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Cjfr-2018-0135.Pdf Canadian Journal of Forest Research Genome-wide systematic characterization and its regularity expression reprogramming process of the bZIP transcription factors during trauma response in Camellia sinensis L. Journal: Canadian Journal of Forest Research Manuscript ID cjfr-2018-0135.R1 Manuscript Type: Article Date Submitted by the 17-Jul-2018 Author: Complete List of Authors: Xue, Yajie; Xinyang Normal University Zhang, Zaibao; Xinyang Normal University Wang, Lei; Xinyang Normal University Yu, Yajun; Xinyang Forestry Work Station Xiao, Jinbin ; Hennan High-Tech Industrial Corporation Hou, Jiajia; Xinyang Normal University Lian, Shuaibin; Xinyang Normal University Yuan, Hongyu; Xinyang Normal University Cheng, Lin; Xinyang Normal University bZIP transcription factor, Camellia sinensis, phylogenetic Keyword: analysis, trauma response, reprogramming Is the invited manuscript Draft for consideration in a Not applicable (regular submission) Special Issue? : https://mc06.manuscriptcentral.com/cjfr-pubs Page 1 of 45 Canadian Journal of Forest Research 1 Genome-wide systematic characterization and its regulatory expression reprogramming 2 process of the bZIP transcription factors during trauma response in Camellia sinensis L. 3 Yajie Xue: College of Life Sciences, Xinyang Normal University, Xinyang, 464000, 4 Henan, China; [email protected]; 5 Zaibao Zhang: College of Life Sciences, Xinyang Normal University, Xinyang, 464000, 6 Henan, China; [email protected]; 7 Lei Wang: College of Life Sciences, Xinyang Normal University, Xinyang, 464000, 8 Henan, China; [email protected]; 9 Yajun Yu: Xinyang Forestry Work Station, Xinyang, 464000, Henan, China; 10 [email protected]; 11 Jinbin Xiao: Henan High-Tech Industrial Corporation, Zhengzhou, 450000, Henan, 12 China; [email protected]; Draft 13 Jiajia Hou: College of Life Sciences, Xinyang Normal University, Xinyang, 464000, 14 Henan, China; [email protected]; 15 Shuaibin Lian: College of Physics and Electronic Engineering, Xinyang Normal 16 University, Xinyang, 464000, Henan, China; [email protected]; 17 Hongyu Yuan: College of Life Sciences, Xinyang Normal University, Xinyang, 464000, 18 Henan, China; [email protected]; 19 Lin Cheng: College of Life Sciences, Xinyang Normal University, Xinyang, 464000, 20 Henan, China; [email protected]; 21 * Corresponding author: Lin Cheng, College of Life Sciences, Xinyang Normal 22 University, Xinyang, 464000, Henan, China; +86 0376-6391380; (email: 23 [email protected]). 24 † Yajie Xue and Zaibao Zhang have contributed equally to this work. 25 26 1 https://mc06.manuscriptcentral.com/cjfr-pubs Canadian Journal of Forest Research Page 2 of 45 27 28 Abstract 29 Basic leucine zipper (bZIP) transcription factor (TF) genes are regulating numerous 30 biological processes as well as biotic and abiotic responses. Although the genome of the 31 tea tree (Camellia sinensis L.) has been released, knowledge regarding the bZIP TF 32 family in C. sinensis, such as phylogenetic relationship, transcriptional gene expression 33 profiles remains limited. In this study, we characterized 77 bZIP genes in C. sinensis 34 based on transcriptomic and genome data, and divided into 11 groups according to their 35 phylogenetic relationship with those in Arabidopsis, which allowed us to identify 14 pairs 36 of orthologous proteins shared by Arabidopsis and C. sinensis and 19 pairs of paralogous 37 proteins in C. sinensis. Conserved motifs CsbZIP proteins were analyzed showing high 38 group-specificity. Our classificationDraft was supported by the predicted specificities based on 39 DNA-binding domains as well as the dimerization property based off characteristic 40 features in the basic and hinge regions and the leucine zipper. Specifically, they indicated 41 that some highly conserved amino acid residues exist across each major group in the tree 42 of land plant life. Expression profiling analyses indicate that the CsbZIP genes are likely 43 involved in response to trauma, and a model was established to display the unique 44 expression of each group during different time intervals after wounding. This work 45 provides useful clues for further functional characterization of the CsbZIP TFs. 46 47 48 Keywords bZIP transcription factor, Camellia sinensis, phylogenetic analysis, trauma 49 response, reprogramming 50 51 52 2 https://mc06.manuscriptcentral.com/cjfr-pubs Page 3 of 45 Canadian Journal of Forest Research 53 54 55 Introduction 56 Transcription factors (TFs) contain one or more sequence-specific DNA-binding 57 domains, which bind to the promoter or enhance target gene expression, play important 58 roles in both development and responses to environmental stresses (Ellenberger et al., 59 1992; Ptashne and Gann, 1997). The basic leucine (Leu) zipper (bZIP) TF family is one 60 of the most diverse and largest families of TFs and is involved in many biological 61 processes including biotic stress responses (Yáñez et al., 2009; Hsieh et al., 2010; 62 Orellana et al., 2010; Bastías et al., 2011; Bastías et al., 2014), wounding, and 63 organ-specific signals (Stanković et al., 2000; Sell and Hehl, 2004; Orellana et al., 2010). 64 The bZIP TFs contain a highly conservedDraft bZIP domain, approximately 60-80 amino 65 acids in length, surrounded by a basic region and Leu zipper (Landschulz et al., 1988). 66 The basic region is responsible for nuclear localization and DNA binding with an 67 invariant motif N-x7-R/K-x9 of around 18 amino acid residues (Landschulz et al., 1988; 68 Ellenberger et al., 1992; Ptashne and Gann, 1997). The Leu zipper motif is made up of 69 several heptad repeats of Leu or other bulky hydrophobic amino acids such as Ile, Val, 70 Phe or Met. Additionally, the Leu zipper is less conserved and mediates the homo- and/or 71 heterodimerization of bZIP proteins for dimerization specificity (Jakoby et al., 2002; Lee 72 et al., 2006; Nijhawan et al., 2008). Several studies have identified or predicted encoding 73 genes for the bZIP TF and have made available entire genome sequences for several 74 plants including cassava (Hu et al., 2016), six legume species (Wang et al., 2015), wheat 75 (Li et al., 2015b), barley (Pourabed et al., 2015), maize (Wei et al., 2012), sorghum 76 (Wang et al., 2011), rice (Nijhawan et al., 2008), castor bean (Jin et al., 2014), cucumber 77 (Baloglu et al., 2014), tomato (Li et al., 2015a), grapevine (Liu et al., 2014), and 78 Arabidopsis (Jakoby et al., 2002). It was also reported for 56 bZIPs members in humans 3 https://mc06.manuscriptcentral.com/cjfr-pubs Canadian Journal of Forest Research Page 4 of 45 79 (Vinson et al., 2002) and 27 in Drosophila (Fassler et al., 2002), respectively. Among all 80 plant species, a small number of bZIP genes have been functionally characterized. 81 Extensive studies have provided strong evidence that members of the bZIP TF family are 82 involved in various biological processes including organ-specific processes 83 (Rodriguez-Uribe and O'Connell, 2006), embryogenesis (Shiota et al., 2008; Guan et al., 84 2009), seed maturation and germination (Izawa et al., 1994; Jakoby et al., 2002; Toh et 85 al., 2012), gene regulation of storage proteins (Lara et al., 2003), floral transition and 86 development (Abe et al., 2005; Wigge et al., 2005; Iven et al., 2010), as well as vascular 87 development through knockout/knockdown and other overexpression methods from 88 model plant species (Yin et al., 1997). While several studies have evaluated bZIPs 89 involvement in plant responses to stress, these studies were mostly performed in annual 90 herbs, whereas little is known aboutDraft bZIPs in woody plants. In order to investigate the 91 role of bZIPs in woody plants, we selected Camellia sinensis as our study species. On the 92 other hand, Camellia sinensis is both an economically important horticultural and 93 agricultural crop as tea ranks in the top three nonalcoholic beverages consumed 94 throughout the world (Rogers et al., 2008). Research suggests that tea consumption 95 [Camellia sinensis (L.)] had positive health advantages such as reducing the incidence of 96 many cancers (Hertog et al., 1993; Soobrattee et al., 2006; Jiang et al., 2013), decreasing 97 both body weight and fat (Nagao et al., 2007; Auvichayapat et al., 2008), improving 98 glucose homeostasis (Crespy and Williamson, 2004; Iso et al., 2006; Kao et al., 2006; 99 Fukino et al., 2008), and enhancing cardiovascular health (Nakachi et al., 2000; Ryu et al., 100 2006). Therefore, understanding the wound-induced response mechanism of tea plants 101 has both theoretical significance and practical application value. 102 Plant responses to wounding and other damage have been widely studied for several 103 species, specifically Arabidopsis (Huffaker et al., 2006; Huffaker et al., 2007), Solanum 104 lycopersicom (Holton et al., 2007) and Nicotiana tobacum (Wu et al., 2007), the 4 https://mc06.manuscriptcentral.com/cjfr-pubs Page 5 of 45 Canadian Journal of Forest Research 105 conclusions from these case studies indicate a complex defense response involving the 106 conversation or reprogramming of transcriptome and metabolome. Little genetic 107 information is available about tea tree, due to its large genome and the lack of developed 108 genetic tools such as tissue culture and transformation (Shi et al., 2011). To investigate 109 the role of bZIP TFs in C. sinensis, we describe the isolation of 77 tea tree bZIP TFs 110 based on a set of transcriptomic data and the whole genome sequences in different 111 species (Xia et al., 2017). We categorized CsbZIP into 11 groups according to their 112 phylogenetic relationships with genes from Arabidopsis. Conserved motifs were 113 identified, since they presented high group specificity and supported the group 114 classification. We were able to predict the DNA-binding patterns and the dimerization 115 properties based on the characteristic features in the basic region and hinge regions and 116 the Leu zipper, respectively. AfterDraft analyzing their expression profiles, we identified 117 candidate CsbZIPs responsive to wound stress by determining CsbZIP genes expressed 118 constitutively or specifically in different tissues in response to mechanical damage.
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