Characterization and expression analysis of the WRKY gene family in moso bamboo

Li, Long; Mu, Shaohua; Cheng, Zhanchao; Cheng, Yuanwen; Zhang, Ying; Miao, Ying; Hou, Cheng‐Lin; Li, Xueping; Gao, Jian

doi:10.1038/s41598-017-06701-2

Cited by 36 publications

(23 citation statements)

References 60 publications

(76 reference statements)

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“…Genomic studies in bamboo, including genome-wide full-length cDNA sequencing ( Peng et al, 2010 ), chloroplast genome sequencing ( Zhang et al, 2011 ), identification of syntenic genes between bamboo and other grasses ( Gui et al, 2010 ), phylogenetic analysis of Bambusoideae subspecies ( Sungkaew et al, 2009 ), and the construction of the draft genome sequence of moso bamboo, laid the foundation for researching and improving stress resistance at the genetic level. So far, various gene families having potential resistance functions in moso bamboo have been analyzed, such as the WRKY TF family ( Li et al, 2017 ; Wu M. et al, 2017 ), homeodomain leucine zipper subfamily ( Chen et al, 2017 ), and AP2/ERF TF family ( Wu et al, 2015 ). The study of TCP TFs remains enigmatic, even though they play significant roles in plant development and growth as well as in stress resistance.…”

Section: Introductionmentioning

confidence: 99%

TCP Transcription Factors in Moso Bamboo (Phyllostachys edulis): Genome-Wide Identification and Expression Analysis

Liu

et al. 2018

Front. Plant Sci.

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TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (T), members of a plant-specific gene family, play significant roles during plant growth and development, as well as in response to environmental stress. However, knowledge about this family in moso bamboo (Phyllostachys edulis) is limited. Therefore, in this study, the first genome-wide identification, classification, characterization, and expression pattern analysis of the TCP transcription factor family in moso bamboo was performed. Sixteen TCP members were identified from the moso bamboo genome using a BLASTP algorithm-based method and verified using the Pfam database. Based on a multiple-sequence alignment, the members were divided into two subfamilies, and members of the same family shared highly conserved motif structures. Subcellular localization and transactivation activity analyses of four selected genes revealed that they were nuclear localized and had self-activation activities. Additionally, the expression levels of several PeTCP members were significantly upregulated under abscisic acid, methyl jasmonate, and salicylic acid treatments, indicating that they play crucial plant hormone transduction roles in the processes of plant growth and development, as well as in responses to environmental stresses. Thus, the current study provides previously lacking information on the TCP family in moso bamboo and reveals the potential functions of this gene family in growth and development.

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Section: Introductionmentioning

confidence: 99%

TCP Transcription Factors in Moso Bamboo (Phyllostachys edulis): Genome-Wide Identification and Expression Analysis

Liu

et al. 2018

Front. Plant Sci.

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“…During growth and development, moso bamboo is exposed to a variety of environmental that may cause death, severely threatening the bamboo industry ( Peng et al, 2013b ; Liu et al, 2017 ). In recent years, a number of gene families involved in the abiotic stress response and plant growth were sequentially identified and analyzed in moso bamboo, such as WRKY, TIFY, IQD and AAAP gene families ( Huang et al, 2016 ; Min et al, 2016 ; Liu et al, 2017 ; Long et al, 2017 ). Peng et al (2013a) noted that MYB proteins are highly expressed in panicles in comparison to the vegetative tissues of P. edulis ( Peng et al, 2013a ).…”

Section: Introductionmentioning

confidence: 99%

The R2R3MYB Gene Family in Phyllostachys edulis: Genome-Wide Analysis and Identification of Stress or Development-Related R2R3MYBs

Hou¹,

Cheng²,

Xie³

et al. 2018

Front. Plant Sci.

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The MYB transcription factor (TF) is one of the largest gene families in plants and involved to multiple biological processes. However, little is known about the MYB family and its functional role in the genome of moso bamboo. In the present study, a total of 114 R2R3MYB genes were first identified from moso bamboo genome and full-length non-chimeric (FLNC) reads. Phylogenetic analysis coupled with gene structure analysis and motif determination resulted in the division of these PheR2R3MYBs into 17 subgroups. The position of eight proteins along an external branch in the phylogenetic tree suggested their relatively ancient origin. The genes in this group were all substituted by (Met, M)/(Arg, R) at conservative W residues in both R2 and R3 repeats, and half were found to possess no transcriptional activation activity. The analysis of evolutionary patterns and divergence suggests that the expansion of PheMYBs was mainly attributable to whole genome duplication (WGD) under different selection pressures. Expressional analysis based on microarray and qRT-PCR data performed diverse expression patterns of R2R3MYBs in response to both various abiotic stimuli and flower development. Furthermore, the co-expression analysis of R2R3MYBs suggested an intricate interplay of growth- and stress-related responses. Finally, we found a hub gene, PheMYB4, was involved in a complex proteins interaction network. Further functional analysis indicated that ectopic overexpression of its homologous gene, PheMYB4-1, could increase tolerance to cold treatment and sensitivity to drought and salt treatment of transgenic Arabidopsis seedlings. These findings provide comprehensive insights into the MYB family members in moso bamboo and offer candidate MYB genes for further studies on their roles in stress resistance.

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“…Morus005757 shows significant up-regulation in response to dehydration stress, salinity stress, and SA and ABA (Abscisic acid) treatments [27]. Similar results were also found in wheat, common bean [28], grape [29], pineapple [30], soybean [31], moso bamboo [32], Caragana intermedia [33], peanut [34], and broomcorn millet [35]. These observations suggest that studying the WRKY gene families may provide valuable insights into the mechanism underlying abiotic stress tolerance in plants.…”

Section: Introductionmentioning

confidence: 66%

Identification of WRKY Gene Family from Dimocarpus longan and Its Expression Analysis during Flower Induction and Abiotic Stress Responses

Jue

Sang

Liu

et al. 2018

IJMS

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Longan is an important fruit tree in the subtropical region of Southeast Asia and Australia. However, its blooming and its yield are susceptible to stresses such as droughts, high salinity, and high and low temperature. To date, the molecular mechanisms of abiotic stress tolerance and flower induction in longan have not been elucidated. WRKY transcription factors (TFs), which have been studied in various plant species, play important regulatory roles in plant growth, development, and responses to stresses. However, there is no report about WRKYs in longan. In this study, we identified 55 WRKY genes with the conserved WRKY domain and zinc finger motif in the longan genome. Based on the structural features of WRKY proteins and topology of the phylogenetic tree, the longan WRKY (DlWRKY) family was classified into three major groups (I–III) and five subgroups (IIa–IIe) in group II. Tissue expression analysis showed that 25 DlWRKYs were highly expressed in almost all organs, suggesting that these genes may be important for plant growth and organ development in longan. Comparative RNA-seq and qRT-PCR-based gene expression analysis revealed that 18 DlWRKY genes showed a specific expression during three stages of flower induction in “Sijimi” (“SJ”), which exhibited the “perpetual flowering” (PF) habit, indicating that these 18 DlWRKY genes may be involved in the flower induction and the genetic control of the perpetual flowering trait in longan. Furthermore, the RT-qPCR analysis illustrated the significant variation of 27, 18, 15, 17, 27, and 23 DlWRKY genes under SA (Salicylic acid), MeJA (Methyl Jasmonate), heat, cold, drought, or high salinity treatment, respectively, implicating that they might be stress- or hormone-responsive genes. In summary, we systematically and comprehensively analyzed the structure, evolution, and expression pattern of the DlWRKY genes. The results presented here increase our understanding of the WRKY family in fruit trees and provide a basis for the further elucidation of the biological function of DlWRKY genes in longan.

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Characterization and expression analysis of the WRKY gene family in moso bamboo

Cited by 36 publications

References 60 publications

TCP Transcription Factors in Moso Bamboo (Phyllostachys edulis): Genome-Wide Identification and Expression Analysis

TCP Transcription Factors in Moso Bamboo (Phyllostachys edulis): Genome-Wide Identification and Expression Analysis

The R2R3MYB Gene Family in Phyllostachys edulis: Genome-Wide Analysis and Identification of Stress or Development-Related R2R3MYBs

Identification of WRKY Gene Family from Dimocarpus longan and Its Expression Analysis during Flower Induction and Abiotic Stress Responses

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