Leaf form diversification in an ornamental heirloom tomato results from alterations in two different HOMEOBOX genes

Nakayama, Hokuto; Rowland, Steven D.; Cheng, Zizhang; Zumstein, Kristina; Kang, Julie; Kondo, Yohei; Sinha, Neelima

doi:10.1016/j.cub.2021.08.023

Cited by 28 publications

(29 citation statements)

References 57 publications

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“…To identify the key genes in GC, we analyzed the network focusing on biological functions. A recent study in plant biology has used DiffCorr to identify a novel community of genes to explain differences in leaf phenotypes which has no enriched GO terms (Nakayama et al, 2021). We carried out our functional research of our key genes by studying the co-expressed genes and referring to previous researches with the help of STRING database.…”

Section: Discussionmentioning

confidence: 99%

Identification and Validation of Key Genes of Differential Correlations in Gastric Cancer

Chen

Xiang

et al. 2022

Front. Cell Dev. Biol.

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Background: Gastric cancer (GC) is aggressive cancer with a poor prognosis. Previously bulk transcriptome analysis was utilized to identify key genes correlated with the development, progression and prognosis of GC. However, due to the complexity of the genetic mutations, there is still an urgent need to recognize core genes in the regulatory network of GC.Methods: Gene expression profiles (GSE66229) were retrieved from the GEO database. Weighted correlation network analysis (WGCNA) was employed to identify gene modules mostly correlated with GC carcinogenesis. R package ‘DiffCorr’ was applied to identify differentially correlated gene pairs in tumor and normal tissues. Cytoscape was adopted to construct and visualize the gene regulatory network.Results: A total of 15 modules were detected in WGCNA analysis, among which three modules were significantly correlated with GC. Then genes in these modules were analyzed separately by “DiffCorr”. Multiple differentially correlated gene pairs were recognized and the network was visualized by the software Cytoscape. Moreover, GEMIN5 and PFDN2, which were rarely discussed in GC, were identified as key genes in the regulatory network and the differential expression was validated by real-time qPCR, WB and IHC in cell lines and GC patient tissues.Conclusions: Our research has shed light on the carcinogenesis mechanism by revealing differentially correlated gene pairs during transition from normal to tumor. We believe the application of this network-based algorithm holds great potential in inferring relationships and detecting candidate biomarkers.

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Section: Discussionmentioning

confidence: 99%

Identification and Validation of Key Genes of Differential Correlations in Gastric Cancer

Chen

Xiang

et al. 2022

Front. Cell Dev. Biol.

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“…YABBY and KAN likely also upregulate and restrict WOX1 expression, respectively ( Nakata et al, 2012 ). Mutants of the WOX1 genes in different model species show inhibited lamina outgrowth, suggesting that WOX1 function in leaf lamina expansion is conserved among species ( Vandenbussche et al, 2009 ; Tadege et al, 2011 ; Nakata et al, 2012 ; Du et al, 2020 ; Zhang et al, 2020 ; Nakayama et al, 2021 ). Altogether, these studies suggest that the ad–ab distribution of auxin, ARF activators, and ARF repressors regulates the expression of WOX1 and PRS , leading to leaf expansion and establishing the mediolateral axis ( Tadege et al, 2011 ; Nakata et al, 2012 ).…”

Section: Basic Mechanism Of Simple Leaf Developmentmentioning

confidence: 99%

“…SiFT has a single-nucleotide deletion in the homeobox motif of the BIP gene, leading to a premature stop codon. This truncated BIP protein leads to enhanced expression of KNOX1 in leaves and a highly complex leaf phenotype ( Nakayama et al, 2021 ). The extreme complexity of the SiFT leaf induced by alteration of the KNOX–BIP interaction likely led to the use of SiFT as an ornamental and landscaping plant ( Figure 3C ).…”

Section: Molecular Mechanisms Underlying Leaf Form Diversificationmentioning

confidence: 99%

“…The first insight was the discovery of the KNOX-GA-CK module in model plants, which regulates morphological diversification both among species and within a species. A variety of factors have altered the KNOX1 pathway, including promoter variation, alterations in effective concentrations, and changes in expression patterns, leading to subsequent morphological changes ( Hay and Tsiantis, 2006 ; Kimura et al, 2008 ; Nakayama et al, 2021 ). Recent progress in transcriptome analysis and the incorporation of network biology has been helpful in furthering our understanding of morphological regulation.…”

Section: Placing the Core Network In Their Ecological Contextmentioning

confidence: 99%

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Molecular mechanisms underlying leaf development, morphological diversification, and beyond

2022

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The basic mechanisms of leaf development have been revealed through a combination of genetics and intense analyses in select model species. The genetic basis for diversity in leaf morphology seen in nature is also being unraveled through recent advances in techniques and technologies related to genomics and transcriptomics, which have had a major impact on these comparative studies. However, this has led to the emergence of new unresolved questions about the mechanisms that generate the diversity of leaf form. Here we provide a review of the current knowledge of the fundamental molecular genetic mechanisms underlying leaf development with an emphasis on natural variation and conserved gene regulatory networks involved in leaf development. Beyond that, we discuss open questions/enigmas in the area of leaf development, how recent technologies can best be deployed to generate a unified understanding of leaf diversity and its evolution, and what untapped fields lie ahead.

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“…Leaves are the main vegetative organs of plants, and their morphological diversity helps plants adapt to environmental changes and complete their life cycle (Demura & Ye, 2010; Nakayama et al., 2021). Leaf shape is determined by numerous factors such as species, developmental stage, environment, and genetics, and the patterning of leaf margins can result in intermittent leaf serrations, lobes, or leaflets (Nicotra et al., 2011; Wang et al., 2021; Zhang et al., 2019).…”

Section: Introductionmentioning

confidence: 99%

CiKN1 and CiKN6 are involved in leaf development in citrus by regulating CimiR164

Zeng

Luo

et al. 2022

The Plant Journal

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Leaf shape is an important agronomic trait that is involved in plant photosynthesis, flowering, disease resistance, and yield. In recent years, many leaf shape-related genes have been identified in model plants, but the precise regulatory network of leaf shape development remains unclear, particularly in woody plants. Transcriptome analysis of trifoliate orange and lemon leaves revealed that two citrus Knotted1-like (CiKN1 and CiKN6) genes might participate in leaf development. Overexpression of CiKN1 displays lobed leaves in simple leaf Arabidopsis and lemon. Further protein interaction analysis revealed that CiKN6 interacted with CiKN1, whose overexpression resulted in deeper lobed leaves in transgenic Arabidopsis and lemon. Suppressing CiKN6 expression also affected the development of lemon leaves. Furthermore, we found that the CiKN1-CiKN6 complex specifically binds to the citrus miR164a promoter and suppresses its expression. In addition, a SQUAMOSA promoter binding protein-like (SPL) gene (CiSPL11) was identified using yeast onehybrid assays and was found to promote CiKN6 transcription by binding to its promoter. Transgenic Arabidopsis showed that CiSPL11 might be involved in the development of citrus leaves. These results suggested that the CiKN1-CiKN6 complex and miR164a interact to regulate leaf development in citrus.

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Leaf form diversification in an ornamental heirloom tomato results from alterations in two different HOMEOBOX genes

Cited by 28 publications

References 57 publications

Identification and Validation of Key Genes of Differential Correlations in Gastric Cancer

Identification and Validation of Key Genes of Differential Correlations in Gastric Cancer

Molecular mechanisms underlying leaf development, morphological diversification, and beyond

CiKN1 and CiKN6 are involved in leaf development in citrus by regulating CimiR164

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