of the SDR gene family in M. truncatula was conducted. A total of 213 MtSDR genes were identified, and they were distributed on all chromosomes unevenly. MtSDR proteins were categorized into seven subgroups based on phylogenetic analysis and three types including 'classic', 'extended', and 'atypical', depending on the cofactor-binding site and active site. Analysis of the data from M. truncatula Gene Expression Atlas (MtGEA) showed that above half of MtSDRs were expressed in at least one organ, and lots of MtSDRs had a preference in a tissue-specific expression. The cis-acting element responsive to plant hormones (salicylic acid, ABA, auxin, MeJA, and gibberellin) and stresses were found in the promoter of some MtSDRs. Many genes of MtSDR7C,MtSDR65C, MtSDR110C, MtSDR114C, and MtSDR108E families were responsive to drought, salt, and cold. The study provides useful information for further investigation on biological functions of MtSDRs, especially in abiotic stress adaptation, in the future.
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Affiliation(s)
| | | | | | | | | | - Zhenfei Guo
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China; (S.Y.); (Q.S.); (J.W.); (P.Z.); (Y.S.)
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13
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Genome-Wide Identification and Analysis of the Polycomb Group Family in Medicago truncatula. Int J Mol Sci 2021; 22:ijms22147537. [PMID: 34299158 PMCID: PMC8303337 DOI: 10.3390/ijms22147537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/01/2021] [Accepted: 07/12/2021] [Indexed: 12/20/2022] Open
Abstract
Polycomb group (PcG) proteins, which are important epigenetic regulators, play essential roles in the regulatory networks involved in plant growth, development, and environmental stress responses. Currently, as far as we know, no comprehensive and systematic study has been carried out on the PcG family in Medicago truncatula. In the present study, we identified 64 PcG genes with distinct gene structures from the M. truncatula genome. All of the PcG genes were distributed unevenly over eight chromosomes, of which 26 genes underwent gene duplication. The prediction of protein interaction network indicated that 34 M. truncatula PcG proteins exhibited protein-protein interactions, and MtMSI1;4 and MtVRN2 had the largest number of protein-protein interactions. Based on phylogenetic analysis, we divided 375 PcG proteins from 27 species into three groups and nine subgroups. Group I and Group III were composed of five components from the PRC1 complex, and Group II was composed of four components from the PRC2 complex. Additionally, we found that seven PcG proteins in M. truncatula were closely related to the corresponding proteins of Cicer arietinum. Syntenic analysis revealed that PcG proteins had evolved more conservatively in dicots than in monocots. M. truncatula had the most collinearity relationships with Glycine max (36 genes), while collinearity with three monocots was rare (eight genes). The analysis of various types of expression data suggested that PcG genes were involved in the regulation and response process of M. truncatula in multiple developmental stages, in different tissues, and for various environmental stimuli. Meanwhile, many differentially expressed genes (DEGs) were identified in the RNA-seq data, which had potential research value in further studies on gene function verification. These findings provide novel and detailed information on the M. truncatula PcG family, and in the future it would be helpful to carry out related research on the PcG family in other legumes.
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Zhang Y, Huang J, Hou Q, Liu Y, Wang J, Deng S. Isolation and Functional Characterization of a Salt-Responsive Calmodulin-Like Gene MpCML40 from Semi-Mangrove Millettia pinnata. Int J Mol Sci 2021; 22:3475. [PMID: 33801703 PMCID: PMC8036263 DOI: 10.3390/ijms22073475] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022] Open
Abstract
Salt stress is a major increasing threat to global agriculture. Pongamia (Millettia pinnata), a semi-mangrove, is a good model to study the molecular mechanism of plant adaptation to the saline environment. Calcium signaling pathways play critical roles in the model plants such as Arabidopsis in responding to salt stress, but little is known about their function in Pongamia. Here, we have isolated and characterized a salt-responsive MpCML40, a calmodulin-like (CML) gene from Pongamia. MpCML40 protein has 140 amino acids and is homologous with Arabidopsis AtCML40. MpCML40 contains four EF-hand motifs and a bipartite NLS (Nuclear Localization Signal) and localizes both at the plasma membrane and in the nucleus. MpCML40 was highly induced after salt treatment, especially in Pongamia roots. Heterologous expression of MpCML40 in yeast cells improved their salt tolerance. The 35S::MpCML40 transgenic Arabidopsis highly enhanced seed germination rate and root length under salt and osmotic stresses. The transgenic plants had a higher level of proline and a lower level of MDA (malondialdehyde) under normal and stress conditions, which suggested that heterologous expression of MpCML40 contributed to proline accumulation to improve salt tolerance and protect plants from the ROS (reactive oxygen species) destructive effects. Furthermore, we did not observe any measurable discrepancies in the development and growth between the transgenic plants and wild-type plants under normal growth conditions. Our results suggest that MpCML40 is an important positive regulator in response to salt stress and of potential application in producing salt-tolerant crops.
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Affiliation(s)
- Yi Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
| | - Jianzi Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China;
| | - Qiongzhao Hou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (Q.H.); (Y.L.)
| | - Yujuan Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (Q.H.); (Y.L.)
| | - Jun Wang
- CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Costal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
| | - Shulin Deng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
- Xiaoliang Research Station for Tropical Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510275, China
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15
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Liu SX, Qin B, Fang QX, Zhang WJ, Zhang ZY, Liu YC, Li WJ, Du C, Liu XX, Zhang YL, Guo YX. Genome-wide identification, phylogeny and expression analysis of the bZIP gene family in Alfalfa ( Medicago sativa). BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1938674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Shu-Xia Liu
- Department of Crop Cultivation, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
- Laboratory of Economic Plants, Crop Cultivation Center, Daqing Branch of Heilongjiang Academy of Sciences, Daqing, Heilongjiang, PR China
| | - Bin Qin
- Department of Crop Cultivation, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Qing-xi Fang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Wen-Jing Zhang
- Department of Crop Cultivation, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Zhe-Yu Zhang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Yang-Cheng Liu
- Department of Crop Cultivation, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Wei-Jia Li
- Department of Crop Cultivation, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Chao Du
- Department of Crop Cultivation, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Xian-xian Liu
- Department of Crop Cultivation, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - You-li Zhang
- Department of Crop Cultivation, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Yong-Xia Guo
- Department of Crop Cultivation, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
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