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Liu S, Xiao M, Fang A, Tian B, Yu Y, Bi C, Ma D, Yang Y. LysM Proteins TaCEBiP and TaLYK5 are Involved in Immune Responses Mediated by Chitin Coreceptor TaCERK1 in Wheat. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13535-13545. [PMID: 37665660 DOI: 10.1021/acs.jafc.3c02686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Plant lysin motif (LysM) ectodomain receptors interact with pathogen-associated molecular patterns (PAMPs) and have critical functions in plant-microbe interactions. In this study, 65 LysM family genes were identified using the recent version of the reference sequence of bread wheat (Triticum aestivum), in which 23, 16, 20, and 6 members belonged to LysM-containing receptor-like kinases (LYKs), LysM-containing receptor-like proteins (LYPs), extracellular LysM proteins (LysMes), and intracellular nonsecretory LysM proteins (LysMns), respectively. The study found that TaCEBiP, TaLYK5, and TaCERK1 were highly responsive to PAMP elicitors and phytopathogens, with TaCEBiP and TaLYK5 binding directly to chitin. TaCERK1 acted as a coreceptor with TaCEBiP and TaLYK5 at the plasma membrane. Overexpression of TaCEBiP, TaLYK5, and TaCERK1 in Nicotiana benthamiana leaves exhibited enhanced resistance to Sclerotinia sclerotiorum. Subsequently, knocking down TaCEBiP, TaLYK5, and TaCERK1 genes with barley stripe mosaic virus-VIGS compromised the wheat defense response to an avirulent strain of Puccinia striiformis. The study concluded that wheat has two synergistic chitin perception systems for detecting pathogen elicitors, with the activated CERK1 intracellular kinase domain leading to signaling transduction. This research provides valuable insights into the functional roles and regulatory mechanisms of wheat LysM members under biotic stress.
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Affiliation(s)
- Saifei Liu
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Muye Xiao
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Anfei Fang
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Binnian Tian
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Yang Yu
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Chaowei Bi
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Dongfang Ma
- Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Yuheng Yang
- College of Plant Protection, Southwest University, Chongqing 400715, China
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Zhang L, Li S, Fang X, An H, Zhang X. Genome-wide analysis of LysM gene family members and their expression in response to Colletotrichum fructicola infection in Octoploid strawberry( Fragaria × ananassa). FRONTIERS IN PLANT SCIENCE 2023; 13:1105591. [PMID: 36756233 PMCID: PMC9900028 DOI: 10.3389/fpls.2022.1105591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/30/2022] [Indexed: 06/18/2023]
Abstract
The cultivated octoploid strawberry (Fragaria × ananassa) is an economically important fruit that is planted worldwide. The lysin motif (LysM) protein family is composed of the major class of plant pattern recognition receptors, which play important roles in sensing pathogen-associated molecular patterns (PAMPs), and subsequently triggers downstream plant immunity. In the present study, a comprehensive, genome-wide analysis of F. × ananassa LysM (FaLysM) genes was performed to investigate gene structures, phylogenic relationships, chromosome location, collinear relationships, transcription factor binding sites, and protein model analysis. We aimed to identify the LysM genes involved in the defense against plant pathogens. A total of 14 FaLysM genes were identified in the F. × ananassa genome and divided into 2 subgroups (LYP and LYK) on the basis of the phylogenetic analysis. The Ka/Ks ratio for the duplicated pair of most FaLysM genes was less than 1, which indicates that the selection pressure was mostly subject to the purifying selection during evolution. The protein model analysis revealed that FaLysM2-10 contain conserved mode of chitin binding, which suggest the potential role of FaLysM2-10 in pathogen perception and plant immunity. The RNA-Seq results showed the differential regulation of 14 FaLysM genes in response to Colletotrichum fructicola infection, implying the complex interaction between C. fructicola and strawberry. Knockout of candidate effector gene CfLysM2, which was previously proved to be highly expressed during C. fructicola infection, resulted in the up-regulation of six FaLysM genes (FaLysM1, FaLysM2, FaLysM3, FaLysM7, FaLysM8, and FaLysM12), indicating the competitive relations between CfLysM2 and FaLysM genes. Overall, this study provides fundamental information on the roles of LysM proteins in octoploid strawberry and its interaction with C. fructicola, laying useful information for further investigation on the C. fructicola-strawberry interaction and strawberry resistance breeding.
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Affiliation(s)
| | | | | | - Haishan An
- *Correspondence: Haishan An, ; Xueying Zhang,
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Ren W, Zhang C, Wang M, Zhang C, Xu X, Huang Y, Chen Y, Lin Y, Lai Z. Genome-wide identification, evolution analysis of LysM gene family members and their expression analysis in response to biotic and abiotic stresses in banana (Musa L.). Gene X 2022; 845:146849. [PMID: 36044944 DOI: 10.1016/j.gene.2022.146849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
LysM (Lysin motif), in response to pathogenic molecular stresses, is a crucial signal recognition gene. To understand the molecular characteristics of banana LysM gene family members, we used a series of bioinformatics methods. Based on the genomic databases of Musa acuminata, Musa balbisiana and Musa itinerans, a total of 53 genes and 55 proteins were identified, with 21 genes and 23 proteins in the M.acuminata, 16 genes and 16 proteins in each of M.balbisiana and M.itinerans, respectively. According to the conserved structural domains, LysM can be divided into five classes, namely LysM&MltD, LYK, LYP, LysMn, and LysMe. The LysM gene was relatively highly conserved in the evolution of the three genomes of banana, and some differences occurred. Expression analysis revealed that MaLysM4-5 was relatively highly expressed under high-temperature stress, low-temperature stress and pathogen infection; at the same time, about one-third of the members were down-regulated under low-temperature stress and high-temperature stress, while the expression of MaLysM10-1 and MaLysM4-5 were up-regulated. After the banana wilt fungus FocTR4 infected the banana roots, MaLysM1 was down-regulated and MaLysM11-1 was up-regulated. In conclusion, our study suggests that MaLysMs may be necessary in the response to high- and low-temperature stresses, as well as the banana wilt fungus infestation. Overall, this paper found that LysM genes may be involved in biotic and abiotic stresses in banana, and provided helpful information about LysM's evolution, expression and properties, which will provide theoretical references for further studies on the functions of LysM genes and resistance breeding in the future.
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Affiliation(s)
- Wenhui Ren
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chengyu Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengge Wang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chunyu Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoqiong Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuji Huang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Xia X, Zhang X, Zhang Y, Wang L, An Q, Tu Q, Wu L, Jiang P, Zhang P, Yu L, Li G, He Y. Characterization of the WAK Gene Family Reveals Genes for FHB Resistance in Bread Wheat (Triticum aestivum L.). Int J Mol Sci 2022; 23:ijms23137157. [PMID: 35806165 PMCID: PMC9266398 DOI: 10.3390/ijms23137157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 12/10/2022] Open
Abstract
Wall-associated kinases (WAKs) are important receptor-like proteins that play major roles in plant defense against pathogens. Fusarium head blight (FHB), one of the most widespread and devastating crop diseases, reduces wheat yield and leads to quality deterioration. Although WAK gene families have been studied in many plants, systematic research on bread wheat (Triticum aestivum) and its role in FHB resistance, in particular, is lacking. In this study, we identified and characterized 320 genes of the TaWAK family in wheat distributed across all chromosomes except 4B and divided them into three phylogenetic groups. Duplication and synteny analyses provided valuable information on the evolutionary characteristics of the TaWAK genes. The gene expression pattern analysis suggested that TaWAK genes play diverse roles in plant biological processes and that at least 30 genes may be involved in the response to Fusarium infection in wheat spikes, with most of the genes contributing to pectin- and chitin-induced defense pathways. Furthermore, 45 TaWAK genes were identified within 17 hcmQTLs that are related to wheat FHB resistance. Our findings provide potential candidate genes for improving FHB resistance and insights into the future functional analysis of TaWAK genes in wheat.
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Affiliation(s)
- Xiaobo Xia
- CIMMYT-JAAS Joint Center for Wheat Diseases, Key Laboratory of Germplasm Innovation in Downstream of Huaihe River (Nanjing), Ministry of Agriculture and Rural Affairs, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (X.X.); (X.Z.); (Y.Z.); (L.W.); (Q.A.); (Q.T.); (L.W.); (P.J.); (P.Z.); (L.Y.)
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Xu Zhang
- CIMMYT-JAAS Joint Center for Wheat Diseases, Key Laboratory of Germplasm Innovation in Downstream of Huaihe River (Nanjing), Ministry of Agriculture and Rural Affairs, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (X.X.); (X.Z.); (Y.Z.); (L.W.); (Q.A.); (Q.T.); (L.W.); (P.J.); (P.Z.); (L.Y.)
| | - Yicong Zhang
- CIMMYT-JAAS Joint Center for Wheat Diseases, Key Laboratory of Germplasm Innovation in Downstream of Huaihe River (Nanjing), Ministry of Agriculture and Rural Affairs, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (X.X.); (X.Z.); (Y.Z.); (L.W.); (Q.A.); (Q.T.); (L.W.); (P.J.); (P.Z.); (L.Y.)
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Lirong Wang
- CIMMYT-JAAS Joint Center for Wheat Diseases, Key Laboratory of Germplasm Innovation in Downstream of Huaihe River (Nanjing), Ministry of Agriculture and Rural Affairs, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (X.X.); (X.Z.); (Y.Z.); (L.W.); (Q.A.); (Q.T.); (L.W.); (P.J.); (P.Z.); (L.Y.)
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Qi An
- CIMMYT-JAAS Joint Center for Wheat Diseases, Key Laboratory of Germplasm Innovation in Downstream of Huaihe River (Nanjing), Ministry of Agriculture and Rural Affairs, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (X.X.); (X.Z.); (Y.Z.); (L.W.); (Q.A.); (Q.T.); (L.W.); (P.J.); (P.Z.); (L.Y.)
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Qiang Tu
- CIMMYT-JAAS Joint Center for Wheat Diseases, Key Laboratory of Germplasm Innovation in Downstream of Huaihe River (Nanjing), Ministry of Agriculture and Rural Affairs, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (X.X.); (X.Z.); (Y.Z.); (L.W.); (Q.A.); (Q.T.); (L.W.); (P.J.); (P.Z.); (L.Y.)
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Lei Wu
- CIMMYT-JAAS Joint Center for Wheat Diseases, Key Laboratory of Germplasm Innovation in Downstream of Huaihe River (Nanjing), Ministry of Agriculture and Rural Affairs, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (X.X.); (X.Z.); (Y.Z.); (L.W.); (Q.A.); (Q.T.); (L.W.); (P.J.); (P.Z.); (L.Y.)
| | - Peng Jiang
- CIMMYT-JAAS Joint Center for Wheat Diseases, Key Laboratory of Germplasm Innovation in Downstream of Huaihe River (Nanjing), Ministry of Agriculture and Rural Affairs, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (X.X.); (X.Z.); (Y.Z.); (L.W.); (Q.A.); (Q.T.); (L.W.); (P.J.); (P.Z.); (L.Y.)
| | - Peng Zhang
- CIMMYT-JAAS Joint Center for Wheat Diseases, Key Laboratory of Germplasm Innovation in Downstream of Huaihe River (Nanjing), Ministry of Agriculture and Rural Affairs, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (X.X.); (X.Z.); (Y.Z.); (L.W.); (Q.A.); (Q.T.); (L.W.); (P.J.); (P.Z.); (L.Y.)
| | - Lixuan Yu
- CIMMYT-JAAS Joint Center for Wheat Diseases, Key Laboratory of Germplasm Innovation in Downstream of Huaihe River (Nanjing), Ministry of Agriculture and Rural Affairs, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (X.X.); (X.Z.); (Y.Z.); (L.W.); (Q.A.); (Q.T.); (L.W.); (P.J.); (P.Z.); (L.Y.)
| | - Gang Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (G.L.); (Y.H.)
| | - Yi He
- CIMMYT-JAAS Joint Center for Wheat Diseases, Key Laboratory of Germplasm Innovation in Downstream of Huaihe River (Nanjing), Ministry of Agriculture and Rural Affairs, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (X.X.); (X.Z.); (Y.Z.); (L.W.); (Q.A.); (Q.T.); (L.W.); (P.J.); (P.Z.); (L.Y.)
- Correspondence: (G.L.); (Y.H.)
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Li F, Yin J, Lu M, Yang Q, Zeng Z, Zhang B, Li Z, Qiu Y, Dai H, Chen Y, Zhu F. ConSIG: consistent discovery of molecular signature from OMIC data. Brief Bioinform 2022; 23:6618243. [PMID: 35758241 DOI: 10.1093/bib/bbac253] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/09/2022] [Accepted: 05/31/2022] [Indexed: 12/12/2022] Open
Abstract
The discovery of proper molecular signature from OMIC data is indispensable for determining biological state, physiological condition, disease etiology, and therapeutic response. However, the identified signature is reported to be highly inconsistent, and there is little overlap among the signatures identified from different biological datasets. Such inconsistency raises doubts about the reliability of reported signatures and significantly hampers its biological and clinical applications. Herein, an online tool, ConSIG, was constructed to realize consistent discovery of gene/protein signature from any uploaded transcriptomic/proteomic data. This tool is unique in a) integrating a novel strategy capable of significantly enhancing the consistency of signature discovery, b) determining the optimal signature by collective assessment, and c) confirming the biological relevance by enriching the disease/gene ontology. With the increasingly accumulated concerns about signature consistency and biological relevance, this online tool is expected to be used as an essential complement to other existing tools for OMIC-based signature discovery. ConSIG is freely accessible to all users without login requirement at https://idrblab.org/consig/.
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Affiliation(s)
- Fengcheng Li
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jiayi Yin
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Mingkun Lu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Qingxia Yang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Zhenyu Zeng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Bing Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhaorong Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Yunqing Qiu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, China
| | - Haibin Dai
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yuzong Chen
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, The Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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Wu W, Zhu S, Xu L, Zhu L, Wang D, Liu Y, Liu S, Hao Z, Lu Y, Yang L, Shi J, Chen J. Genome-wide identification of the Liriodendron chinense WRKY gene family and its diverse roles in response to multiple abiotic stress. BMC PLANT BIOLOGY 2022; 22:25. [PMID: 35012508 PMCID: PMC8744262 DOI: 10.1186/s12870-021-03371-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/29/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Liriodendron chinense (Lchi) is a tree species within the Magnoliaceae family and is considered a basal angiosperm. The too low or high temperature or soil drought will restrict its growth as the adverse environmental conditions, thus improving L. chinense abiotic tolerance was the key issues to study. WRKYs are a major family of plant transcription factors known to often be involved in biotic and abiotic stress responses. So far, it is still largely unknown if and how the LchiWRKY gene family is tied to regulating L. chinense stress responses. Therefore, studying the involvement of the WRKY gene family in abiotic stress regulation in L. chinense could be very informative in showing how this tree deals with such stressful conditions. RESULTS In this research, we performed a genome-wide analysis of the Liriodendron chinense (Lchi) WRKY gene family, studying their classification relationships, gene structure, chromosomal locations, gene duplication, cis-element, and response to abiotic stress. The 44 members of the LchiWRKY gene family contain a significant amount of sequence diversity, with their lengths ranging from 525 bp to 40,981 bp. Using classification analysis, we divided the 44 LchiWRKY genes into three phylogenetic groups (I, II, II), with group II then being further divided into five subgroups (IIa, IIb, IIc, IId, IIe). Comparative phylogenetic analysis including the WRKY families from 17 plant species suggested that LchiWRKYs are closely related to the Magnolia Cinnamomum kanehirae WRKY family, and has fewer family members than higher plants. We found the LchiWRKYs to be evenly distributed across 15 chromosomes, with their duplication events suggesting that tandem duplication may have played a major role in LchiWRKY gene expansion model. A Ka/Ks analysis indicated that they mainly underwent purifying selection and distributed in the group IId. Motif analysis showed that LchiWRKYs contained 20 motifs, and different phylogenetic groups contained conserved motif. Gene ontology (GO) analysis showed that LchiWRKYs were mainly enriched in two categories, i.e., biological process and molecular function. Two group IIc members (LchiWRKY10 and LchiWRKY37) contain unique WRKY element sequence variants (WRKYGKK and WRKYGKS). Gene structure analysis showed that most LchiWRKYs possess 3 exons and two different types of introns: the R- and V-type which are both contained within the WRKY domain (WD). Additional promoter cis-element analysis indicated that 12 cis-elements that play different functions in environmental adaptability occur across all LchiWRKY groups. Heat, cold, and drought stress mainly induced the expression of group II and I LchiWRKYs, some of which had undergone gene duplication during evolution, and more than half of which had three exons. LchiWRKY33 mainly responded to cold stress and LchiWRKY25 mainly responded to heat stress, and LchiWRKY18 mainly responded to drought stress, which was almost 4-fold highly expressed, while 5 LchiWRKYs (LchiWRKY5, LchiWRKY23, LchiWRKY14, LchiWRKY27, and LchiWRKY36) responded equally three stresses with more than 6-fold expression. Subcellular localization analysis showed that all LchiWRKYs were localized in the nucleus, and subcellular localization experiments of LchiWRKY18 and 36 also showed that these two transcription factors were expressed in the nucleus. CONCLUSIONS This study shows that in Liriodendron chinense, several WRKY genes like LchiWRKY33, LchiWRKY25, and LchiWRKY18, respond to cold or heat or drought stress, suggesting that they may indeed play a role in regulating the tree's response to such conditions. This information will prove a pivotal role in directing further studies on the function of the LchiWRKY gene family in abiotic stress response and provides a theoretical basis for popularizing afforestation in different regions of China.
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Affiliation(s)
- Weihuang Wu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Sheng Zhu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Lin Xu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Liming Zhu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Dandan Wang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yang Liu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Siqin Liu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Ye Lu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.
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Analyses of Lysin-motif Receptor-like Kinase ( LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study. Cells 2021; 11:cells11010037. [PMID: 35011598 PMCID: PMC8750388 DOI: 10.3390/cells11010037] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/10/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022] Open
Abstract
The LysM receptor-like kinases (LysM-RLKs) play a crucial role in plant symbiosis and response to environmental stresses. Brassica napus, B. rapa, and B. oleracea are utilized as valuable vegetables. Different biotic and abiotic stressors affect these crops, resulting in yield losses. Therefore, genome-wide analysis of the LysM-RLK gene family was conducted. From the genome of the examined species, 33 LysM-RLK have been found. The conserved domains of Brassica LysM-RLKs were divided into three groups: LYK, LYP, and LysMn. In the BrassicaLysM-RLK gene family, only segmental duplication has occurred. The Ka/Ks ratio for the duplicated pair of genes was less than one indicating that the genes’ function had not changed over time. The BrassicaLysM-RLKs contain 70 cis-elements, indicating that they are involved in stress response. 39 miRNA molecules were responsible for the post-transcriptional regulation of 12 Brassica LysM-RLKs. A total of 22 SSR loci were discovered in 16 Brassica LysM-RLKs. According to RNA-seq data, the highest expression in response to biotic stresses was related to BnLYP6. According to the docking simulations, several residues in the active sites of BnLYP6 are in direct contact with the docked chitin and could be useful in future studies to develop pathogen-resistant B. napus. This research reveals comprehensive information that could lead to the identification of potential genes for Brassica species genetic manipulation.
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Zhao D, Chen Z, Xu L, Zhang L, Zou Q. Genome-Wide Analysis of the MADS-Box Gene Family in Maize: Gene Structure, Evolution, and Relationships. Genes (Basel) 2021; 12:genes12121956. [PMID: 34946905 PMCID: PMC8701013 DOI: 10.3390/genes12121956] [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: 11/07/2021] [Revised: 11/24/2021] [Accepted: 12/02/2021] [Indexed: 12/24/2022] Open
Abstract
The MADS-box gene family is one of the largest families in plants and plays an important roles in floral development. The MADS-box family includes the SRF-like domain and K-box domain. It is considered that the MADS-box gene family encodes a DNA-binding domain that is generally related to transcription factors, and plays important roles in regulating floral development. Our study identified 211 MADS-box protein sequences in the Zea mays proteome and renamed all the genes based on the gene annotations. All the 211 MADS-box protein sequences were coded by 98 expressed genes. Phylogenetic analysis of the MADS-box genes showed that all the family members were categorized into five subfamilies: MIKC-type, Mα, Mβ, Mγ, and Mδ. Gene duplications are regarded as products of several types of errors during the period of DNA replication and reconstruction; in our study all the 98 MADS-box genes contained 22 pairs of segmentally duplicated events which were distributed on 10 chromosomes. We compared expression data in different tissues from the female spikelet, silk, pericarp aleurone, ear primordium, leaf zone, vegetative meristem, internode, endosperm crown, mature pollen, embryo, root cortex, secondary root, germination kernels, primary root, root elongation zone, and root meristem. According to analysis of gene ontology pathways, we found a total of 41 pathways in which MADS-box genes in maize are involved. All the studies we conducted provided an overview of MADS-box gene family members in maize and showed multiple functions as transcription factors. The related research of MADS-box domains has provided the theoretical basis of MADS-box domains for agricultural applications.
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Affiliation(s)
- Da Zhao
- School of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen 518055, China; (D.Z.); (Z.C.); (L.Z.)
| | - Zheng Chen
- School of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen 518055, China; (D.Z.); (Z.C.); (L.Z.)
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen 518055, China
- Correspondence: (L.X.); (Q.Z.)
| | - Lijun Zhang
- School of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen 518055, China; (D.Z.); (Z.C.); (L.Z.)
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
- Correspondence: (L.X.); (Q.Z.)
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Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum. Genes (Basel) 2021; 12:genes12121867. [PMID: 34946815 PMCID: PMC8701280 DOI: 10.3390/genes12121867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/21/2021] [Accepted: 11/23/2021] [Indexed: 11/17/2022] Open
Abstract
WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.
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