Genome-Wide Identification of the MdKNOX Gene Family and Characterization of Its Transcriptional Regulation in Malus domestica

Jia, Peng; Zhang, Chenguang; Xing, Libo; Li, Youmei; Shah, Kamran; Zuo, Xia; Zhang, Dong; An, Na; Han, Mingyu; Ren, Xiaolin

doi:10.3389/fpls.2020.00128

Cited by 26 publications

(24 citation statements)

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“…Subsequently, more KNOX genes were identified and characterized in other plant species [13]. The KNOX genes seem to have a limited number in different species, for example, 8 in Arabidopsis, 13 in rice, 12 in maize, 15 in poplar [12], 10 in peach [10], 22 in apple [27], and 18 in pear [24]. Furthermore, the number of KNOX genes among different plant species seems not to correlate with their genome sizes, which was further confirmed in the present study.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, both in the natural context of KNOX function in the SAM and upon ectopic KNOX expression in Arabidopsis leaves, reducing activity of the GA growth regulators could promotes meristematic activity [38]. Recently, studies in apple indicated that expressions of KNOX genes are also inducible by exogenous phytohormones [17,27]. For example, MdKNOX19, a Class II KNOX gene regulating apple fruit and seed developments through ABA signaling, was significantly up-regulated when applied ABA to apple leaves, fruits, and seeds [17].…”

Section: Discussionmentioning

confidence: 99%

“…For example, MdKNOX19, a Class II KNOX gene regulating apple fruit and seed developments through ABA signaling, was significantly up-regulated when applied ABA to apple leaves, fruits, and seeds [17]. Furthermore, expressions of the fourteen MdKNOX genes that strongly exhibited expressions in the floral bud of apple were also more or less affected by the applications of exogenous phytohormones of 6-BA, GA 3 , ABA, and SA during the flower induction period [27]. In the present study, phytohormoneassociated cis-elements, including auxin, abscisic acid, gibberellin, and ethylene-responsive elements were also shown within the promoters of AsKNOX genes (depicted in Figure 3), which might indicate the involvement of AsKNOX genes in these related phytohormone signaling pathways.…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Identification and Characterization of KNOTTED-Like Homeobox (KNOX) Homologs in Garlic (Allium sativum L.) and Their Expression Profilings Responding to Exogenous Cytokinin and Gibberellin

Zhang

Pan

Zhi

et al. 2021

IJMS

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Garlic (Allium sativum L.) is an important vegetable and is cultivated and consumed worldwide for its economic and medicinal values. Garlic cloves, the major reproductive and edible organs, are derived from the axillary meristems. KNOTTED-like homeobox (KNOX) proteins, such as SHOOT MERISTEM-LESS (STM), play important roles in axillary meristem formation and development. However, the KNOX proteins in garlic are still poorly known. Here, 10 AsKNOX genes, scattered on 5 of the 8 chromosomes, were genome-wide identified and characterized based on the newly released garlic genome. The typical conserved domains of KNOX proteins were owned by all these 10 AsKNOX homologs, which were divided into two Classes (Class I and Class II) based on the phylogenetic analysis. Prediction and verification of the subcellular localizations revealed the diverse subcellular localization of these 10 AsKNOX proteins. Cis-element prediction, tissue expression analysis, and expression profilings in responding to exogenous GA3 and 6-BA showed the potential involvement of AsKNOX genes in the gibberellin and cytokinin signaling pathways. Overall, the results of this work provided a better understanding of AsKNOX genes in garlic and laid an important foundation for their further functional studies.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Identification and Characterization of KNOTTED-Like Homeobox (KNOX) Homologs in Garlic (Allium sativum L.) and Their Expression Profilings Responding to Exogenous Cytokinin and Gibberellin

Zhang

Pan

Zhi

et al. 2021

IJMS

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“…The class II subfamily lacks phenotypic due to mutations; however, there have been relatively few previous studies. In brief, KNOX genes are involved in the growth and development of different tissues and organs in different species [ 26 , 27 , 28 ]. Plants must constantly adjust their physiological processes to adapt to changes in the external environment [ 29 ].…”

Section: Introductionmentioning

confidence: 99%

Functional divergence and adaptive selection of KNOX gene family in plants

Meng

Liu

et al. 2020

Open Life Sciences

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AbstractKNOTTED-like homeodomain (KNOX) genes are transcriptional regulators that play an important role in morphogenesis. In the present study, a comparative analysis was performed to investigate the molecular evolution of the characteristics of the KNOX gene family in 10 different plant species. We identified 129 KNOX gene family members, which were categorized into two subfamilies based on multiple sequence alignment and phylogenetic tree reconstruction. Several segmental duplication pairs were found, indicating that different species share a common expansion model. Functional divergence analysis identified the 15 and 52 amino acid sites with significant changes in evolutionary rates and amino acid physicochemical properties as functional divergence sites. Additional selection analysis showed that 14 amino acid sites underwent positive selection during evolution, and two groups of co-evolutionary amino acid sites were identified by Coevolution Analysis using Protein Sequences software. These sites could play critical roles in the molecular evolution of the KNOX gene family in these species. In addition, the expression profiles of KNOX duplicated genes demonstrated functional divergence. Taken together, these results provide novel insights into the structural and functional evolution of the KNOX gene family.

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“…The first KNOX gene to be identified in plants was Knotted1 (Kn1) in maize (Vollbrecht et al, 1991). Following this discovery, the KNOX gene was identified in more and more plants (Gao et al, 2015), such as Arabidopsis, rice, poplar, cotton, apple and so on, and the functions of some KNOX genes have been deeply studied (Mukherjee et al, 2009;Xiong et al, 2018;Ma et al, 2019;Jia et al, 2020). However, little information is available on the KNOX gene family in the important food crop wheat (Triticum aestivum L.).…”

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confidence: 99%

Identification and Bioinformatics Analysis of <i>KNOX</i> Gene Family in Wheat (<i>Triticum aestivum</i> L.)

Song¹,

Liang²,

An³

et al. 2021

mpb

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KNOTTED-like homeodomain (KNOX) gene family is a transcription factor encoding homeobox protein, which plays an important role in plant growth and morphogenesis. However, little information is available on the KNOX gene family in wheat (Triticum aestivum L.). In this study, 36 KNOX genes with KNOX1 or KNOX2 domain distributed on 18 chromosomes were identified from wheat genome using bioinformatics methods. The phylogenetic evolution, gene structure, protein domains, cis-acting elements and gene expression patterns were analyzed in the present study. Based on the phylogenetic tree, the 36 TaKNOX genes were divided into two major subclasses, Class I and Class II, and the two subclasses were further divided into five evolutionary branches. Most TaKNOX genes contain four typical conserved protein domains: KNOX1, KNOX2, ELK and HOX. Some cis-acting elements are associated with hormonal, plant development and stress in TaKNOX promoters. The analysis result of transcriptome data from wheat different tissue showed that Class I KNOX genes had obvious tissue specificity, while Class II KNOX genes expressed widely in different wheat tissues. The study results provide important information for future analysis of the regulation and functions of the TaKNOX gene family. Keywords Wheat; KNOX gene family; Gene structure; Gene expression KNOX (KNOTTED1-like homeobox) transcription factor family is a subfamily of the homeobox gene TALE (Three amino acid loop extension) protein superfamily, which is widely involved in the regulation of plant growth and development (Hamant and Pautot, 2010). Most KNOX proteins contain four typical conserved domains:

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Genome-Wide Identification of the MdKNOX Gene Family and Characterization of Its Transcriptional Regulation in Malus domestica

Cited by 26 publications

References 68 publications

Genome-Wide Identification and Characterization of KNOTTED-Like Homeobox (KNOX) Homologs in Garlic (Allium sativum L.) and Their Expression Profilings Responding to Exogenous Cytokinin and Gibberellin

Genome-Wide Identification and Characterization of KNOTTED-Like Homeobox (KNOX) Homologs in Garlic (Allium sativum L.) and Their Expression Profilings Responding to Exogenous Cytokinin and Gibberellin

Functional divergence and adaptive selection of KNOX gene family in plants

Identification and Bioinformatics Analysis of <i>KNOX</i> Gene Family in Wheat (<i>Triticum aestivum</i> L.)

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