scholarly journals Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants

2019 ◽  
Vol 20 (14) ◽  
pp. 3591 ◽  
Author(s):  
Ming-Ming Liu ◽  
Mang-Mang Wang ◽  
Jin Yang ◽  
Jing Wen ◽  
Peng-Cheng Guo ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Higher Plants ◽  
Protein Complexes ◽  
Expression Patterns ◽  
Interaction Network ◽  
Land Plants ◽  
Terrestrial Plants ◽  
Functional Studies ◽  
Transcription Factor Genes ◽  
Tcp Family

The plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) transcription factor genes are involved in plants’ development, hormonal pathways, and stress response but their evolutionary history is uncertain. The genome-wide analysis performed here for 47 plant species revealed 535 TCP candidates in terrestrial plants and none in aquatic plants, and that TCP family genes originated early in the history of land plants. Phylogenetic analysis divided the candidate genes into Classes I and II, and Class II was further divided into CYCLOIDEA (CYC) and CINCINNATA (CIN) clades; CYC is more recent and originated from CIN in angiosperms. Protein architecture, intron pattern, and sequence characteristics were conserved in each class or clade supporting this classification. The two classes significantly expanded through whole-genome duplication during evolution. Expression analysis revealed the conserved expression of TCP genes from lower to higher plants. The expression patterns of Class I and CIN genes in different stages of the same tissue revealed their function in plant development and their opposite effects in the same biological process. Interaction network analysis showed that TCP proteins tend to form protein complexes, and their interaction networks were conserved during evolution. These results contribute to further functional studies on TCP family genes.

scholarly journals Genome-wide characterization and expression profiling of NAC transcription factor genes under abiotic stresses in radish (Raphanus sativus L.)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4172 ◽  
Author(s):  
Bernard Kinuthia Karanja ◽  
Liang Xu ◽  
Yan Wang ◽  
Everlyne M’mbone Muleke ◽  
Bashir Mohammed Jabir ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Hormone Signaling ◽  
Preferential Expression ◽  
Genome Wide ◽  
Raphanus Sativus L ◽  
Transcription Factor Genes ◽  
Membrane Bound ◽  
Polymerase Chain

NAC (NAM, no apical meristem; ATAF, Arabidopsis transcription activation factor and CUC, cup-shaped cotyledon) proteins are among the largest transcription factor (TF) families playing fundamental biological processes, including cell expansion and differentiation, and hormone signaling in response to biotic and abiotic stresses. In this study, 172 RsNACs comprising 17 membrane-bound members were identified from the whole radish genome. In total, 98 RsNAC genes were non-uniformly distributed across the nine radish chromosomes. In silico analysis revealed that expression patterns of several NAC genes were tissue-specific such as a preferential expression in roots and leaves. In addition, 21 representative NAC genes were selected to investigate their responses to heavy metals (HMs), salt, heat, drought and abscisic acid (ABA) stresses using real-time polymerase chain reaction (RT-qPCR). As a result, differential expressions among these genes were identified where RsNAC023 and RsNAC080 genes responded positively to all stresses except ABA, while RsNAC145 responded more actively to salt, heat and drought stresses compared with other genes. The results provides more valuable information and robust candidate genes for future functional analysis for improving abiotic stress tolerances in radish.

scholarly journals Transcriptional profiling of gametogenesis in the green seaweed Ulva mutabilis identifies an RWP‐RK transcription factors linked to reproduction

2021 ◽  
Author(s):  
Xiaojie Liu ◽  
Jonas Blomme ◽  
Kenny Bogaert ◽  
Sofie D’hondt ◽  
Thomas Wichard ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Sexual Reproduction ◽  
Higher Plants ◽  
Crop Improvement ◽  
Functional Characterization ◽  
Land Plants ◽  
Alternative Source ◽  
Starting Point ◽  
Green Seaweed

Abstract Background The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of functional food and feedstock for energy applications. Results Gametogenesis of Ulva mutabilis, a model organism for green seaweeds, is studied. We analyze transcriptome dynamics at different time points during gametogenesis following induction of reproduction by fragmentation and removal of sporulation inhibitors. Analyses demonstrate that 45% of the genes in the genome are differentially expressed during gametogenesis. We identified several transcription factors that potentially play a key role in the early gametogenesis of Ulva given the function of their homologs in higher plants and microalgae. In particular, the detailed expression pattern of an evolutionary conserved transcription factor containing an RWP-RK domain suggests a key role during Ulva gametogenesis. Conclusions Transcriptomic analyses of gametogenesis in the green seaweed Ulva highlight the importance of a conserved RWP-RK transcription factor in induction of sexual reproduction. The identification of putative master regulators of gametogenesis provides a starting point for further functional characterization.

scholarly journals Gene co-expression networks identify novel candidate genes for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)

2021 ◽  
Author(s):  
Zhaoran Zhou ◽  
Christiane Eichner ◽  
Frank Nilsen ◽  
Inge Jonassen ◽  
Michael Dondrup
Keyword(s):  
Transcription Factor ◽  
Rna Interference ◽  
Atlantic Salmon ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Transcriptional Level ◽  
Lepeophtheirus Salmonis ◽  
Salmon Louse ◽  
Transcription Factor Genes ◽  
Regulatory Impact

Background: The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod, living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better understanding of the mechanisms of moulting and development of the salmon louse at the transcriptional level is required. Methods: Three weighted gene co-expression networks were constructed based on the pairwise correlations of salmon louse gene expression profiles at different life stages. Network-based approaches and gene annotation information were applied to identify genes that might be important for the moulting and development of the salmon louse. RNA interference was performed for validation. Regulatory impact factors were calculated for all the transcription factor genes by examining the changes in co-expression patterns between transcription factor genes and deferentially expressed genes in middle stages and moulting stages. Results: Eight gene modules were predicted as important, and 10 genes from six of the eight modules have been found to show observable phenotypes in RNA interference experiments. We knocked down five hub genes from three modules and observed phenotypic consequences in all experiments. In the infection trial, no copepodids with the RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. Also, a FOXO-like gene obtained highest scores in the regulatory impact factor calculation. Conclusions: We propose a gene co-expression network-based approach to identify genes playing an important role in the moulting and development of salmon louse. The RNA interference experiments confirmed the effectiveness of our approach and demonstrated the indispensable role of RAB1A-like gene in the development of salmon louse. In addition to salmon louse, this approach could be generalized to identify important genes associated with a phenotype of interest in other organisms.

scholarly journals Transcriptional dynamics of gametogenesis in the green seaweed Ulva mutabilis identifies an RWP-RK transcription factor linked to reproduction

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaojie Liu ◽  
Jonas Blomme ◽  
Kenny A. Bogaert ◽  
Sofie D’hondt ◽  
Thomas Wichard ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Sexual Reproduction ◽  
Higher Plants ◽  
Crop Improvement ◽  
Functional Characterization ◽  
Model Organism ◽  
Land Plants ◽  
Alternative Source ◽  
Starting Point ◽  
Green Seaweed

Abstract Background The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of functional food and feedstock for energy applications. Results Gametogenesis of Ulva mutabilis, a model organism for green seaweeds, was studied. We analyzed transcriptome dynamics at different time points during gametogenesis following induction of reproduction by fragmentation and removal of sporulation inhibitors. Analyses demonstrated that 45% of the genes in the genome were differentially expressed during gametogenesis. We identified several transcription factors that potentially play a key role in the early gametogenesis of Ulva given the function of their homologs in higher plants and microalgae. In particular, the detailed expression pattern of an evolutionarily conserved transcription factor containing an RWP-RK domain suggested a key role during Ulva gametogenesis. Conclusions Transcriptomic analyses of gametogenesis in the green seaweed Ulva highlight the importance of a conserved RWP-RK transcription factor in the induction of sexual reproduction. The identification of putative master regulators of gametogenesis provides a starting point for further functional characterization.

scholarly journals Metallothionein and bZIP Transcription Factor Genes from Velvetleaf and Their Differential Expression Following Colletotrichum coccodes Infection

2006 ◽  
Vol 96 (10) ◽  
pp. 1116-1123 ◽  
Author(s):  
Amélie L. Dauch ◽  
Suha H. Jabaji-Hare
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Bzip Transcription Factor ◽  
Colletotrichum Coccodes ◽  
Transcription Factor Genes ◽  
Pathogen Attack ◽  
Fungal Genes ◽  
Type 3

Colletotrichum coccodes is a biocontrol agent of velvetleaf (Abutilon theophrasti), a noxious weed of corn and soybean. Metallothioneins (MTs) and basic region/leucine zipper motif (bZIP) are heavy-metal-binding proteins and transcription factors, respectively, that have been related to several plant processes, including the responses of plants to pathogen attack. Previous investigation of the determinants involved in the velvet-leaf-C. coccodes interaction had shed light on particular plant and fungal genes expressed in this pathosystem. Here, we report on the temporal expression patterns of two distinct types (2 and 3) of MT and bZIP transcription factor genes in velvetleaf leaves following infection with C. coccodes using quantitative reverse-transcription polymerase chain reaction. Gene expression ratios were significantly upregulated 1 day after infection (DAI), a time at which velvetleaf leaves appeared symptomless. At 2 DAI, bZIP and type 3 MT expression ratios dropped to levels significantly lower than those estimated for noninfected plants. Necrotic symptoms appeared 5 DAI and increased with time, during which gene expression levels were maintained either below or at levels observed in the control. These findings indicate that C. coccodes altered the expression of type 2 and 3 MT and bZIP genes. In addition, this is the first report on induction of a type 3 MT in plants in response to a pathogen attack.

scholarly journals Evolution Analyses of CAMTA Transcription Factor in Plants and Its Enhancing Effect on Cold-tolerance

2021 ◽  
Vol 12 ◽  
Author(s):  
Peixuan Xiao ◽  
Jia-Wu Feng ◽  
Xi-Tong Zhu ◽  
Junxiang Gao
Keyword(s):  
Transcription Factor ◽  
Cold Tolerance ◽  
Regulatory Networks ◽  
Target Genes ◽  
Higher Plants ◽  
Expression Patterns ◽  
Evolutionary Process ◽  
Functional Differentiation ◽  
Transcription Activator ◽  
Structure Variation

The calmodulin binding transcription activator (CAMTA) is a transcription factor that is widely present in eukaryotes with conserved structure. It contributes to the response to biotic and abiotic stresses and promotes the growth and development of plants. Although previous studies have investigated the number and function of CAMTAs in some species, there is still a lack of comprehensive understanding of the evolutionary process, phylogenetic relationship, expression patterns, and functions of CAMTAs in plants. Here we identified 465 CMATA genes from 112 plants and systematically studied the origin of CAMTA family, gene expansion, functional differentiation, gene structure, and conservative motif distribution. Based on these analyses, we presented the evidence that CAMTA family was originated from chlorophyta, and we speculated that CAMTA might experience obvious structure variation during its early evolution, and that the number of CAMTA genes might gradually increase in higher plants. To reveal potential functions of CAMTA genes, we analyzed the expression patterns of 12 representative species and found significant species specificity, tissue specificity, and developmental stage specificity of CAMTAs. The results also indicated that the CAMTA genes might promote the maturation and senescence. The expression levels and regulatory networks of CAMTAs revealed that CAMTAs could enhance cold tolerance of rice by regulating carbohydrate metabolism-related genes to accumulate carbohydrates or by modulating target genes together with other transcription factors. Our study provides an insight into the molecular evolution of CAMTA family and lays a foundation for further study of related biological functions.

scholarly journals Comparative Analysis of 3D Expression Patterns of Transcription Factor Genes and Digit Fate Maps in the Developing Chick Wing

PLoS ONE ◽  
2011 ◽  
Vol 6 (4) ◽  
pp. e18661 ◽  
Author(s):  
Malcolm Fisher ◽  
Helen Downie ◽  
Monique C. M. Welten ◽  
Irene Delgado ◽  
Andrew Bain ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Comparative Analysis ◽  
Expression Patterns ◽  
Transcription Factor Genes

scholarly journals Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 20
Author(s):  
Fernando Manuel Matias Hurtado ◽  
Maísa de Siqueira Pinto ◽  
Perla Novais de Oliveira ◽  
Diego Mauricio Riaño-Pachón ◽  
Laura Beatriz Inocente ◽  
...  
Keyword(s):  
Cell Wall ◽  
Transcription Factor ◽  
Secondary Cell Wall ◽  
Expression Patterns ◽  
Wood Quality ◽  
Tectona Grandis ◽  
Wood Formation ◽  
Xylem Differentiation ◽  
Transcription Factor Genes ◽  
Tectona Grandis L.F

NAC proteins are one of the largest families of plant-specific transcription factors (TFs). They regulate diverse complex biological processes, including secondary xylem differentiation and wood formation. Recent genomic and transcriptomic studies of Tectona grandis L.f. (teak), one of the most valuable hardwood trees in the world, have allowed identification and analysis of developmental genes. In the present work, T. grandis NAC genes were identified and analyzed regarding to their evolution and expression profile during wood formation. We analyzed the recently published T. grandis genome, and identified 130 NAC proteins that are coded by 107 gene loci. These proteins were classified into 23 clades of the NAC family, together with Populus, Eucalyptus, and Arabidopsis. Data on transcript expression revealed specific temporal and spatial expression patterns for the majority of teak NAC genes. RT-PCR indicated expression of VND genes (Tg11g04450-VND2 and Tg15g08390-VND4) related to secondary cell wall formation in xylem vessels of 16-year-old juvenile trees. Our findings open a way to further understanding of NAC transcription factor genes in T. grandis wood biosynthesis, while they are potentially useful for future studies aiming to improve biomass and wood quality using biotechnological approaches.

scholarly journals A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhaoran Zhou ◽  
Christiane Eichner ◽  
Frank Nilsen ◽  
Inge Jonassen ◽  
Michael Dondrup
Keyword(s):  
Transcription Factor ◽  
Rna Interference ◽  
Atlantic Salmon ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Transcriptional Level ◽  
Lepeophtheirus Salmonis ◽  
Salmon Louse ◽  
Transcription Factor Genes ◽  
Regulatory Impact

Abstract Background The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better understanding of the mechanisms of moulting and development of the salmon louse at the transcriptional level is required. Methods Three weighted gene co-expression networks were constructed based on the pairwise correlations of salmon louse gene expression profiles at different life stages. Network-based approaches and gene annotation information were applied to identify genes that might be important for the moulting and development of the salmon louse. RNA interference was performed for validation. Regulatory impact factors were calculated for all the transcription factor genes by examining the changes in co-expression patterns between transcription factor genes and deferentially expressed genes in middle stages and moulting stages. Results Eight gene modules were predicted as important, and 10 genes from six of the eight modules have been found to show observable phenotypes in RNA interference experiments. We knocked down five hub genes from three modules and observed phenotypic consequences in all experiments. In the infection trial, no copepodids with a RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. Also, a FOXO-like transcription factor obtained highest scores in the regulatory impact factor calculation. Conclusions We propose a gene co-expression network-based approach to identify genes playing an important role in the moulting and development of salmon louse. The RNA interference experiments confirm the effectiveness of our approach and demonstrated the indispensable role of a RAB1A-like gene in the development of the salmon louse. We propose that our approach could be generalized to identify important genes associated with a phenotype of interest in other organisms.

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