Genome-wide identification and characterization of <i>WOX</i> genes in <i>Cucumis sativus</i>

Han, Ni; Tang, Rui; Chen, Xueqian; Xu, Zhixuan; Ren, Zhonghai; Wang, Lina

doi:10.1139/gen-2020-0029

Cited by 20 publications

(19 citation statements)

References 64 publications

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“…To explore the function of NAC genes in K. obovata , the expression patterns of all KoNAC s in various organs were determined. In contrast to the constitutive expression patterns of other gene families [ 56 , 57 , 58 ], KoNAC genes were differentially and preferentially expressed in different organs. For instance, there were 28 Ko NAC genes expressed highly in roots, 18 Ko NAC genes expressed preferentially in leaves, and 13 Ko NAC genes expressed mainly in fruits.…”

Section: Discussionmentioning

confidence: 75%

Genome-Wide Identification and Expression Analysis of the NAC Gene Family in Kandelia obovata, a Typical Mangrove Plant

Sun

Liu²,

Huang

et al. 2022

CIMB

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The NAC (NAM, ATAF1/2, and CUC2) gene family, one of the largest transcription factor families in plants, acts as positive or negative regulators in plant response and adaption to various environmental stresses, including cold stress. Multiple reports on the functional characterization of NAC genes in Arabidopsis thaliana and other plants are available. However, the function of the NAC genes in the typical woody mangrove (Kandelia obovata) remains poorly understood. Here, a comprehensive analysis of NAC genes in K. obovata was performed with a pluri-disciplinary approach including bioinformatic and molecular analyses. We retrieved a contracted NAC family with 68 genes from the K. obovata genome, which were unevenly distributed in the chromosomes and classified into ten classes. These KoNAC genes were differentially and preferentially expressed in different organs, among which, twelve up-regulated and one down-regulated KoNAC genes were identified. Several stress-related cis-regulatory elements, such as LTR (low-temperature response), STRE (stress response element), ABRE (abscisic acid response element), and WUN (wound-responsive element), were identified in the promoter regions of these 13 KoNAC genes. The expression patterns of five selected KoNAC genes (KoNAC6, KoNAC15, KoNAC20, KoNAC38, and KoNAC51) were confirmed by qRT-PCR under cold treatment. These results strongly implied the putative important roles of KoNAC genes in response to chilling and other stresses. Collectively, our findings provide valuable information for further investigations on the function of KoNAC genes.

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Section: Discussionmentioning

confidence: 75%

Genome-Wide Identification and Expression Analysis of the NAC Gene Family in Kandelia obovata, a Typical Mangrove Plant

Sun

Liu²,

Huang

et al. 2022

CIMB

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“…This may be due to the gene loss in the evolution of Actinidia species. The lost of WOX6 homologous gene has also been reported in many plants including Orchidaceae species ( Kanchan & Sembi, 2020 ; Victorathisayam et al, 2020 ), Solanaceae species ( Li et al, 2018 ), and cucumber ( Han et al, 2021 ). AtWOX6 regulates ovule development and plays a role in freezing tolerance in Arabidopsis ( Park et al, 2005 ).…”

Section: Discussionmentioning

confidence: 83%

In silico identification, characterization expression profile of WUSCHEL-Related Homeobox (WOX) gene family in two species of kiwifruit

Feng

Zou

Gao

et al. 2021

PeerJ

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The WUSCHEL (WUS)-related homeobox (WOX) gene family is a class of plant-specific transcriptional factors and plays a crucial role in forming the shoot apical meristem and embryonic development, stem cell maintenance, and various other developmental processes. However, systematic identification and characterization of the kiwifruit WOX gene family have not been studied. This study identified 17 and 10 WOX genes in A. chinensis (Ac) and A. eriantha (Ae) genomes, respectively. Phylogenetic analysis classified kiwifruit WOX genes from two species into three clades. Analysis of phylogenetics, synteny patterns, and selection pressure inferred that WOX gene families in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in WOX gene number and distribution. Ten conserved motifs were identified in the kiwifruit WOX genes, and motif architectures of WOXs belonging to different clades highly diverged. The cis-element analysis and expression profiles investigation indicated the functional differentiation of WOX genes and identified the potential WOXs in response to stresses. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit WOXs.

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“…In addition, members of the WUS clade possess a motif of two amino acids (Threonine and Leucine) at the beginning of the WUS-box, whereas the WOX proteins belonging to the other clades show amino acid variations in the beginning position. Some WOX proteins contain a series of amino acids between the HD and the WUS-box that could potentially act as an activation domain, and/or show a carboxy-terminal ERF-associated Amphiphilic Repression (EAR) domain (Figure 2A) [88,[93][94][95][96][97][98][99][100][101][102][103]. The EAR motif structure identified in Arabidopsis is [LVI]-X-[LVI]-X-[LVI] (where V represents Valine).…”

Section: Nomenclature and Molecular Characteristic Motifsmentioning

confidence: 99%

Induction of Somatic Embryogenesis in Plants: Different Players and Focus on WUSCHEL and WUS-RELATED HOMEOBOX (WOX) Transcription Factors

Fambrini

Usai

Pugliesi

2022

IJMS

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In plants, other cells can express totipotency in addition to the zygote, thus resulting in embryo differentiation; this appears evident in apomictic and epiphyllous plants. According to Haberlandt’s theory, all plant cells can regenerate a complete plant if the nucleus and the membrane system are intact. In fact, under in vitro conditions, ectopic embryos and adventitious shoots can develop from many organs of the mature plant body. We are beginning to understand how determination processes are regulated and how cell specialization occurs. However, we still need to unravel the mechanisms whereby a cell interprets its position, decides its fate, and communicates it to others. The induction of somatic embryogenesis might be based on a plant growth regulator signal (auxin) to determine an appropriate cellular environment and other factors, including stress and ectopic expression of embryo or meristem identity transcription factors (TFs). Still, we are far from having a complete view of the regulatory genes, their target genes, and their action hierarchy. As in animals, epigenetic reprogramming also plays an essential role in re-establishing the competence of differentiated cells to undergo somatic embryogenesis. Herein, we describe the functions of WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors in regulating the differentiation–dedifferentiation cell process and in the developmental phase of in vitro regenerated adventitious structures.

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Genome-wide identification and characterization of WOX genes in Cucumis sativus

Cited by 20 publications

References 64 publications

Genome-Wide Identification and Expression Analysis of the NAC Gene Family in Kandelia obovata, a Typical Mangrove Plant

Genome-Wide Identification and Expression Analysis of the NAC Gene Family in Kandelia obovata, a Typical Mangrove Plant

In silico identification, characterization expression profile of WUSCHEL-Related Homeobox (WOX) gene family in two species of kiwifruit

Induction of Somatic Embryogenesis in Plants: Different Players and Focus on WUSCHEL and WUS-RELATED HOMEOBOX (WOX) Transcription Factors

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