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Li D, Wu D, Li S, Dai Y, Cao Y. Evolutionary and functional analysis of the plant-specific NADPH oxidase gene family in Brassica rapa L. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181727. [PMID: 30891283 PMCID: PMC6408365 DOI: 10.1098/rsos.181727] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/31/2019] [Indexed: 05/13/2023]
Abstract
NADPH oxidases (NOXs) have been known as respiratory burst oxidase homologues (RBOHs) in plants. To characterize the evolutionary relationships and functions of RBOHs in Brassica rapa, 134 RBOH homologues were identified from 13 plant species, including 14 members (namely BrRBOH01-14) from B. rapa. There presented 47 gene-pairs among 14 BrRBOHs and other RBOHs, consisting of five pairs within B. rapa, and 15 pairs between B. rapa and Arabidopsis thaliana. Together with phylogenetic analysis, the results suggested that whole-genome duplication might have played an important role in BrRBOH gene expansion, and these duplication events occurred after the divergence of the eudicot and the monocot lineages examined. Furthermore, gene expression of RBOHs in both A. thaliana and B. rapa were assayed via qRT-PCR. An RBOH gene, BrRBOH13 in B. rapa, was transformed into wild-type Arabidopsis plants. The transgenic lines with the overexpressed level of BrRBOH13 conferred to be more tolerant to heavy metal lead (0.05 mM) than wild-type plants. Overall, this integrated analysis at genome-wide level has provided some information on the evolutionary relationships among plant-specific NOXs and the coordinated diversification of gene structure and function in B. rapa.
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Affiliation(s)
- Dahui Li
- Author for correspondence: Dahui Li e-mail:
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Liu Z, Qanmber G, Lu L, Qin W, Liu J, Li J, Ma S, Yang Z, Yang Z. Genome-wide analysis of BES1 genes in Gossypium revealed their evolutionary conserved roles in brassinosteroid signaling. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1566-1582. [PMID: 30607883 DOI: 10.1007/s11427-018-9412-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/23/2018] [Indexed: 01/11/2023]
Abstract
Brassinosteroids (BRs), which are essential phytohormones for plant growth and development, are important for cotton fiber development. Additionally, BES1 transcription factors are critical for BR signal transduction. However, cotton BES1 family genes have not been comprehensively characterized. In this study, we identified 11 BES1 genes in G. arboreum, 11 in G. raimondii, 16 in G. barbadense, and 22 in G. hirsutum. The BES1 sequences were significantly conserved in the Arabidopsis thaliana, rice, and upland cotton genomes. A total of 94 BES1 genes from 10 different plant species were divided into three clades according to the neighbor-joining and minimum-evolution methods. Moreover, the exon/intron patterns and motif distributions were highly conserved among the A. thaliana and cotton BES1 genes. The collinearity among the orthologs from the At and Dt subgenomes was estimated. Segmental duplications in the At and Dt subgenomes were primarily responsible for the expansion of the cotton BES1 gene family. Of the GhBES1 genes, GhBES1.4_At/Dt exhibited BL-induced expression and was predominantly expressed in fibers. Furthermore, Col-0/mGhBES1.4_At plants produced curled leaves with long and bent petioles. These transgenic plants also exhibited decreased hypocotyl sensitivity to brassinazole and constitutive BR induced/repressed gene expression patterns. The constitutive BR responses of the plants overexpressing mGhBES1.4_At were similar to those of the bes1-D mutant.
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Affiliation(s)
- Zhao Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lili Lu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wenqiang Qin
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jie Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Shuya Ma
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhaoen Yang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China. .,School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China.
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Jiu S, Haider MS, Kurjogi MM, Zhang K, Zhu X, Fang J. Genome-wide Characterization and Expression Analysis of Sugar Transporter Family Genes in Woodland Strawberry. THE PLANT GENOME 2018; 11:170103. [PMID: 30512042 DOI: 10.3835/plantgenome2017.11.0103] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In higher plants, sugars are nutrients and important signal molecules. Sugar transporters (STs) facilitate sugar transport across membranes and are associated with loading and unloading of the conducting complex. Strawberry ( Duchesne ex Rozier) is one of the most economically important and widely cultivated fruit crop and a model plant among fleshy fruits worldwide. In this study, 66 woodland strawberry ( L.) ST (FvST) genes were identified and further classified into eight distinct subfamilies in the woodland strawberry genome based on the phylogenetic analysis. In the promoter sequences of FvST gene families, a search for -regulatory elements suggested that some of them might probably be regulated by plant hormones (e.g., salicylic acid, abscisic acid, and auxin), abiotic (e.g., drought, excessive cold, and light), and biotic stress factors. Exon-intron analysis showed that each subfamily manifested closely associated gene architectural features based on similar number or length of exons. Moreover, to comprehend the potential evolution mechanism of FvST gene family, the analysis of genome duplication events was performed. The segmental and tandem duplication analysis elucidated that some of ST genes arose through whole-genome duplication (WGD) or segmental duplication, accompanied by tandem duplications. The expression analysis of 24 FvST genes in vegetative and during fruit development has shown that the expression of several ST genes was tissue and developmental stage specific. Generally, our findings are important in understanding of the allocation of photo assimilates from source to sink cell and provide insights into the genomic organization and expression profiling of FvST gene families in woodland strawberry.
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Gupta S, Mishra VK, Kumari S, Raavi, Chand R, Varadwaj PK. Deciphering genome-wide WRKY gene family of Triticum aestivum L. and their functional role in response to Abiotic stress. Genes Genomics 2018; 41:79-94. [PMID: 30238225 DOI: 10.1007/s13258-018-0742-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/11/2018] [Indexed: 12/18/2022]
Abstract
WRKY transcription factors (TFs) act in regulating plant growth and development as well as in response to different stress. Some earlier studies done by individual researchers reported different wheat WRKY TFs. Although, the recently released wheat genome has opened an avenue to investigate wheat WRKYs (TaWRKY) TFs. Prime objective of this study to performed genome-wide classifications of TaWRKYs and their functional annotation. The classification of 107 individual identified characterized sequences of TaWRKY (IICS-TaWRKY) and 160 uncharacterized draft sequences of TaWRKY (UDS-TaWRKY), along with their gene structures and motifs analysis was performed. Along with comparative sequence analysis and microarray analysis was performed to mimic out TaWRKYs functions in response to different abiotic stresses, accompanied by in-vitro validation. The comparative phylogenetic analysis and estimation of Ka/Ks ratio with Triticum urartu, illustrate group based clasifications of TaWRKYs and evolutionary divergences. Furthermore, motif-based and protein-DNA interaction analysis of TaWRKYs helps to identify, their putative function in target DNA recognition sites. Subsequently, results of microarray and comparative sequence analysis provides the evidence of TaWRKYs involved in heat and/or drought stress. Further, in-vitro results validates that TaWRKY014, TaWRKY090 are found to participate in response of drought stress, whereas TaWRKY008, TaWRKY122, and WRKY45 are involved in response of heat and drought stress. These findings can be utilized in developing novel heat and drought-tolerant wheat cultivars using marker-assisted breeding and transgenic development.
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Affiliation(s)
- Saurabh Gupta
- Department of Applied Sciences, Indian Institute of Information Technology, Deoghat, Jhalwa, Allahabad, 211015, India.,AgriGenome Labs Pvt. Ltd., Hyderabad, 500078, India
| | - Vinod Kumar Mishra
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Sunita Kumari
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Raavi
- Molecular Biology, Cell Biology and Biochemistry Program, Boston University, Boston, 02215, USA
| | - Ramesh Chand
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Pritish Kumar Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology, Deoghat, Jhalwa, Allahabad, 211015, India.
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Li W, Ren Z, Wang Z, Sun K, Pei X, Liu Y, He K, Zhang F, Song C, Zhou X, Zhang W, Ma X, Yang D. Evolution and Stress Responses of Gossypium hirsutum SWEET Genes. Int J Mol Sci 2018; 19:E769. [PMID: 29517986 PMCID: PMC5877630 DOI: 10.3390/ijms19030769] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 02/21/2018] [Accepted: 02/26/2018] [Indexed: 02/07/2023] Open
Abstract
The SWEET (sugars will eventually be exported transporters) proteins are sugar efflux transporters containing the MtN3_saliva domain, which affects plant development as well as responses to biotic and abiotic stresses. These proteins have not been functionally characterized in the tetraploid cotton, Gossypium hirsutum, which is a widely cultivated cotton species. In this study, we comprehensively analyzed the cotton SWEET gene family. A total of 55 putative G. hirsutumSWEET genes were identified. The GhSWEET genes were classified into four clades based on a phylogenetic analysis and on the examination of gene structural features. Moreover, chromosomal localization and an analysis of homologous genes in Gossypium arboreum, Gossypium raimondii, and G. hirsutum suggested that a whole-genome duplication, several tandem duplications, and a polyploidy event contributed to the expansion of the cotton SWEET gene family, especially in Clade III and IV. Analyses of cis-acting regulatory elements in the promoter regions, expression profiles, and artificial selection revealed that the GhSWEET genes were likely involved in cotton developmental processes and responses to diverse stresses. These findings may clarify the evolution of G. hirsutum SWEET gene family and may provide a foundation for future functional studies of SWEET proteins regarding cotton development and responses to abiotic stresses.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhongying Ren
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhenyu Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Kuan Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xiaoyu Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yangai Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Kunlun He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Fei Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Chengxiang Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xiaojian Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Wensheng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xiongfeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Daigang Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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Genome-Wide Identification and Comparative Analysis of the 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Gossypium. Molecules 2018; 23:molecules23020193. [PMID: 29364830 PMCID: PMC6017885 DOI: 10.3390/molecules23020193] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/19/2018] [Accepted: 01/21/2018] [Indexed: 11/25/2022] Open
Abstract
Terpenes are the largest and most diverse class of secondary metabolites in plants and play a very important role in plant adaptation to environment. 3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is a rate-limiting enzyme in the process of terpene biosynthesis in the cytosol. Previous study found the HMGR genes underwent gene expansion in Gossypium raimondii, but the characteristics and evolution of the HMGR gene family in Gossypium genus are unclear. In this study, genome-wide identification and comparative study of HMGR gene family were carried out in three Gossypium species with genome sequences, i.e., G. raimondii, Gossypium arboreum, and Gossypium hirsutum. In total, nine, nine and 18 HMGR genes were identified in G. raimondii, G. arboreum, and G. hirsutum, respectively. The results indicated that the HMGR genes underwent gene expansion and a unique gene cluster containing four HMGR genes was found in all the three Gossypium species. The phylogenetic analysis suggested that the expansion of HMGR genes had occurred in their common ancestor. There was a pseudogene that had a 10-bp deletion resulting in a frameshift mutation and could not be translated into functional proteins in G. arboreum and the A-subgenome of G. hirsutum. The expression profiles of the two pseudogenes showed that they had tissue-specific expression. Additionally, the expression pattern of the pseudogene in the A-subgenome of G. hirsutum was similar to its paralogous gene in the D-subgenome of G. hirsutum. Our results provide useful information for understanding cytosolic terpene biosynthesis in Gossypium species.
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Yang Y, Zhou Y, Chi Y, Fan B, Chen Z. Characterization of Soybean WRKY Gene Family and Identification of Soybean WRKY Genes that Promote Resistance to Soybean Cyst Nematode. Sci Rep 2017; 7:17804. [PMID: 29259331 PMCID: PMC5736691 DOI: 10.1038/s41598-017-18235-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 12/08/2017] [Indexed: 12/03/2022] Open
Abstract
WRKY proteins are a superfamily of plant transcription factors with important roles in plants. WRKY proteins have been extensively analyzed in plant species including Arabidopsis and rice. Here we report characterization of soybean WRKY gene family and their functional analysis in resistance to soybean cyst nematode (SCN), the most important soybean pathogen. Through search of the soybean genome, we identified 174 genes encoding WRKY proteins that can be classified into seven groups as established in other plants. WRKY variants including a WRKY-related protein unique to legumes have also been identified. Expression analysis reveals both diverse expression patterns in different soybean tissues and preferential expression of specific WRKY groups in certain tissues. Furthermore, a large number of soybean WRKY genes were responsive to salicylic acid. To identify soybean WRKY genes that promote soybean resistance to SCN, we first screened soybean WRKY genes for enhancing SCN resistance when over-expressed in transgenic soybean hairy roots. To confirm the results, we transformed five WRKY genes into a SCN-susceptible soybean cultivar and generated transgenic soybean lines. Transgenic soybean lines overexpressing three WRKY transgenes displayed increased resistance to SCN. Thus, WRKY genes could be explored to develop new soybean cultivars with enhanced resistance to SCN.
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Affiliation(s)
- Yan Yang
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Yuan Zhou
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Yingjun Chi
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Baofang Fan
- Department of Botany and Plant Pathology and Purdue Center for Plant Biology, 915 W. State Street, Purdue University, West Lafayette, IN, 47907, USA
| | - Zhixiang Chen
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China.
- Department of Botany and Plant Pathology and Purdue Center for Plant Biology, 915 W. State Street, Purdue University, West Lafayette, IN, 47907, USA.
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Zhang M, Shen Z, Meng G, Lu Y, Wang Y. Genome-wide analysis of the Brachypodium distachyon (L.) P. Beauv. Hsp90 gene family reveals molecular evolution and expression profiling under drought and salt stresses. PLoS One 2017; 12:e0189187. [PMID: 29216330 PMCID: PMC5720741 DOI: 10.1371/journal.pone.0189187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/21/2017] [Indexed: 01/31/2023] Open
Abstract
The structure, evolution, and function of heat shock proteins 90 (Hsp90s) have been investigated in great detail in fungi and animals. However, studies on the Hsp90 genes in plants are generally limited. Brachypodium distachyon (L.) P. Beauv., as a model plant for cereal crops, has become a potential biofuel grass. During its long evolution, the Hsp90 gene family in Brachypodium has developed some strategies to cope with adverse environments. How the Hsp90 gene family in Brachypodium evolved in different plant lineages and what its role is in plant responses to drought and salt stresses remains to be elucidated. We used a set of different bioinformatics tools to identify 94 Hsp90 genes from 10 species representing four plant lineages and classified into three subgroups. Eight BdHsp90 genes were detected from B. distachyon. The number of exon-intron structures differed in each subgroup, and the motif analysis revealed that these genes were relatively conservative in each group. The fragments duplication and tandem duplication, which are the prime powers for functional diversity, generally occurred during the duplication of the whole plant genome. Transcriptional analysis of the BdHsp90 genes under salt and drought stress conditions indicated that the expression of these genes was delayed or increased at different stress time points; The expression was more affected in that of Bradi3g39630, Bradi4g06370, and Bradi1g30130. Our findings suggest the involvement of BdHsp90s in plant abiotic stress response, and further consolidate our views on the stress response mechanism of Hsp90 in general.
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Affiliation(s)
- Ming Zhang
- College of Life Science, Heze University, Shandong, China
| | - Zhiwei Shen
- College of Life Science, Heze University, Shandong, China
| | - Guoqing Meng
- College of Life Science, Heze University, Shandong, China
| | - Yu Lu
- College of Life Science, Heze University, Shandong, China
| | - Yilei Wang
- College of Life Science, Heze University, Shandong, China
- * E-mail:
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Wytynck P, Rougé P, Van Damme EJM. Genome-wide screening of Oryza sativa ssp. japonica and indica reveals a complex family of proteins with ribosome-inactivating protein domains. PHYTOCHEMISTRY 2017; 143:87-97. [PMID: 28797946 DOI: 10.1016/j.phytochem.2017.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/08/2017] [Accepted: 07/22/2017] [Indexed: 06/07/2023]
Abstract
Ribosome-inactivating proteins (RIPs) are cytotoxic enzymes capable of halting protein synthesis by irreversible modification of ribosomes. Although RIPs are widespread they are not ubiquitous in the plant kingdom. The physiological importance of RIPs is not fully elucidated, but evidence suggests a role in the protection of the plant against biotic and abiotic stresses. Searches in the rice genome revealed a large and highly complex family of proteins with a RIP domain. A comparative analysis retrieved 38 RIP sequences from the genome sequence of Oryza sativa subspecies japonica and 34 sequences from the subspecies indica. The RIP sequences are scattered over different chromosomes but are mostly found on the third chromosome. The phylogenetic tree revealed the pairwise clustering of RIPs from japonica and indica. Molecular modeling and sequence analysis yielded information on the catalytic site of the enzyme, and suggested that a large part of RIP domains probably possess N-glycosidase activity. Several RIPs are differentially expressed in plant tissues and in response to specific abiotic stresses. This study provides an overview of RIP motifs in rice and will help to understand their biological role(s) and evolutionary relationships.
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Affiliation(s)
- Pieter Wytynck
- Lab Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Pierre Rougé
- UMR152 PHARMA-DEV, Université de Toulouse, IRD, UPS, Chemin des Maraîchers 35, 31400, Toulouse, France
| | - Els J M Van Damme
- Lab Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium.
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Zhang C, Wang D, Yang C, Kong N, Shi Z, Zhao P, Nan Y, Nie T, Wang R, Ma H, Chen Q. Genome-wide identification of the potato WRKY transcription factor family. PLoS One 2017; 12:e0181573. [PMID: 28727761 PMCID: PMC5519183 DOI: 10.1371/journal.pone.0181573] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/03/2017] [Indexed: 12/05/2022] Open
Abstract
WRKY transcription factors play pivotal roles in regulation of stress responses. This study identified 79 WRKY genes in potato (Solanum tuberosum). Based on multiple sequence alignment and phylogenetic relationships, WRKY genes were classified into three major groups. The majority of WRKY genes belonged to Group II (52 StWRKYs), Group III had 14 and Group I consisted of 13. The phylogenetic tree further classified Group II into five sub-groups. All StWRKY genes except StWRKY79 were mapped on potato chromosomes, with eight tandem duplication gene pairs and seven segmental duplication gene pairs found from StWRKY family genes. The expression analysis of 22 StWRKYs showed their differential expression levels under various stress conditions. Cis-element prediction showed that a large number of elements related to drought, heat and salicylic acid were present in the promotor regions of StWRKY genes. The expression analysis indicated that seven StWRKYs seemed to respond to stress (heat, drought and salinity) and salicylic acid treatment. These genes are candidates for abiotic stress signaling for further research.
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Affiliation(s)
- Chao Zhang
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Dongdong Wang
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Chenghui Yang
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Nana Kong
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Zheng Shi
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Peng Zhao
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Yunyou Nan
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Tengkun Nie
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Ruoqiu Wang
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Haoli Ma
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
- * E-mail: (HM); (QC)
| | - Qin Chen
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
- * E-mail: (HM); (QC)
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Yang Z, Gong Q, Qin W, Yang Z, Cheng Y, Lu L, Ge X, Zhang C, Wu Z, Li F. Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses. BMC PLANT BIOLOGY 2017; 17:113. [PMID: 28683794 PMCID: PMC5501002 DOI: 10.1186/s12870-017-1065-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/25/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND WUSCHEL-related homeobox (WOX) family members play significant roles in plant growth and development, such as in embryo patterning, stem-cell maintenance, and lateral organ formation. The recently published cotton genome sequences allow us to perform comprehensive genome-wide analysis and characterization of WOX genes in cotton. RESULTS In this study, we identified 21, 20, and 38 WOX genes in Gossypium arboreum (2n = 26, A2), G. raimondii (2n = 26, D5), and G. hirsutum (2n = 4x = 52, (AD)t), respectively. Sequence logos showed that homeobox domains were significantly conserved among the WOX genes in cotton, Arabidopsis, and rice. A total of 168 genes from three typical monocots and six dicots were naturally divided into three clades, which were further classified into nine sub-clades. A good collinearity was observed in the synteny analysis of the orthologs from At and Dt (t represents tetraploid) sub-genomes. Whole genome duplication (WGD) and segmental duplication within At and Dt sub-genomes played significant roles in the expansion of WOX genes, and segmental duplication mainly generated the WUS clade. Copia and Gypsy were the two major types of transposable elements distributed upstream or downstream of WOX genes. Furthermore, through comparison, we found that the exon/intron pattern was highly conserved between Arabidopsis and cotton, and the homeobox domain loci were also conserved between them. In addition, the expression pattern in different tissues indicated that the duplicated genes in cotton might have acquired new functions as a result of sub-functionalization or neo-functionalization. The expression pattern of WOX genes under different stress treatments showed that the different genes were induced by different stresses. CONCLUSION In present work, WOX genes, classified into three clades, were identified in the upland cotton genome. Whole genome and segmental duplication were determined to be the two major impetuses for the expansion of gene numbers during the evolution. Moreover, the expression patterns suggested that the duplicated genes might have experienced a functional divergence. Together, these results shed light on the evolution of the WOX gene family, and would be helpful in future research.
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Affiliation(s)
- Zhaoen Yang
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830052, China
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Qian Gong
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wenqiang Qin
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830052, China
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zuoren Yang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuan Cheng
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lili Lu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaoyang Ge
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chaojun Zhang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhixia Wu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fuguang Li
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830052, China.
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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Liu Y, Wei H. Genome-wide identification and evolution of the PIN-FORMED (PIN) gene family in Glycine max. Genome 2017; 60:564-571. [PMID: 28314115 DOI: 10.1139/gen-2016-0141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Soybean (Glycine max) is one of the most important crop plants. Wild and cultivated soybean varieties have significant differences worth further investigation, such as plant morphology, seed size, and seed coat development; these characters may be related to auxin biology. The PIN gene family encodes essential transport proteins in cell-to-cell auxin transport, but little research on soybean PIN genes (GmPIN genes) has been done, especially with respect to the evolution and differences between wild and cultivated soybean. In this study, we retrieved 23 GmPIN genes from the latest updated G. max genome database; six GmPIN protein sequences were changed compared with the previous database. Based on the Plant Genome Duplication Database, 18 GmPIN genes have been involved in segment duplication. Three pairs of GmPIN genes arose after the second soybean genome duplication, and six occurred after the first genome duplication. The duplicated GmPIN genes retained similar expression patterns. All the duplicated GmPIN genes experienced purifying selection (Ka/Ks < 1) to prevent accumulation of non-synonymous mutations and thus remained more similar. In addition, we also focused on the artificial selection of the soybean PIN genes. Five artificially selected GmPIN genes were identified by comparing the genome sequence of 17 wild and 14 cultivated soybean varieties. Our research provides useful and comprehensive basic information for understanding GmPIN genes.
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Affiliation(s)
- Yuan Liu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Haichao Wei
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
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63
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Cao Y, Han Y, Meng D, Li G, Li D, Abdullah M, Jin Q, Lin Y, Cai Y. Genome-Wide Analysis Suggests the Relaxed Purifying Selection Affect the Evolution of WOX Genes in Pyrus bretschneideri, Prunus persica, Prunus mume, and Fragaria vesca. Front Genet 2017; 8:78. [PMID: 28663757 PMCID: PMC5471313 DOI: 10.3389/fgene.2017.00078] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/29/2017] [Indexed: 12/22/2022] Open
Abstract
WUSCHEL-related homeobox (WOX) family is one of the largest group of transcription factors (TFs) specifically found in plant kingdom. WOX TFs play an important role in plant development processes and evolutionary novelties. Although the roles of WOXs in Arabidopsis and rice have been well-studied, however, little are known about the relationships among the main clades in the molecular evolution of these genes in Rosaceae. Here, we carried out a genome-wide analysis and identified 14, 10, 10, and 9 of WOX genes from four Rosaceae species (Fragaria vesca, Prunus persica, Prunus mume, and Pyrus bretschneideri, respectively). According to evolutionary analysis, as well as amino acid sequences of their homodomains, these genes were divided into three clades with nine subgroups. Furthermore, due to the conserved structural patterns among these WOX genes, it was proposed that there should exist some highly conserved regions of microsynteny in the four Rosaceae species. Moreover, most of WOX gene pairs were presented with the conserved orientation among syntenic genome regions. In addition, according to substitution models analysis using PMAL software, no significant positive selection was detected, but type I functional divergence was identified among certain amino acids in WOX protein. These results revealed that the relaxed purifying selection might be the main driving force during the evolution of WOX genes in the tested Rosaceae species. Our result will be useful for further precise research on evolution of the WOX genes in family Rosaceae.
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Affiliation(s)
- Yunpeng Cao
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yahui Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural UniversityHefei, China
| | - Dandan Meng
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Guohui Li
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Dahui Li
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Muhammad Abdullah
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural UniversityHefei, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yi Lin
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
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64
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Gu Y, Li W, Jiang H, Wang Y, Gao H, Liu M, Chen Q, Lai Y, He C. Differential expression of a WRKY gene between wild and cultivated soybeans correlates to seed size. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2717-2729. [PMID: 28472462 PMCID: PMC5853923 DOI: 10.1093/jxb/erx147] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/08/2017] [Indexed: 05/24/2023]
Abstract
Soybean (Glycine max) probably originated from the wild soybean (Glycine soja). Glycine max has a significantly larger seed size, but the underlying genomic changes are largely unknown. Candidate regulatory genes were preliminarily proposed by data co-localizing RNA sequencing with the quantitative loci (QTLs) for seed size. The soybean gene locus SoyWRKY15a and its orthologous genes from G. max (GmWRKY15a) and G. soja (GsWRKY15a) were analyzed in detail. The coding sequences were nearly identical between the two orthologs, but GmWRKY15a was significantly more highly expressed than GsWRKY15a. Four haplotypes (H1-H4) were found and they varied in the size of a CT-core microsatellite locus in the 5'-untranslated region of this gene. H1 (with six CT-repeats) was the only allelic version found in G. max, while H3 (with five CT-repeats) was the dominant G. soja allele. Differential expression of this gene in soybean pods was correlated with CT-repeat variation, and manipulation of the CT copy number altered the reporter gene expression, suggesting a regulatory role for the simple sequence repeats. Seed weight of wild soybeans harboring H1 was significantly greater than that of soybeans having haplotypes H2, H3, or H4, and seed weight was correlated with gene expression, suggesting the influence of GsWRKY15a in controlling seed size. However, the seed size might be refractory to increased SoyWRKY15a expression in cultivated soybeans. The evolutionary significance of SoyWRKY15a variation in soybean seed domestication is discussed.
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Affiliation(s)
- Yongzhe Gu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Hongwei Jiang
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Huihui Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Miao Liu
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yongcai Lai
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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65
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Lakhssassi N, Liu S, Bekal S, Zhou Z, Colantonio V, Lambert K, Barakat A, Meksem K. Characterization of the Soluble NSF Attachment Protein gene family identifies two members involved in additive resistance to a plant pathogen. Sci Rep 2017; 7:45226. [PMID: 28338077 PMCID: PMC5364553 DOI: 10.1038/srep45226] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/21/2017] [Indexed: 11/15/2022] Open
Abstract
Proteins with Tetratricopeptide-repeat (TPR) domains are encoded by large gene families and distributed in all plant lineages. In this study, the Soluble NSF-Attachment Protein (SNAP) subfamily of TPR containing proteins is characterized. In soybean, five members constitute the SNAP gene family: GmSNAP18, GmSNAP11, GmSNAP14, GmSNAP02, and GmSNAP09. Recently, GmSNAP18 has been reported to mediate resistance to soybean cyst nematode (SCN). Using a population of recombinant inbred lines from resistant and susceptible parents, the divergence of the SNAP gene family is analysed over time. Phylogenetic analysis of SNAP genes from 22 diverse plant species showed that SNAPs were distributed in six monophyletic clades corresponding to the major plant lineages. Conservation of the four TPR motifs in all species, including ancestral lineages, supports the hypothesis that SNAPs were duplicated and derived from a common ancestor and unique gene still present in chlorophytic algae. Syntenic analysis of regions harbouring GmSNAP genes in soybean reveals that this family expanded from segmental and tandem duplications following a tetraploidization event. qRT-PCR analysis of GmSNAPs indicates a co-regulation following SCN infection. Finally, genetic analysis demonstrates that GmSNAP11 contributes to an additive resistance to SCN. Thus, GmSNAP11 is identified as a novel minor gene conferring resistance to SCN.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Sadia Bekal
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Vincent Colantonio
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Kris Lambert
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Abdelali Barakat
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
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66
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Ma J, Gao X, Liu Q, Shao Y, Zhang D, Jiang L, Li C. Overexpression of TaWRKY146 Increases Drought Tolerance through Inducing Stomatal Closure in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:2036. [PMID: 29225611 PMCID: PMC5706409 DOI: 10.3389/fpls.2017.02036] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/14/2017] [Indexed: 05/02/2023]
Abstract
As a superfamily of transcription factors, the tryptophan-arginine-lysine-tyrosine (WRKY) transcription factors have been found to be essential for abiotic and biotic stress responses in plants. Currently, only 76 WRKY transcription factors in wheat could be identified in the NCBI database, among which only a few have been functionally analyzed. Herein, a total of 188 WRKY transcription factors were identified from the wheat genome database, which included 123 full-length coding sequences, and all of them were used for detailed evolution studies. By bioinformatics analysis, a WRKY transcription factor, named TaWRKY146, was found to be the homologous gene of AtWRKY46, overexpression of which leads to hypersensitivity to drought and salt stress in Arabidopsis. Consequently, the full length of TaWRKY146 was cloned, and the expression levels of TaWRKY146 were found significantly up-regulated in the leaves and roots of wheat seedlings, which were subjected to osmotic stress. Overexpression of TaWRKY146 in Arabidopsis was shown to enhance drought tolerance by the induction of stomatal closure that reduced the transpiration rate. All these results provide a firm foundation for further identification of WRKY transcription factors with important functions in wheat.
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Affiliation(s)
| | | | | | | | | | - Lina Jiang
- *Correspondence: Chunxi Li, ; Lina Jiang,
| | - Chunxi Li
- *Correspondence: Chunxi Li, ; Lina Jiang,
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67
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Lakhssassi N, Zhou Z, Liu S, Colantonio V, AbuGhazaleh A, Meksem K. Characterization of the FAD2 Gene Family in Soybean Reveals the Limitations of Gel-Based TILLING in Genes with High Copy Number. FRONTIERS IN PLANT SCIENCE 2017; 8:324. [PMID: 28348573 PMCID: PMC5346563 DOI: 10.3389/fpls.2017.00324] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/23/2017] [Indexed: 05/21/2023]
Abstract
Soybean seed oil typically contains 18-20% oleic acid. Increasing the content of oleic acid is beneficial for health and biodiesel production. Mutations in FAD2-1 genes have been reported to increase seed oleic acid content. A subset of 1,037 mutant families from a mutagenized soybean cultivar (cv.) Forrest population was screened using reverse genetics (TILLING) to identify mutations within FAD2 genes. Although no fad2 mutants were identified using gel-based TILLING, four fad2-1A and one fad2-1B mutants were identified to have high seed oleic acid content using forward genetic screening and subsequent target sequencing. TILLING has been successfully used as a non-transgenic reverse genetic approach to identify mutations in genes controlling important agronomic traits. However, this technique presents limitations in traits such as oil composition due to gene copy number and similarities within the soybean genome. In soybean, FAD2 are present as two copies, FAD2-1 and FAD2-2. Two FAD2-1 members: FAD2-1A and FAD2-1B; and three FAD2-2 members: FAD2-2A, FAD2-2B, and FAD2-2C have been reported. Syntenic, phylogenetic, and in silico analysis revealed two additional members constituting the FAD2 gene family: GmFAD2-2D and GmFAD2-2E, located on chromosomes 09 and 15, respectively. They are presumed to have diverged from other FAD2-2 members localized on chromosomes 19 (GmFAD2-2A and GmFAD2-2B) and 03 (GmFAD2-2C). This work discusses alternative solutions to the limitations of gel-based TILLING in functional genomics due to high copy number and multiple paralogs of the FAD2 gene family in soybean.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois UniversityCarbondale, IL, USA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural Systems, Southern Illinois UniversityCarbondale, IL, USA
| | - Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois UniversityCarbondale, IL, USA
| | - Vincent Colantonio
- Department of Plant, Soil and Agricultural Systems, Southern Illinois UniversityCarbondale, IL, USA
| | - Amer AbuGhazaleh
- Department of Animal Science, Food and Nutrition, Southern Illinois UniversityCarbondale, IL, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois UniversityCarbondale, IL, USA
- *Correspondence: Khalid Meksem
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68
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Wu J, Chen J, Wang L, Wang S. Genome-Wide Investigation of WRKY Transcription Factors Involved in Terminal Drought Stress Response in Common Bean. FRONTIERS IN PLANT SCIENCE 2017; 8:380. [PMID: 28386267 PMCID: PMC5362628 DOI: 10.3389/fpls.2017.00380] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/06/2017] [Indexed: 05/03/2023]
Abstract
WRKY transcription factor plays a key role in drought stress. However, the characteristics of the WRKY gene family in the common bean (Phaseolus vulgaris L.) are unknown. In this study, we identified 88 complete WRKY proteins from the draft genome sequence of the "G19833" common bean. The predicted genes were non-randomly distributed in all chromosomes. Basic information, amino acid motifs, phylogenetic tree and the expression patterns of PvWRKY genes were analyzed, and the proteins were classified into groups 1, 2, and 3. Group 2 was further divided into five subgroups: 2a, 2b, 2c, 2d, and 2e. Finally, we detected 19 WRKY genes that were responsive to drought stress using qRT-PCR; 11 were down-regulated, and 8 were up-regulated under drought stress. This study comprehensively examines WRKY proteins in the common bean, a model food legume, and it provides a foundation for the functional characterization of the WRKY family and opportunities for understanding the mechanisms of drought stress tolerance in this plant.
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Affiliation(s)
- Jing Wu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences,Beijing, China
| | - Jibao Chen
- College of Agricultural Engineering, Nanyang Normal University,Nanyang, China
| | - Lanfen Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences,Beijing, China
| | - Shumin Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences,Beijing, China
- *Correspondence: Shumin Wang,
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69
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Mamoon Rehman H, Amjad Nawaz M, Bao L, Hussain Shah Z, Lee JM, Ahmad MQ, Chung G, Yang SH. Genome-wide analysis of Family-1 UDP-glycosyltransferases in soybean confirms their abundance and varied expression during seed development. JOURNAL OF PLANT PHYSIOLOGY 2016; 206:87-97. [PMID: 27721120 DOI: 10.1016/j.jplph.2016.08.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 08/23/2016] [Accepted: 08/28/2016] [Indexed: 05/13/2023]
Abstract
Family-1 UDP-glycosyltransferases (EC 2.4.1.x; UGTs) are enzymes that glycosylate aglycones into glycoside-associated compounds with improved transport and water solubility. This glycosylation mechanism is vital to plant functions, such as regulation of hormonal homeostasis, growth and development, xenobiotic detoxification, stress response, and biosynthesis of secondary metabolites. Here, we report a genome-wide analysis of soybean that identified 149 putative UGTs based on 44 conserved plant secondary product glycosyl-transferase (PSPG) motif amino acid sequences. Phylogenetic analysis against 22 referenced UGTs from Arabidopsis and maize clustered the putative UGTs into 15 major groups (A-O); J, K, and N were not represented, but the UGTs were distributed across all chromosomes except chromosome 04. Leucine was the most abundant amino acid across all 149 UGT peptide sequences. Two conserved introns (C1 and C2) were detected in the most intron-containing UGTs. Publicly available microarray data on their maximum expression in the seed developmental stage were further confirmed using Affymetrix soybean IVT array and RNA sequencing data. The UGT expression models were designed, based on reads per kilobase of gene model per million mapped read (RPKM) values confirmed their maximally varied expression at globular and early maturation stages of seed development.
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Affiliation(s)
- Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 550-749, Republic of Korea
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 550-749, Republic of Korea
| | - Le Bao
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 550-749, Republic of Korea
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, King Abdul-Aziz University Jeddah, Saudi Arabia
| | - Jae-Min Lee
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 550-749, Republic of Korea
| | - Muhammad Qadir Ahmad
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan 6000, Pakistan
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 550-749, Republic of Korea.
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 550-749, Republic of Korea
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70
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Dias LP, de Oliveira-Busatto LA, Bodanese-Zanettini MH. The differential expression of soybean [Glycine max (L.) Merrill] WRKY genes in response to water deficit. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 107:288-300. [PMID: 27343875 DOI: 10.1016/j.plaphy.2016.06.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/13/2016] [Accepted: 06/14/2016] [Indexed: 05/21/2023]
Abstract
Drought is today, and perhaps even more in the future, the main challenge for grain crops, resulting in a drastic yield reduction. Thus, it is of great interest to obtain soybean genotypes tolerant to water deficit. The drought tolerance trait is difficult to obtain through classical breeding due to its polygenic basis. In this context, genetic engineering is presented as a way to achieve this attribute. The ability to modulate the expression of many genes placed the transcription factors as promising biotechnological targets to develop stress tolerant cultivars. The WRKY proteins form a large family of transcription factors that are involved in important physiological and biochemical processes in plants, including the response to water deficit. In this study, the expression pattern determined by qPCR showed that, GmWRKY6, GmWRKY46, GmWRKY56, GmWRKY106 and GmWRKY149 genes are differentially expressed between a drought tolerant and a susceptible soybean genotype in water stress conditions. The in silico promoter and coexpression analysis indicate that these genes act in a stress physiological background.
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Affiliation(s)
- Letícia Pereira Dias
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil.
| | - Luisa Abruzzi de Oliveira-Busatto
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil.
| | - Maria Helena Bodanese-Zanettini
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil.
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71
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Wang L, Bei X, Gao J, Li Y, Yan Y, Hu Y. The similar and different evolutionary trends of MATE family occurred between rice and Arabidopsis thaliana. BMC PLANT BIOLOGY 2016; 16:207. [PMID: 27669820 PMCID: PMC5037600 DOI: 10.1186/s12870-016-0895-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 07/19/2016] [Indexed: 05/02/2023]
Abstract
BACKGROUND Multidrug and toxic compound extrusion (MATE) transporter proteins are present in all organisms. Although the functions of some MATE gene family members have been studied in plants, few studies have investigated the gene expansion patterns, functional divergence, or the effects of positive selection. RESULTS Forty-five MATE genes from rice and 56 from Arabidopsis were identified and grouped into four subfamilies. MATE family genes have similar exon-intron structures in rice and Arabidopsis; MATE gene structures are conserved in each subfamily but differ among subfamilies. In both species, the MATE gene family has expanded mainly through tandem and segmental duplications. A transcriptome atlas showed considerable differences in expression among the genes, in terms of transcript abundance and expression patterns under normal growth conditions, indicating wide functional divergence in this family. In both rice and Arabidopsis, the MATE genes showed consistent functional divergence trends, with highly significant Type-I divergence in each subfamily, while Type-II divergence mainly occurred in subfamily III. The Type-II coefficients between rice subfamilies I/III, II/III, and IV/III were all significantly greater than zero, while only the Type-II coefficient between Arabidopsis IV/III subfamilies was significantly greater than zero. A site-specific model analysis indicated that MATE genes have relatively conserved evolutionary trends. A branch-site model suggested that the extent of positive selection on each subfamily of rice and Arabidopsis was different: subfamily II of Arabidopsis showed higher positive selection than other subfamilies, whereas in rice, positive selection was highest in subfamily III. In addition, the analyses identified 18 rice sites and 7 Arabidopsis sites that were responsible for positive selection and for Type-I and Type-II functional divergence; there were no common sites between rice and Arabidopsis. Five coevolving amino acid sites were identified in rice and three in Arabidopsis; these sites might have important roles in maintaining local structural stability and protein functional domains. CONCLUSIONS We demonstrate that the MATE gene family expanded through tandem and segmental duplication in both rice and Arabidopsis. Overall, the results of our analyses contribute to improved understanding of the molecular evolution and functions of the MATE gene family in plants.
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Affiliation(s)
- Lihui Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Xiujuan Bei
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Jiansheng Gao
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Yaxuan Li
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Yueming Yan
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Yingkao Hu
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
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72
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Liu X, Song Y, Xing F, Wang N, Wen F, Zhu C. GhWRKY25, a group I WRKY gene from cotton, confers differential tolerance to abiotic and biotic stresses in transgenic Nicotiana benthamiana. PROTOPLASMA 2016; 253:1265-81. [PMID: 26410829 DOI: 10.1007/s00709-015-0885-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 09/16/2015] [Indexed: 05/03/2023]
Abstract
WRKY transcription factors are involved in various processes, ranging from plant growth to abiotic and biotic stress responses. Group I WRKY members have been rarely reported compared with group II or III members, particularly in cotton (Gossypium hirsutum). In this study, a group I WRKY gene, namely, GhWRKY25, was cloned from cotton and characterized. Expression analysis revealed that GhWRKY25 can be induced or deduced by the treatments of abiotic stresses and multiple defense-related signaling molecules. Overexpression of GhWRKY25 in Nicotiana benthamiana reduced plant tolerance to drought stress but enhanced tolerance to salt stress. Moreover, more MDA and ROS accumulated in transgenic plants after drought treatment with lower activities of SOD, POD, and CAT. Our study further demonstrated that GhWRKY25 overexpression in plants enhanced sensitivity to the fungal pathogen Botrytis cinerea by reducing the expression of SA or ET signaling related genes and inducing the expression of genes involved in the JA signaling pathway. These results indicated that GhWRKY25 plays negative or positive roles in response to abiotic stresses, and the reduced pathogen resistance may be related to the crosstalk of the SA and JA/ET signaling pathways.
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Affiliation(s)
- Xiufang Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China
| | - Yunzhi Song
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China
| | - Fangyu Xing
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China
| | - Ning Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China
| | - Fujiang Wen
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China
| | - Changxiang Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China.
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73
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Meng D, Li Y, Bai Y, Li M, Cheng L. Genome-wide identification and characterization of WRKY transcriptional factor family in apple and analysis of their responses to waterlogging and drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 103:71-83. [PMID: 26970718 DOI: 10.1016/j.plaphy.2016.02.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 02/05/2016] [Accepted: 02/05/2016] [Indexed: 05/23/2023]
Abstract
As one of the largest transcriptional factor families in plants, WRKY genes play significant roles in various biotic and abiotic stress responses. Although the WRKY gene family has been characterized in a few plant species, the details remain largely unknown in the apple (Malus domestica Borkh.). In this study, we identified a total of 127 MdWRKYs from the apple genome, which were divided into four subgroups according to the WRKY domains and zinc finger motif. Most of them were mapped onto the apple's 17 chromosomes and were expressed in more than one tissue, including shoot tips, mature leaves, fruit and apple calli. We then contrasted WRKY expression patterns between calli grown in solid medium (control) and liquid medium (representing waterlogging stress) and found that 34 WRKY genes were differentially expressed between the two growing conditions. Finally, we determined the expression patterns of 10 selected WRKY genes in an apple rootstock, G41, in response to waterlogging and drought stress, which identified candidate genes involved in responses to water stress for functional analysis. Our data provide interesting candidate MdWRKYs for future functional analysis and demonstrate that apple callus is a useful system for characterizing gene expression and function in apple.
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Affiliation(s)
- Dong Meng
- Department of Horticulture, Cornell University, 134A Plant Science, Ithaca, NY 14853, USA
| | - Yuanyuan Li
- Department of Horticulture, Cornell University, 134A Plant Science, Ithaca, NY 14853, USA; College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Yang Bai
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Mingjun Li
- Department of Horticulture, Cornell University, 134A Plant Science, Ithaca, NY 14853, USA; College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lailiang Cheng
- Department of Horticulture, Cornell University, 134A Plant Science, Ithaca, NY 14853, USA.
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74
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Song H, Wang P, Lin JY, Zhao C, Bi Y, Wang X. Genome-Wide Identification and Characterization of WRKY Gene Family in Peanut. FRONTIERS IN PLANT SCIENCE 2016; 7:534. [PMID: 27200012 PMCID: PMC4845656 DOI: 10.3389/fpls.2016.00534] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/04/2016] [Indexed: 05/18/2023]
Abstract
WRKY, an important transcription factor family, is widely distributed in the plant kingdom. Many reports focused on analysis of phylogenetic relationship and biological function of WRKY protein at the whole genome level in different plant species. However, little is known about WRKY proteins in the genome of Arachis species and their response to salicylic acid (SA) and jasmonic acid (JA) treatment. In this study, we identified 77 and 75 WRKY proteins from the two wild ancestral diploid genomes of cultivated tetraploid peanut, Arachis duranensis and Arachis ipaënsis, using bioinformatics approaches. Most peanut WRKY coding genes were located on A. duranensis chromosome A6 and A. ipaënsis chromosome B3, while the least number of WRKY genes was found in chromosome 9. The WRKY orthologous gene pairs in A. duranensis and A. ipaënsis chromosomes were highly syntenic. Our analysis indicated that segmental duplication events played a major role in AdWRKY and AiWRKY genes, and strong purifying selection was observed in gene duplication pairs. Furthermore, we translate the knowledge gained from the genome-wide analysis result of wild ancestral peanut to cultivated peanut to reveal that gene activities of specific cultivated peanut WRKY gene were changed due to SA and JA treatment. Peanut WRKY7, 8 and 13 genes were down-regulated, whereas WRKY1 and 12 genes were up-regulated with SA and JA treatment. These results could provide valuable information for peanut improvement.
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Affiliation(s)
- Hui Song
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Biotechnology Research Center, Shandong Academy of Agricultural SciencesJinan, China
| | - Pengfei Wang
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Biotechnology Research Center, Shandong Academy of Agricultural SciencesJinan, China
| | - Jer-Young Lin
- Department of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Chuanzhi Zhao
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Biotechnology Research Center, Shandong Academy of Agricultural SciencesJinan, China
| | - Yuping Bi
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Biotechnology Research Center, Shandong Academy of Agricultural SciencesJinan, China
| | - Xingjun Wang
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Biotechnology Research Center, Shandong Academy of Agricultural SciencesJinan, China
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75
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Ghosh A, Islam T. Genome-wide analysis and expression profiling of glyoxalase gene families in soybean (Glycine max) indicate their development and abiotic stress specific response. BMC PLANT BIOLOGY 2016; 16:87. [PMID: 27083416 PMCID: PMC4833937 DOI: 10.1186/s12870-016-0773-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 04/11/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Glyoxalase pathway consists of two enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII) which detoxifies a highly cytotoxic metabolite methylglyoxal (MG) to its non-toxic form. MG may form advanced glycation end products with various cellular macro-molecules such as proteins, DNA and RNA; that ultimately lead to their inactivation. Role of glyoxalase enzymes has been extensively investigated in various plant species which showed their crucial role in salinity, drought and heavy metal stress tolerance. Previously genome-wide analysis of glyoxalase genes has been conducted in model plants Arabidopsis and rice, but no such study was performed in any legume species. RESULTS In the present study, a comprehensive genome database analysis of soybean was performed and identified a total of putative 41 GLYI and 23 GLYII proteins encoded by 24 and 12 genes, respectively. Detailed analysis of these identified members was conducted including their nomenclature and classification, chromosomal distribution and duplication, exon-intron organization, and protein domain(s) and motifs identification. Expression profiling of these genes has been performed in different tissues and developmental stages as well as under salinity and drought stresses using publicly available RNAseq and microarray data. The study revealed that GmGLYI-7 and GmGLYII-8 have been expressed intensively in all the developmental stages and tissues; while GmGLYI-6, GmGLYI-9, GmGLYI-20, GmGLYII-5 and GmGLYII-10 were highly abiotic stress responsive members. CONCLUSIONS The present study identifies the largest family of glyoxalase proteins to date with 41 GmGLYI and 23 GmGLYII members in soybean. Detailed analysis of GmGLYI and GmGLYII genes strongly indicates the genome-wide segmental and tandem duplication of the glyoxalase members. Moreover, this study provides a strong basis about the biological role and function of GmGLYI and GmGLYII members in soybean growth, development and stress physiology.
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MESH Headings
- Adaptation, Physiological/genetics
- Adaptation, Physiological/physiology
- Amino Acid Sequence
- Chromosome Mapping
- Chromosomes, Plant/genetics
- Droughts
- Exons
- Gene Expression Profiling/methods
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Plant
- Genome, Plant/genetics
- Introns
- Lactoylglutathione Lyase/chemistry
- Lactoylglutathione Lyase/classification
- Lactoylglutathione Lyase/genetics
- Models, Molecular
- Multigene Family
- Phylogeny
- Plant Proteins/classification
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Promoter Regions, Genetic/genetics
- Protein Domains
- Reverse Transcriptase Polymerase Chain Reaction
- Salinity
- Sequence Homology, Amino Acid
- Glycine max/enzymology
- Glycine max/genetics
- Glycine max/growth & development
- Stress, Physiological
- Thiolester Hydrolases/chemistry
- Thiolester Hydrolases/classification
- Thiolester Hydrolases/genetics
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Affiliation(s)
- Ajit Ghosh
- />Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
| | - Tahmina Islam
- />Plant Breeding and Biotechnology Laboratory, Department of Botany, Dhaka University, Dhaka, 1000 Bangladesh
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76
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Kumar K, Srivastava V, Purayannur S, Kaladhar VC, Cheruvu PJ, Verma PK. WRKY domain-encoding genes of a crop legume chickpea (Cicer arietinum): comparative analysis with Medicago truncatula WRKY family and characterization of group-III gene(s). DNA Res 2016; 23:225-39. [PMID: 27060167 PMCID: PMC4909309 DOI: 10.1093/dnares/dsw010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/20/2016] [Indexed: 11/16/2022] Open
Abstract
The WRKY genes have been identified as important transcriptional modulators predominantly during the environmental stresses, but they also play critical role at various stages of plant life cycle. We report the identification of WRKY domain (WD)-encoding genes from galegoid clade legumes chickpea (Cicer arietinum L.) and barrel medic (Medicago truncatula). In total, 78 and 98 WD-encoding genes were found in chickpea and barrel medic, respectively. Comparative analysis suggests the presence of both conserved and unique WRKYs, and expansion of WRKY family in M. truncatula primarily by tandem duplication. Exclusively found in galegoid legumes, CaWRKY16 and its orthologues encode for a novel protein having a transmembrane and partial Exo70 domains flanking a group-III WD. Genomic region of galegoids, having CaWRKY16, is more dynamic when compared with millettioids. In onion cells, fused CaWRKY16-EYFP showed punctate fluorescent signals in cytoplasm. The chickpea WRKY group-III genes were further characterized for their transcript level modulation during pathogenic stress and treatments of abscisic acid, jasmonic acid, and salicylic acid (SA) by real-time PCR. Differential regulation of genes was observed during Ascochyta rabiei infection and SA treatment. Characterization of A. rabiei and SA inducible gene CaWRKY50 showed that it localizes to plant nucleus, binds to W-box, and have a C-terminal transactivation domain. Overexpression of CaWRKY50 in tobacco plants resulted in early flowering and senescence. The in-depth comparative account presented here for two legume WRKY genes will be of great utility in hastening functional characterization of crop legume WRKYs and will also help in characterization of Exo70Js.
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Affiliation(s)
- Kamal Kumar
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vikas Srivastava
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Savithri Purayannur
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - V Chandra Kaladhar
- School of Life Sciences, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
| | - Purnima Jaiswal Cheruvu
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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77
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Wang N, Xia EH, Gao LZ. Genome-wide analysis of WRKY family of transcription factors in common bean, Phaseolus vulgaris: Chromosomal localization, structure, evolution and expression divergence. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2015.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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78
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Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis. PLoS One 2016; 11:e0148771. [PMID: 26859686 PMCID: PMC4747569 DOI: 10.1371/journal.pone.0148771] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/22/2016] [Indexed: 11/19/2022] Open
Abstract
Bambara groundnut (Vigna subterranea (L.) Verdc.) is an African legume and is a promising underutilized crop with good seed nutritional values. Low temperature stress in a number of African countries at night, such as Botswana, can effect the growth and development of bambara groundnut, leading to losses in potential crop yield. Therefore, in this study we developed a computational pipeline to identify and analyze the genes and gene modules associated with low temperature stress responses in bambara groundnut using the cross-species microarray technique (as bambara groundnut has no microarray chip) coupled with network-based analysis. Analyses of the bambara groundnut transcriptome using cross-species gene expression data resulted in the identification of 375 and 659 differentially expressed genes (p<0.01) under the sub-optimal (23°C) and very sub-optimal (18°C) temperatures, respectively, of which 110 genes are commonly shared between the two stress conditions. The construction of a Highest Reciprocal Rank-based gene co-expression network, followed by its partition using a Heuristic Cluster Chiseling Algorithm resulted in 6 and 7 gene modules in sub-optimal and very sub-optimal temperature stresses being identified, respectively. Modules of sub-optimal temperature stress are principally enriched with carbohydrate and lipid metabolic processes, while most of the modules of very sub-optimal temperature stress are significantly enriched with responses to stimuli and various metabolic processes. Several transcription factors (from MYB, NAC, WRKY, WHIRLY & GATA classes) that may regulate the downstream genes involved in response to stimulus in order for the plant to withstand very sub-optimal temperature stress were highlighted. The identified gene modules could be useful in breeding for low-temperature stress tolerant bambara groundnut varieties.
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79
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Cao Y, Han Y, Jin Q, Lin Y, Cai Y. Comparative Genomic Analysis of the GRF Genes in Chinese Pear ( Pyrus bretschneideri Rehd), Poplar ( Populous), Grape ( Vitis vinifera), Arabidopsis and Rice ( Oryza sativa). FRONTIERS IN PLANT SCIENCE 2016; 7:1750. [PMID: 27933074 PMCID: PMC5121280 DOI: 10.3389/fpls.2016.01750] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/07/2016] [Indexed: 05/20/2023]
Abstract
Growth-regulating factors (GRFs) are plant-specific transcription factors that have important functions in regulating plant growth and development. Previous studies on GRF family members focused either on a single or a small set of genes. Here, a comparative genomic analysis of the GRF gene family was performed in poplar (a model tree species), Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots), rice (a model plant for monocots) and Chinese pear (one of the economical fruit crops). In total, 58 GRF genes were identified, 12 genes in rice (Oryza sativa), 8 genes in grape (Vitis vinifera), 9 genes in Arabidopsis thaliana, 19 genes in poplar (Populus trichocarpa) and 10 genes in Chinese pear (Pyrus bretschneideri). The GRF genes were divided into five subfamilies based on the phylogenetic analysis, which was supported by their structural analysis. Furthermore, microsynteny analysis indicated that highly conserved regions of microsynteny were identified in all of the five species tested. And Ka/Ks analysis revealed that purifying selection plays an important role in the maintenance of GRF genes. Our results provide basic information on GRF genes in five plant species and lay the foundation for future research on the functions of these genes.
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Affiliation(s)
- Yunpeng Cao
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yahui Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural UniversityHefei, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yi Lin
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
- *Correspondence: Yongping Cai,
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80
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Song H, Wang P, Hou L, Zhao S, Zhao C, Xia H, Li P, Zhang Y, Bian X, Wang X. Global Analysis of WRKY Genes and Their Response to Dehydration and Salt Stress in Soybean. FRONTIERS IN PLANT SCIENCE 2016; 7:9. [PMID: 26870047 PMCID: PMC4740950 DOI: 10.3389/fpls.2016.00009] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/07/2016] [Indexed: 05/19/2023]
Abstract
WRKY proteins are plant specific transcription factors involved in various developmental and physiological processes, especially in biotic and abiotic stress resistance. Although previous studies suggested that WRKY proteins in soybean (Glycine max var. Williams 82) involved in both abiotic and biotic stress responses, the global information of WRKY proteins in the latest version of soybean genome (Wm82.a2v1) and their response to dehydration and salt stress have not been reported. In this study, we identified 176 GmWRKY proteins from soybean Wm82.a2v1 genome. These proteins could be classified into three groups, namely group I (32 proteins), group II (120 proteins), and group III (24 proteins). Our results showed that most GmWRKY genes were located on Chromosome 6, while chromosome 11, 12, and 20 contained the least number of this gene family. More GmWRKY genes were distributed on the ends of chromosomes to compare with other regions. The cis-acting elements analysis suggested that GmWRKY genes were transcriptionally regulated upon dehydration and salt stress. RNA-seq data analysis indicated that three GmWRKY genes responded negatively to dehydration, and 12 genes positively responded to salt stress at 1, 6, and 12 h, respectively. We confirmed by qRT-PCR that the expression of GmWRKY47 and GmWRKY 58 genes was decreased upon dehydration, and the expression of GmWRKY92, 144 and 165 genes was increased under salt treatment.
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81
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Wang L, Wu N, Zhu Y, Song W, Zhao X, Li Y, Hu Y. The divergence and positive selection of the plant-specific BURP-containing protein family. Ecol Evol 2015; 5:5394-5412. [PMID: 30151141 PMCID: PMC6102523 DOI: 10.1002/ece3.1792] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 09/13/2015] [Accepted: 09/17/2015] [Indexed: 11/21/2022] Open
Abstract
BURP domain-containing proteins belong to a plant-specific protein family and have diverse roles in plant development and stress responses. However, our understanding about the genetic divergence patterns and evolutionary rates of these proteins remain inadequate. In this study, 15 plant genomes were explored to elucidate the genetic origins, divergence, and functions of these proteins. One hundred and twenty-five BURP protein-encoding genes were identified from four main plant lineages, including 13 higher plant species. The absence of BURP family genes in unicellular and multicellular algae suggests that this family (1) appeared when plants shifted from relatively stable aquatic environments to land, where conditions are more variable and stressful, and (2) is critical in the adaptation of plants to adverse environments. Promoter analysis revealed that several responsive elements to plant hormones and external environment stresses are concentrated in the promoter region of BURP protein-encoding genes. This finding confirms that these genes influence plant stress responses. Several segmentally and tandem-duplicated gene pairs were identified from eight plant species. Thus, in general, BURP domain-containing genes have been subject to strong positive selection, even though these genes have conformed to different expansion models in different species. Our study also detected certain critical amino acid sites that may have contributed to functional divergence among groups or subgroups. Unexpectedly, all of the critical amino acid residues of functional divergence and positive selection were exclusively located in the C-terminal region of the BURP domain. In conclusion, our results contribute novel insights into the genetic divergence patterns and evolutionary rates of BURP proteins.
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Affiliation(s)
- Lihui Wang
- College of Life SciencesCapital Normal UniversityBeijing100048China
| | - Ningning Wu
- College of Life SciencesCapital Normal UniversityBeijing100048China
| | - Yan Zhu
- College of Life SciencesCapital Normal UniversityBeijing100048China
| | - Wanlu Song
- College of Life SciencesCapital Normal UniversityBeijing100048China
| | - Xin Zhao
- College of Life SciencesCapital Normal UniversityBeijing100048China
| | - Yaxuan Li
- College of Life SciencesCapital Normal UniversityBeijing100048China
| | - Yingkao Hu
- College of Life SciencesCapital Normal UniversityBeijing100048China
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82
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Zhu G, Chen G, Zhu J, Zhu Y, Lu X, Li X, Hu Y, Yan Y. Molecular Characterization and Expression Profiling of NAC Transcription Factors in Brachypodium distachyon L. PLoS One 2015; 10:e0139794. [PMID: 26444425 PMCID: PMC4596864 DOI: 10.1371/journal.pone.0139794] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 09/17/2015] [Indexed: 12/19/2022] Open
Abstract
NAC (NAM, ATAF1/2, CUC2) transcription factors are involved in regulating plant developmental processes and response to environmental stresses. Brachypodium distachyon is an emerging model system for cereals, temperate grasses and biofuel crops. In this study, a comprehensive investigation of the molecular characterizations, phylogenetics and expression profiles under various abiotic stresses of the NAC gene family in Brachypodium distachyon was performed. In total, 118 BNAC genes in B. distachyon were identified, of which 22 (18.64%) were tandemly duplicated and segmentally duplicated, respectively. The Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC) algorithms showed that they were divided into two clades and fourteen subfamilies, supported by similar motif compositions within one subfamily. Some critical amino acids detected using DIVERGE v3.0 might contribute to functional divergence among subfamilies. The different exon-intron organizations among subfamilies revealed structural differentiation. Promoter sequence predictions showed that the BNAC genes were involved in various developmental processes and diverse stress responses. Three NAC domain-encoding genes (BNAC012, BNAC078 and BNAC108), orthologous of NAC1, were targeted by five miRNA164 (Bdi-miR164a-c, e, f), suggesting that they might function in lateral organ enlargement, floral development and the responses to abiotic stress. Eleven (~9.32%) BNAC proteins containing α-helical transmembrane motifs were identified. 23 representative BNAC genes were analyzed by quantitative real-time PCR, showing different expression patterns under various abiotic stresses, of which 18, 17 and 11 genes were up-regulated significantly under drought, H2O2 and salt stresses, respectively. Only four and two genes were up-regulated under cold and cadmium stresses, respectively. Dynamic transcriptional expression analysis revealed that six genes showed constitutive expression and period-specific expression. The current results provide novel insights into the structure and function of the plant NAC gene family.
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Affiliation(s)
- Gengrui Zhu
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Guanxing Chen
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Jiantang Zhu
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Yan Zhu
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Xiaobing Lu
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Xiaohui Li
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Yingkao Hu
- College of Life Science, Capital Normal University, Beijing, 100048, China
- * E-mail: (YH); (YY)
| | - Yueming Yan
- College of Life Science, Capital Normal University, Beijing, 100048, China
- * E-mail: (YH); (YY)
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83
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Li JM, Zheng DM, Li LT, Qiao X, Wei SW, Bai B, Zhang SL, Wu J. Genome-Wide Function, Evolutionary Characterization and Expression Analysis of Sugar Transporter Family Genes in Pear (Pyrus bretschneideri Rehd). PLANT & CELL PHYSIOLOGY 2015; 56:1721-37. [PMID: 26079674 DOI: 10.1093/pcp/pcv090] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 06/10/2015] [Indexed: 05/22/2023]
Abstract
The sugar transporter (ST) plays an important role in plant growth, development and fruit quality. In this study, a total of 75 ST genes were identified in the pear (Pyrus bretschneideri Rehd) genome based on systematic analysis. Furthermore, all ST genes identified were grouped into eight subfamilies according to conserved domains and phylogenetic analysis. Analysis of cis-regulatory element sequences of all ST genes identified the MYBCOREATCYCB1 promoter in sucrose transporter (SUT) and monosaccharide transporter (MST) genes of pear, while in grape it is exclusively found in SUT subfamily members, indicating divergent transcriptional regulation in different species. Gene duplication event analysis indicated that whole-genome duplication (WGD) and segmental duplication play key roles in ST gene amplification, followed by tandem duplication. Estimation of positive selection at codon sites of ST paralog pairs indicated that all plastidic glucose translocator (pGlcT) subfamily members have evolved under positive selection. In addition, the evolutionary history of ST gene duplications indicated that the ST genes have experienced significant expansion in the whole ST gene family after the second WGD, especially after apple and pear divergence. According to the global RNA sequencing results of pear fruit development, gene expression profiling showed the expression of 53 STs. Combined with quantitative real-time PCR (qRT-PCR) analysis, two polyol/monosaccharide transporter (PLT) and three tonoplast monosaccharide transporter (tMT) members were identified as candidate genes, which may play important roles in sugar accumulation during pear fruit development and ripening. Identification of highly expressed STs in fruit is important for finding novel genes contributing to enhanced levels of sugar content in pear fruit.
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Affiliation(s)
- Jia-Ming Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Dan-man Zheng
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Lei-ting Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shu-wei Wei
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Bai
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shao-ling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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Zhao TT, Zhang J, Liang LS, Ma QH, Chen X, Zong JW, Wang GX. Expression and Functional Analysis of WRKY Transcription Factors in Chinese Wild Hazel, Corylus heterophylla Fisch. PLoS One 2015; 10:e0135315. [PMID: 26270529 PMCID: PMC4536078 DOI: 10.1371/journal.pone.0135315] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/20/2015] [Indexed: 12/03/2022] Open
Abstract
Plant WRKY transcription factors are known to regulate various biotic and abiotic stress responses. In this study we identified a total of 30 putative WRKY unigenes in a transcriptome dataset of the Chinese wild Hazel, Corylus heterophylla, a species that is noted for its cold tolerance. Thirteen full-length of these ChWRKY genes were cloned and found to encode complete protein sequences, and they were divided into three groups, based on the number of WRKY domains and the pattern of zinc finger structures. Representatives of each of the groups, Unigene25835 (group I), Unigene37641 (group II) and Unigene20441 (group III), were transiently expressed as fusion proteins with yellow fluorescent fusion protein in Nicotiana benthamiana, where they were observed to accumulate in the nucleus, in accordance with their predicted roles as transcriptional activators. An analysis of the expression patterns of all 30 WRKY genes revealed differences in transcript abundance profiles following exposure to cold, drought and high salinity conditions. Among the stress-inducible genes, 23 were up-regulated by all three abiotic stresses and the WRKY genes collectively exhibited four different patterns of expression in flower buds during the overwintering period from November to April. The organ/tissue related expression analysis showed that 18 WRKY genes were highly expressed in stem but only 2 (Unigene9262 and Unigene43101) were greatest in male anthotaxies. The expression of Unigene37641, a member of the group II WRKY genes, was substantially up-regulated by cold, drought and salinity treatments, and its overexpression in Arabidopsis thaliana resulted in better seedling growth, compared with wild type plants, under cold treatment conditions. The transgenic lines also had exhibited higher soluble protein content, superoxide dismutase and peroxidase activiety and lower levels of malondialdehyde, which collectively suggets that Unigene37641 expression promotes cold tolerance.
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Affiliation(s)
- Tian-Tian Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Li-Song Liang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Qing-Hua Ma
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xin Chen
- Shandong Institute of Pomology, Shandong Provincial Key Laboratory of Fruit Tree Biotechnology Breeding, Tai’an, Shandong, China
| | - Jian-Wei Zong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Gui-Xi Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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85
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Chen L, Yang Y, Liu C, Zheng Y, Xu M, Wu N, Sheng J, Shen L. Characterization of WRKY transcription factors in Solanum lycopersicum reveals collinearity and their expression patterns under cold treatment. Biochem Biophys Res Commun 2015. [DOI: 10.1016/j.bbrc.2015.07.085] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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86
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Brown AV, Hudson KA. Developmental profiling of gene expression in soybean trifoliate leaves and cotyledons. BMC PLANT BIOLOGY 2015; 15:169. [PMID: 26149852 PMCID: PMC4492100 DOI: 10.1186/s12870-015-0553-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 06/15/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Immediately following germination, the developing soybean seedling relies on the nutrient reserves stored in the cotyledons to sustain heterotrophic growth. During the seed filling period, developing seeds rely on the transport of nutrients from the trifoliate leaves. In soybean, both cotyledons and leaves develop the capacity for photosynthesis, and subsequently senesce and abscise once their function has ended. Before this occurs, the nutrients they contain are mobilized and transported to other parts of the plant. These processes are carefully orchestrated by genetic regulation throughout the development of the leaf or cotyledon. RESULTS To identify genes involved in the processes of leaf or cotyledon development and senescence in soybean, we used RNA-seq to profile multiple stages of cotyledon and leaf tissues. Differentially expressed genes between stages of leaf or cotyledon development were determined, major patterns of gene expression were defined, and shared genes were identified. Over 38,000 transcripts were expressed during the course of leaf and cotyledon development. Of those transcripts, 5,000 were expressed in a tissue specific pattern. Of the genes that were differentially expressed between both later stage tissues, 90 % had the same direction of change, suggesting that the mechanisms of senescence are conserved between tissues. Analysis of the enrichment of biological functions within genes sharing common expression profiles highlights the main processes occurring within these defined temporal windows of leaf and cotyledon development. Over 1,000 genes were identified with predicted regulatory functions that may have a role in control of leaf or cotyledon senescence. CONCLUSIONS The process of leaf and cotyledon development can be divided into distinct stages characterized by the expression of specific gene sets. The importance of the WRKY, NAC, and GRAS family transcription factors as major regulators of plant senescence is confirmed for both soybean leaf and cotyledon tissues. These results help validate functional annotation for soybean genes and promoters.
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Affiliation(s)
- Anne V Brown
- Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.
| | - Karen A Hudson
- USDA-ARS Crop Production and Pest Control Research Unit, 915 West State Street, West Lafayette, IN, 47907, USA.
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87
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Chi Y, Yang Y, Li G, Wang F, Fan B, Chen Z. Identification and characterization of a novel group of legume-specific, Golgi apparatus-localized WRKY and Exo70 proteins from soybean. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3055-70. [PMID: 25805717 PMCID: PMC4449531 DOI: 10.1093/jxb/erv104] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Many plant genes belong to families that arise from extensive proliferation and diversification allowing the evolution of functionally new proteins. Here we report the characterization of a group of proteins evolved from WRKY and exocyst complex subunit Exo70 proteins through fusion with a novel transmembrane (TM) domain in soybean (Glycine max). From the soybean genome, we identified a novel WRKY-related protein (GmWRP1) that contains a WRKY domain with no binding activity for W-box sequences. GFP fusion revealed that GmWRP1 was targeted to the Golgi apparatus through its N-terminal TM domain. Similar Golgi-targeting TM domains were also identified in members of a new subfamily of Exo70J proteins involved in vesicle trafficking. The novel TM domains are structurally most similar to the endosomal cytochrome b561 from birds and close homologues of GmWRP1 and GmEx070J proteins with the novel TM domain have only been identified in legumes. Transient expression of some GmExo70J proteins or the Golgi-targeting TM domain in tobacco altered the subcellular structures labelled by a fluorescent Golgi marker. GmWRP1 transcripts were detected at high levels in roots, flowers, pods, and seeds, and the expression levels of GmWRP1 and GmExo70J genes were elevated with increased age in leaves. The legume-specific, Golgi apparatus-localized GmWRP1 and GmExo70J proteins are probably involved in Golgi-mediated vesicle trafficking of biological molecules that are uniquely important to legumes.
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Affiliation(s)
- Yingjun Chi
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Yan Yang
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Guiping Li
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Fei Wang
- Department of Botany and Plant Pathology, 915W. State Street, Purdue University, West Lafayette, IN 47907, USA
| | - Baofang Fan
- Department of Botany and Plant Pathology, 915W. State Street, Purdue University, West Lafayette, IN 47907, USA
| | - Zhixiang Chen
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China Department of Botany and Plant Pathology, 915W. State Street, Purdue University, West Lafayette, IN 47907, USA
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88
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Cabreira C, Cagliari A, Bücker-Neto L, Margis-Pinheiro M, de Freitas LB, Bodanese-Zanettini MH. The phylogeny and evolutionary history of the Lesion Simulating Disease (LSD) gene family in Viridiplantae. Mol Genet Genomics 2015; 290:2107-19. [DOI: 10.1007/s00438-015-1060-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 05/03/2015] [Indexed: 12/23/2022]
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89
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Yang X, Deng C, Zhang Y, Cheng Y, Huo Q, Xue L. The WRKY transcription factor genes in eggplant (Solanum melongena L.) and Turkey Berry (Solanum torvum Sw.). Int J Mol Sci 2015; 16:7608-26. [PMID: 25853261 PMCID: PMC4425038 DOI: 10.3390/ijms16047608] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 03/02/2015] [Accepted: 03/10/2015] [Indexed: 11/16/2022] Open
Abstract
WRKY transcription factors, which play critical roles in stress responses, have not been characterized in eggplant or its wild relative, turkey berry. The recent availability of RNA-sequencing data provides the opportunity to examine WRKY genes from a global perspective. We identified 50 and 62 WRKY genes in eggplant (SmelWRKYs) and turkey berry (StorWRKYs), respectively, all of which could be classified into three groups (I–III) based on the WRKY protein structure. The SmelWRKYs and StorWRKYs contain ~76% and ~95% of the number of WRKYs found in other sequenced asterid species, respectively. Positive selection analysis revealed that different selection constraints could have affected the evolution of these groups. Positively-selected sites were found in Groups IIc and III. Branch-specific selection pressure analysis indicated that most WRKY domains from SmelWRKYs and StorWRKYs are conserved and have evolved at low rates since their divergence. Comparison to homologous WRKY genes in Arabidopsis revealed several potential pathogen resistance-related SmelWRKYs and StorWRKYs, providing possible candidate genetic resources for improving stress tolerance in eggplant and probably other Solanaceae plants. To our knowledge, this is the first report of a genome-wide analyses of the SmelWRKYs and StorWRKYs.
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Affiliation(s)
- Xu Yang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China.
| | - Cao Deng
- DNA Stories Bioinformatics Services Co., Ltd., Chengdu 610000, China.
| | - Yu Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China.
| | - Yufu Cheng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China.
| | - Qiuyue Huo
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China.
| | - Linbao Xue
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China.
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90
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Li C, Li D, Shao F, Lu S. Molecular cloning and expression analysis of WRKY transcription factor genes in Salvia miltiorrhiza. BMC Genomics 2015; 16:200. [PMID: 25881056 PMCID: PMC4371873 DOI: 10.1186/s12864-015-1411-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 02/27/2015] [Indexed: 12/02/2022] Open
Abstract
Background WRKY proteins comprise a large family of transcription factors and play important regulatory roles in plant development and defense response. The WRKY gene family in Salvia miltiorrhiza has not been characterized. Results A total of 61 SmWRKYs were cloned from S. miltiorrhiza. Multiple sequence alignment showed that SmWRKYs could be classified into 3 groups and 8 subgroups. Sequence features, the WRKY domain and other motifs of SmWRKYs are largely conserved with Arabidopsis AtWRKYs. Each group of WRKY domains contains characteristic conserved sequences, and group-specific motifs might attribute to functional divergence of WRKYs. A total of 17 pairs of orthologous SmWRKY and AtWRKY genes and 21 pairs of paralogous SmWRKY genes were identified. Maximum likelihood analysis showed that SmWRKYs had undergone strong selective pressure for adaptive evolution. Functional divergence analysis suggested that the SmWRKY subgroup genes and many paralogous SmWRKY gene pairs were divergent in functions. Various critical amino acids contributed to functional divergence among subgroups were detected. Of the 61 SmWRKYs, 22, 13, 4 and 1 were predominantly expressed in roots, stems, leaves, and flowers, respectively. The other 21 were mainly expressed in at least two tissues analyzed. In S. miltiorrhiza roots treated with MeJA, significant changes of gene expression were observed for 49 SmWRKYs, of which 26 were up-regulated, 18 were down-regulated, while the other 5 were either up-regulated or down-regulated at different time-points of treatment. Analysis of published RNA-seq data showed that 42 of the 61 identified SmWRKYs were yeast extract and Ag+-responsive. Through a systematic analysis, SmWRKYs potentially involved in tanshinone biosynthesis were predicted. Conclusion These results provide insights into functional conservation and diversification of SmWRKYs and are useful information for further elucidating SmWRKY functions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1411-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China.
| | - Dongqiao Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China.
| | - Fenjuan Shao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China.
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China.
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91
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Van Holle S, Van Damme EJM. Distribution and evolution of the lectin family in soybean (Glycine max). Molecules 2015; 20:2868-91. [PMID: 25679048 PMCID: PMC6272470 DOI: 10.3390/molecules20022868] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 02/06/2015] [Indexed: 01/02/2023] Open
Abstract
Lectins are a diverse group of proteins that bind specific carbohydrates and are found throughout all kingdoms. In plants, lectins are involved in a range of important processes such as plant defense and stress signaling. Although the genome sequence of Glycine max (soybean) has been published, little is known about the abundance and expansion patterns of lectin genes in soybean. Using BLAST and hidden Markov models, a total of 359 putative lectin genes have been identified. Furthermore, these sequences could be classified in nine of the twelve plant lectin families identified today. Analysis of the domain organization demonstrated that most of the identified lectin genes encode chimerolectins, consisting of one or multiple lectin domains combined with other known protein domains. Both tandem and segmental duplication events have contributed to the expansion of the lectin gene family. These data provide a detailed understanding of the domain architecture and molecular evolution of the lectin gene family in soybean.
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Affiliation(s)
- Sofie Van Holle
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
| | - Els J M Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
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92
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Ma J, Zhang D, Shao Y, Liu P, Jiang L, Li C. Genome-Wide Analysis of the WRKY Transcription Factors in Aegilops tauschii. Cytogenet Genome Res 2015; 144:243-53. [DOI: 10.1159/000370172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2014] [Indexed: 11/19/2022] Open
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93
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Wu N, Zhu Y, Song W, Li Y, Yan Y, Hu Y. Unusual tandem expansion and positive selection in subgroups of the plant GRAS transcription factor superfamily. BMC PLANT BIOLOGY 2014; 14:373. [PMID: 25524588 PMCID: PMC4279901 DOI: 10.1186/s12870-014-0373-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 12/08/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND GRAS proteins belong to a plant transcription factor family that is involved with multifarious roles in plants. Although previous studies of this protein family have been reported for Arabidopsis, rice, Chinese cabbage and other species, investigation of expansion patterns and evolutionary rate on the basis of comparative genomics in different species remains inadequate. RESULTS A total of 289 GRAS genes were identified in Arabidopsis, B. distachyon, rice, soybean, S. moellendorffii, and P. patens and were grouped into seven subfamilies, supported by the similarity of their exon-intron patterns and structural motifs. All of tandem duplicated genes were found in group II except one cluster of rice, indicating that tandem duplication greatly promoted the expansion of group II. Furthermore, segment duplications were mainly found in the soybean genome, whereas no single expansion pattern dominated in other plant species indicating that GRAS genes from these five species might be subject to a more complex evolutionary mechanism. Interestingly, branch-site model analyses of positive selection showed that a number of sites were positively selected under foreground branches I and V. These results strongly indicated that these groups were experiencing higher positive selection pressure. Meanwhile, the site-specific model revealed that the GRAS genes were under strong positive selection in P. patens. DIVERGE v2.0 was used to detect critical amino acid sites, and the results showed that the shifted evolutionary rate was mainly attributed to the functional divergence between the GRAS genes in the two groups. In addition, the results also demonstrated the expression divergence of the GRAS duplicated genes in the evolution. In short, the results above provide a solid foundation for further functional dissection of the GRAS gene superfamily. CONCLUSIONS In this work, differential expression, evolutionary rate, and expansion patterns of the GRAS gene family in the six species were predicted. Especially, tandem duplication events played an important role in expansion of group II. Together, these results contribute to further functional analysis and the molecular evolution of the GRAS gene superfamily.
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Affiliation(s)
- Ningning Wu
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Yan Zhu
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Wanlu Song
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Yaxuan Li
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Yueming Yan
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Yingkao Hu
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
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94
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Hyun TK, Eom SH, Han X, Kim JS. Evolution and expression analysis of the soybean glutamate decarboxylase gene family. J Biosci 2014; 39:899-907. [PMID: 25431418 DOI: 10.1007/s12038-014-9484-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Glutamate decarboxylase (GAD) is an enzyme that catalyses the conversion of L-glutamate into gamma-aminobutyric acid (GABA), which is a four-carbon non-protein amino acid present in all organisms. Although plant GAD plays important roles in GABA biosynthesis, our knowledge concerning GAD gene family members and their evolutionary relationship remains limited. Therefore, in this study, we have analysed the evolutionary mechanisms of soybean GAD genes and suggested that these genes expanded in the soybean genome partly due to segmental duplication events. The approximate dates of duplication events were calculated using the synonymous substitution rate, and we suggested that the segmental duplication of GAD genes in soybean originated 9.47 to 11.84 million years ago (Mya). In addition, all segmental duplication pairs (GmGAD1/3 and GmGAD2/4) are subject to purifying selection. Furthermore, GmGAD genes displayed differential expression either in their transcript abundance or in their expression patterns under abiotic stress conditions like salt, drought, and cold. The expression pattern of paralogous pairs suggested that they might have undergone neofunctionalization during the subsequent evolution process. Taken together, our results provide valuable information for the evolution of the GAD gene family and represent the basis for future research on the functional characterization of GAD genes in higher plants.
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Affiliation(s)
- Tae Kyung Hyun
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
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95
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Abstract
Glutamate decarboxylase (GAD) is an enzyme that catalyses the conversion of L-glutamate into gamma-aminobutyric acid (GABA), which is a four-carbon non-protein amino acid present in all organisms. Although plant GAD plays important roles in GABA biosynthesis, our knowledge concerning GAD gene family members and their evolutionary relationship remains limited. Therefore, in this study, we have analysed the evolutionary mechanisms of soybean GAD genes and suggested that these genes expanded in the soybean genome partly due to segmental duplication events. The approximate dates of duplication events were calculated using the synonymous substitution rate, and we suggested that the segmental duplication of GAD genes in soybean originated 9.47 to 11.84 million years ago (Mya). In addition, all segmental duplication pairs (GmGAD1/3 and GmGAD2/4) are subject to purifying selection. Furthermore, GmGAD genes displayed differential expression either in their transcript abundance or in their expression patterns under abiotic stress conditions like salt, drought, and cold. The expression pattern of paralogous pairs suggested that they might have undergone neofunctionalization during the subsequent evolution process. Taken together, our results provide valuable information for the evolution of the GAD gene family and represent the basis for future research on the functional characterization of GAD genes in higher plants.
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96
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Leisner CP, Ming R, Ainsworth EA. Distinct transcriptional profiles of ozone stress in soybean (Glycine max) flowers and pods. BMC PLANT BIOLOGY 2014; 14:335. [PMID: 25430603 PMCID: PMC4263021 DOI: 10.1186/s12870-014-0335-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 11/14/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Tropospheric ozone (O3) is a secondary air pollutant and anthropogenic greenhouse gas. Concentrations of tropospheric O3 ([O3] have more than doubled since the Industrial Revolution, and are high enough to damage plant productivity. Soybean (Glycine max L. Merr.) is the world's most important legume crop and is sensitive to O3. Current ground-level [O3] are estimated to reduce global soybean yields by 6% to 16%. In order to understand transcriptional mechanisms of yield loss in soybean, we examined the transcriptome of soybean flower and pod tissues exposed to elevated [O3] using RNA-Sequencing. RESULTS Elevated [O3] elicited a strong transcriptional response in flower and pod tissues, with increased expression of genes involved in signaling in both tissues. Flower tissues also responded to elevated [O3] by increasing expression of genes encoding matrix metalloproteinases (MMPs). MMPs are zinc- and calcium-dependent endopeptidases that have roles in programmed cell death, senescence and stress response in plants. Pod tissues responded to elevated [O3] by increasing expression of xyloglucan endotransglucosylase/hydrolase genes, which may be involved with increased pod dehiscence in elevated [O3]. CONCLUSIONS This study established that gene expression in reproductive tissues of soybean are impacted by elevated [O3], and flowers and pods have distinct transcriptomic responses to elevated [O3].
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Affiliation(s)
- Courtney P Leisner
- Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Ray Ming
- Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Elizabeth A Ainsworth
- Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA.
- USDA ARS Global Change and Photosynthesis Research Unit, 1201 W. Gregory Drive, Urbana, IL, 61801, USA.
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97
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The CarERF genes in chickpea (Cicer arietinum L.) and the identification of CarERF116 as abiotic stress responsive transcription factor. Funct Integr Genomics 2014; 15:27-46. [PMID: 25274312 DOI: 10.1007/s10142-014-0399-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/21/2014] [Accepted: 08/31/2014] [Indexed: 10/24/2022]
Abstract
The AP2/ERF family is one of the largest transcription factor gene families that are involved in various plant processes, especially in response to biotic and abiotic stresses. Complete genome sequences of one of the world's most important pulse crops chickpea (Cicer arietinum L.), has provided an important opportunity to identify and characterize genome-wide ERF genes. In this study, we identified 120 putative ERF genes from chickpea. The genomic organization of the chickpea ERF genes suggested that the gene family might have been expanded through the segmental duplications. The 120 member ERF family was classified into eleven distinct groups (I-X and VI-L). Transcriptional factor CarERF116, which is differentially expressed between drought tolerant and susceptible chickpea cultivar under terminal drought stress has been identified and functionally characterized. The CarERF116 encodes a putative protein of 241 amino acids and classified into group IX of ERF family. An in vitro CarERF116 protein-DNA binding assay demonstrated that CarERF116 protein specifically interacts with GCC box. We demonstrate that CarERF116 is capable of transactivation activity of and show that the functional transcriptional domain lies at the C-terminal region of the CarERF116. In transgenic Arabidopsis plants overexpressing CarERF116, significant up-regulation of several stress related genes were observed. These plants also exhibit resistance to osmotic stress and reduced sensitivity to ABA during seed germination. Based on these findings, we conclude that CarERF116 is an abiotic stress responsive gene, which plays an important role in stress tolerance. In addition, the present study leads to genome-wide identification and evolutionary analyses of chickpea ERF gene family, which will facilitate further research on this important group of genes and provides valuable resources for comparative genomics among the grain legumes.
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98
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Song W, Qin Y, Zhu Y, Yin G, Wu N, Li Y, Hu Y. Delineation of plant caleosin residues critical for functional divergence, positive selection and coevolution. BMC Evol Biol 2014; 14:124. [PMID: 24913827 PMCID: PMC4057654 DOI: 10.1186/1471-2148-14-124] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 06/03/2014] [Indexed: 11/22/2022] Open
Abstract
Background The caleosin genes encode proteins with a single conserved EF hand calcium-binding domain and comprise small gene families found in a wide range of plant species. These proteins may be involved in many cellular and biological processes coupled closely to the synthesis, degradation, or stability of oil bodies. Although previous studies of this protein family have been reported for Arabidopsis and other species, understanding of the evolution of the caleosin gene family in plants remains inadequate. Results In this study, comparative genomic analysis was performed to investigate the phylogenetic relationships, evolutionary history, functional divergence, positive selection, and coevolution of caleosins. First, 84 caleosin genes were identified from five main lineages that included 15 species. Phylogenetic analysis placed these caleosins into five distinct subfamilies (sub I–V), including two subfamilies that have not been previously identified. Among these subfamilies, sub II coincided with the distinct P-caleosin isoform recently identified in the pollen oil bodies of lily; caleosin genes from the same lineage tended to be clustered together in the phylogenetic tree. A special motif was determined to be related with the classification of caleosins, which may have resulted from a deletion in sub I and sub III occurring after the evolutionary divergence of monocot and dicot species. Additionally, several segmentally and tandem-duplicated gene pairs were identified from seven species, and further analysis revealed that caleosins of different species did not share a common expansion model. The ages of each pair of duplications were calculated, and most were consistent with the time of genome-wide duplication events in each species. Functional divergence analysis showed that changes in functional constraints have occurred between subfamilies I/IV, II/IV, and II/V, and some critical amino acid sites were identified during the functional divergence. Additional analyses revealed that caleosins were under positive selection during evolution, and seven candidate amino acid sites (70R, 74G, 88 L, 89G, 100 K, 106A, 107S) for positive selection were identified. Interestingly, the critical amino acid residues of functional divergence and positive selection were mainly located in C-terminal domain. Finally, three groups of coevolved amino acid sites were identified. Among these coevolved sites, seven from group 2 were located in the Ca2+-binding region of crucial importance. Conclusion In this study, the evolutionary and expansion patterns of the caleosin gene family were predicted, and a series of amino acid sites relevant to their functional divergence, adaptive evolution, and coevolution were identified. These findings provide data to facilitate further functional analysis of caleosin gene families in the plant lineage.
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Affiliation(s)
| | | | | | | | | | | | - Yingkao Hu
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
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Zhu Y, Wu N, Song W, Yin G, Qin Y, Yan Y, Hu Y. Soybean (Glycine max) expansin gene superfamily origins: segmental and tandem duplication events followed by divergent selection among subfamilies. BMC PLANT BIOLOGY 2014; 14:93. [PMID: 24720629 PMCID: PMC4021193 DOI: 10.1186/1471-2229-14-93] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 03/27/2014] [Indexed: 05/05/2023]
Abstract
BACKGROUND Expansins are plant cell wall loosening proteins that are involved in cell enlargement and a variety of other developmental processes. The expansin superfamily contains four subfamilies; namely, α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA), and expansin-like B (EXLB). Although the genome sequencing of soybeans is complete, our knowledge about the pattern of expansion and evolutionary history of soybean expansin genes remains limited. RESULTS A total of 75 expansin genes were identified in the soybean genome, and grouped into four subfamilies based on their phylogenetic relationships. Structural analysis revealed that the expansin genes are conserved in each subfamily, but are divergent among subfamilies. Furthermore, in soybean and Arabidopsis, the expansin gene family has been mainly expanded through tandem and segmental duplications; however, in rice, segmental duplication appears to be the dominant process that generates this superfamily. The transcriptome atlas revealed notable differential expression in either transcript abundance or expression patterns under normal growth conditions. This finding was consistent with the differential distribution of the cis-elements in the promoter region, and indicated wide functional divergence in this superfamily. Moreover, some critical amino acids that contribute to functional divergence and positive selection were detected. Finally, site model and branch-site model analysis of positive selection indicated that the soybean expansin gene superfamily is under strong positive selection, and that divergent selection constraints might have influenced the evolution of the four subfamilies. CONCLUSION This study demonstrated that the soybean expansin gene superfamily has expanded through tandem and segmental duplication. Differential expression indicated wide functional divergence in this superfamily. Furthermore, positive selection analysis revealed that divergent selection constraints might have influenced the evolution of the four subfamilies. In conclusion, the results of this study contribute novel detailed information about the molecular evolution of the expansin gene superfamily in soybean.
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Affiliation(s)
- Yan Zhu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Ningning Wu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Wanlu Song
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Guangjun Yin
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yajuan Qin
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yueming Yan
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yingkao Hu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
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Chen X, Chen Z, Zhao H, Zhao Y, Cheng B, Xiang Y. Genome-wide analysis of soybean HD-Zip gene family and expression profiling under salinity and drought treatments. PLoS One 2014; 9:e87156. [PMID: 24498296 PMCID: PMC3911943 DOI: 10.1371/journal.pone.0087156] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 12/18/2013] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Homeodomain-leucine zipper (HD-Zip) proteins, a group of homeobox transcription factors, participate in various aspects of normal plant growth and developmental processes as well as environmental responses. To date, no overall analysis or expression profiling of the HD-Zip gene family in soybean (Glycine max) has been reported. METHODS AND FINDINGS An investigation of the soybean genome revealed 88 putative HD-Zip genes. These genes were classified into four subfamilies, I to IV, based on phylogenetic analysis. In each subfamily, the constituent parts of gene structure and motif were relatively conserved. A total of 87 out of 88 genes were distributed unequally on 20 chromosomes with 36 segmental duplication events, indicating that segmental duplication is important for the expansion of the HD-Zip family. Analysis of the Ka/Ks ratios showed that the duplicated genes of the HD-Zip family basically underwent purifying selection with restrictive functional divergence after the duplication events. Analysis of expression profiles showed that 80 genes differentially expressed across 14 tissues, and 59 HD-Zip genes are differentially expressed under salinity and drought stress, with 20 paralogous pairs showing nearly identical expression patterns and three paralogous pairs diversifying significantly under drought stress. Quantitative real-time RT-PCR (qRT-PCR) analysis of six paralogous pairs of 12 selected soybean HD-Zip genes under both drought and salinity stress confirmed their stress-inducible expression patterns. CONCLUSIONS This study presents a thorough overview of the soybean HD-Zip gene family and provides a new perspective on the evolution of this gene family. The results indicate that HD-Zip family genes may be involved in many plant responses to stress conditions. Additionally, this study provides a solid foundation for uncovering the biological roles of HD-Zip genes in soybean growth and development.
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Affiliation(s)
- Xue Chen
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Zhu Chen
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Hualin Zhao
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Yang Zhao
- Key Laboratory of Crop Biology of Anhui Agriculture University, Hefei, China
| | - Beijiu Cheng
- Key Laboratory of Crop Biology of Anhui Agriculture University, Hefei, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
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