Identification and Transcript Analysis of the TCP Transcription Factors in the Diploid Woodland Strawberry Fragaria vesca

Systematic Analysis of the Betula platyphylla TCP Gene Family and Its Expression Profile Identifies Potential Key Candidate Genes Involved in Abiotic Stress Responses

The TCP transcription factor (TF) family is a vital set of plant-specific regulators involved in plant growth, development, and responses to environmental stresses. Despite the extensive research on TCP transcription factors in numerous plant species, the functions they fulfill in Betula platyphylla are still not well understood. In this study, 21 BpTCP genes were identified via genome-wide analysis. Bioinformatics analysis was used to examine the physicochemical properties of these transcription factors, including molecular weight, isoelectric point, chromosomal distribution, and predicted subcellular localization. We expected that most BpTCP transcription factors would be located in the nucleus. Collinearity analysis revealed that gene fragment duplication events played a major role in the evolutionary expansion and diversification of the BpTCP gene family. Promoter analysis identified diverse cis-acting elements in BpTCP, suggesting that they play a role in stress responses, hormonal regulation, and plant growth and development. qRT-PCR analysis showed that BpTCP genes displayed tissue-specific expression patterns in the roots, stems, and leaves, displaying remarkable differences in expression levels when subjected to abiotic stresses, including drought and high- and low-temperature conditions. Notably, BpTCP17 and BpTCP18 showed markedly higher expression levels under multiple stress conditions. Subcellular localization experiments confirmed that both BpTCP17 and BpTCP18 localize in the nucleus, consistent with bioinformatic predictions. These findings emphasize the potential roles of BpTCP17 and BpTCP18 in mediating abiotic stress responses, highlighting their potential as candidate genes for improving stress tolerance in B. platyphylla.

Unveiling kiwifruit TCP genes: evolution, functions, and expression insights

The TEOSINTE-BRANCHED1/CYCLOIDEA/PROLEFERATING-CELL-FACTORS (TCP) gene family is a plant-specific transcriptional factor family involved in leaf morphogenesis and senescence, lateral branching, hormone crosstalk, and stress responses. To date, a systematic study on the identification and characterization of the TCP gene family in kiwifruit has not been reported. Additionally, the function of kiwifruit TCPs in regulating kiwifruit responses to the ethylene treatment and bacterial canker disease pathogen (Pseudomonas syringae pv. actinidiae, Psa) has not been investigated. Here, we identified 40 and 26 TCP genes in Actinidia chinensis (Ac) and A. eriantha (Ae) genomes, respectively. The synteny analysis of AcTCPs illustrated that whole-genome duplication accounted for the expansion of the TCP family in Ac. Phylogenetic, conserved domain, and selection pressure analysis indicated that TCP family genes in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in TCP gene number and distribution. Our results also suggested that protein structure and cis-element architecture in promoter regions of TCP genes have driven the function divergence of duplicated gene pairs. Three and four AcTCP genes significantly affected kiwifruit responses to the ethylene treatment and Psa invasion, respectively. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit TCPs.

Genome-Wide Identification and Analysis of BrTCP Transcription Factor Family Genes Involved in Cold Stress Tolerance in Winter Rapeseed (Brassica rapa L.)

TCP transcription factors are important during plant growth and stress responses. However, their role in the cold stress response of Brassica rapa L. remains poorly understood. In this research, we identified the TCPs gene family in B. rapa to learn the features of the BrTCP gene family, functionally annotating the interacting proteins of TCP4 and analyzing their expression levels. Our results illustrated the presence of 19 members of the BrTCPs family in B. rapa, exhibiting molecular weights ranging from 27,367.45 to 59,433.64 Da. All identified proteins were classified as unstable, with isoelectric points ranging from 5.5 to 9.48. Subcellular localization forecasted that TCP proteins were all positioned in the nucleus. The BrTCP gene structure is relatively simple, with only seven members possessing introns, and none of the members contain UTR regions. BrTCPs comprise hormone-, light-, and stress-responsive elements. We found that the frequency of photoresponsive elements was greatest in the promoter region, suggesting that BrTCP genes are regulated by light signals and function synergistically with plant growth and development. In addition, five candidate interaction proteins of BrTCP4 were identified using yeast two-hybrid screening. RNA-Seq and q-PCR analyses of the interacting genes revealed differential expression of BrTCP family genes across various tissues following cold stress. Significant responses were observed under low-temperature stress, drought stress, and rehydration treatment, suggesting that these genes play crucial roles as regulators of the molecular network mechanisms responding to stress. This study enhances our understanding of the BrTCP family and provides significant insights into the stress tolerance mechanisms of B. rapa.

Evolution and Functional Dynamics of TCP Transcription Factor Gene Family in Passion Fruit (Passiflora edulis)

Passion fruit is a valued tropical fruit crop that faces environment-related growth strains. TCP genes are important for both growth modulation and stress prevention in plants. Herein, we systematically analyzed the TCP gene family in passion fruit, recognizing 30 members. Genes exhibiting closer phylogenetic relationships exhibited similar protein and gene structures. Gene members of the TCP family showed developmental-stage- or tissue-specific expression profiles during the passion fruit life cycle. Transcriptome data also demonstrated that many PeTCPs showed induced expression in response to hormonal treatments and cold, heat, and salt stress. Based on transcriptomics data, eight candidate genes were chosen for preferential gene expression confirmation under cold stress conditions. The qRT-PCR assays suggested PeTCP15/16/17/19/23 upregulation, while PeTCP1/11/25 downregulation after cold stress. Additionally, TCP19/20/29/30 exhibited in silico binding with cold-stress-related miRNA319s. GFP subcellular localization assays exhibited PeTCP19/1 were localized at the nucleus. This study will aid in the establishment of novel germplasm, as well as the further investigation of the roles of PeTCPs and their cold stress resistance characteristics.

Class I TCP in fruit development: much more than growth

Fruit development can be viewed as the succession of three main steps consisting of the fruit initiation, growth and ripening. These processes are orchestrated by different factors, notably the successful fertilization of flowers, the environmental conditions and the hormones whose action is coordinated by a large variety of transcription factors. Among the different transcription factor families, TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTOR (TCP) family has received little attention in the frame of fruit biology despite its large effects on several developmental processes and its action as modulator of different hormonal pathways. In this respect, the comprehension of TCP functions in fruit development remains an incomplete puzzle that needs to be assembled. Building on the abundance of genomic and transcriptomic data, this review aims at collecting available TCP expression data to allow their integration in the light of the different functional genetic studies reported so far. This reveals that several Class I TCP genes, already known for their involvement in the cell proliferation and growth, display significant expression levels in developing fruit, although clear evidence supporting their functional significance in this process remains scarce. The extensive expression data compiled in our study provide convincing elements that shed light on the specific involvement of Class I TCP genes in fruit ripening, once these reproductive organs acquire their mature size. They also emphasize their putative role in the control of specific biological processes such as fruit metabolism and hormonal dialogue.

Sweet cherry TCP gene family analysis reveals potential functions of PavTCP1, PavTCP2 and PavTCP3 in fruit light responses

BACKGROUND

TCP proteins are plant specific transcription factors that play important roles in plant growth and development. Despite the known significance of these transcription factors in general plant development, their specific role in fruit growth remains largely uncharted. Therefore, this study explores the potential role of TCP transcription factors in the growth and development of sweet cherry fruits.

RESULTS

Thirteen members of the PavTCP family were identified within the sweet cherry plant, with two, PavTCP1 and PavTCP4, found to contain potential target sites for Pav-miR159, Pav-miR139a, and Pav-miR139b-3p. Analyses of cis-acting elements and Arabidopsis homology prediction analyses that the PavTCP family comprises many light-responsive elements. Homologs of PavTCP1 and PavTCP3 in Arabidopsis TCP proteins were found to be crucial to light responses. Shading experiments showed distinct correlation patterns between PavTCP1, 2, and 3 and total anthocyanins, soluble sugars, and soluble solids in sweet cherry fruits. These observations suggest that these genes may contribute significantly to sweet cherry light responses. In particular, PavTCP1 could play a key role, potentially mediated through Pav-miR159, Pav-miR139a, and Pav-miR139b-3p.

CONCLUSION

This study is the first to unveil the potential function of TCP transcription factors in the light responses of sweet cherry fruits, paving the way for future investigations into the role of this transcription factor family in plant fruit development.

Genome-wide identification of the TCP gene family in Chrysanthemum lavandulifolium and its homologs expression patterns during flower development in different Chrysanthemum species

TCP proteins, part of the transcription factors specific to plants, are recognized for their involvement in various aspects of plant growth and development. Nevertheless, a thorough investigation of TCPs in Chrysanthemum lavandulifolium, a prominent ancestral species of cultivated chrysanthemum and an excellent model material for investigating ray floret (RF) and disc floret (DF) development in Chrysanthemum, remains unexplored yet. Herein, a comprehensive study was performed to analyze the genome-wide distribution of TCPs in C. lavandulifolium. In total, 39 TCPs in C. lavandulifolium were identified, showing uneven distribution on 8 chromosomes. Phylogenetic and gene structural analyses revealed that ClTCPs were grouped into classes I and II. The class II genes were subdivided into two subclades, the CIN and CYC/TB1 subclades, with members of each clade having similar conserved motifs and gene structures. Four CIN subclade genes (ClTCP24, ClTCP25, ClTCP26, and ClTCP27) contained the potential miR319 target sites. Promoter analysis revealed that ClTCPs had numerous cis-regulatory elements associated with phytohormone responses, stress responses, and plant growth/development. The expression patterns of ClTCPs during capitulum development and in two different florets were determined using RNA-seq and qRT-PCR. The expression levels of TCPs varied in six development stages of capitula; 25 out of the 36 TCPs genes were specifically expressed in flowers. Additionally, we identified six key ClCYC2 genes, which belong to the class II TCP subclade, with markedly upregulated expression in RFs compared with DFs, and these genes exhibited similar expression patterns in the two florets of Chrysanthemum species. It is speculated that they may be responsible for RFs and DFs development. Subcellular localization and transactivation activity analyses of six candidate genes demonstrated that all of them were localized in the nucleus, while three exhibited self-activation activities. This research provided a better understanding of TCPs in C. lavandulifolium and laid a foundation for unraveling the mechanism by which important TCPs involved in the capitulum development.

Genome-Wide Identification and Expression Analysis of the TCP Gene Family Related to Developmental and Abiotic Stress in Ginger

Ginger (Zingiber officinale Roscoe), a widely consumed edible and medicinal plant, possesses significant nutritional and economic value. Abiotic stresses such as drought and low temperatures can impact the growth and development of ginger. The plant-specific transcription factor Teosinte branched1/cycloidea/proliferating cell factor (TCP) has progressively been identified in various plants for its role in regulating plant growth and development as well as conferring resistance to abiotic stresses. However, limited information on the TCP family is available in ginger. In this study, we identified 20 TCP members in the ginger genome, which were randomly distributed across 9 chromosomes. Based on phylogenetic analysis, these ginger TCP were classified into two subfamilies: Class I (PCF) and Class II (CIN, CYC/TB). The classification of the identified ginger TCPs was supported by a multi-species phylogenetic tree and motif structure analysis, suggesting that the amplification of the ginger TCP gene family occurred prior to the differentiation of angiosperms. The promoter region of ginger TCP genes was found to contain numerous cis-acting elements associated with plant growth, development, and abiotic stress response. Among these elements, the stress response element, anaerobic induction, and MYB binding site play a dominant role in drought responsiveness. Additionally, expression pattern analysis revealed variations in the expression of ginger TCP gene among different tissues and in response to diverse abiotic stresses (drought, low temperature, heat, and salt). Our research offers a thorough examination of TCP members within the ginger plant. This analysis greatly contributes to the understanding of how TCP genes regulate tissue development and response to stress, opening up new avenues for further exploration in this field.

Genome-Wide Analysis of TCP Transcription Factors and Their Expression Pattern Analysis of Rose Plants (Rosa chinensis)

The plant-specific transcription factor TEOSINTE BRANCHED, CYCLOIDEA, AND PROLIFERATING CELL FACTOR (TCP) gene family plays vital roles in various biological processes, including growth and development, hormone signaling, and stress responses. However, there is a limited amount of information regarding the TCP gene family in roses (Rosa sp.). In this study, we identified 18 TCP genes in the rose genome, which were further classified into two subgroups (Group A and Group B) via phylogenetic analysis. Comprehensive characterization of these TCP genes was performed, including gene structure, motif composition, chromosomal location, and expression profiles. Synteny analysis revealed that a few TCP genes are involved in segmental duplication events, indicating that these genes played an important role in the expansion of the TCP gene family in roses. This suggests that segmental duplication events have caused the evolution of the TCP gene family and may have generated new functions. Our study provides an insight into the evolutionary and functional characteristics of the TCP gene family in roses and lays a foundation for the future exploration of the regulatory mechanisms of TCP genes in plant growth and development.

Genome-wide identification and analysis of TCP family genes in Medicago sativa reveal their critical roles in Na+/K+ homeostasis

BACKGROUND

Medicago sativa is the most important forage world widely, and is characterized by high quality and large biomass. While abiotic factors such as salt stress can negatively impact the growth and productivity of alfalfa. Maintaining Na⁺/K⁺ homeostasis in the cytoplasm helps reduce cell damage and nutritional deprivation, which increases a salt-tolerance of plant. Teosinte Branched1/ Cycloidea/ Proliferating cell factors (TCP) family genes, a group of plant-specific transcription factors (TFs), involved in regulating plant growth and development and abiotic stresses. Recent studies have shown TCPs control the Na⁺/K⁺ concentration of plants during salt stress. In order to improve alfalfa salt tolerance, it is important to identify alfalfa TCP genes and investigate if and how they regulate alfalfa Na⁺/K⁺ homeostasis.

RESULTS

Seventy-one MsTCPs including 23 non-redundant TCP genes were identified in the database of alfalfa genome (C.V XinJiangDaYe), they were classified into class I PCF (37 members) and class II: CIN (28 members) and CYC/TB1 (9 members). Their distribution on chromosome were unequally. MsTCPs belonging to PCF were expressed specifically in different organs without regularity, which belonging to CIN class were mainly expressed in mature leaves. MsTCPs belongs to CYC/TB1 clade had the highest expression level at meristem. Cis-elements in the promoter of MsTCPs were also predicted, the results indicated that most of the MsTCPs will be induced by phytohormone and stress treatments, especially by ABA-related stimulus including salinity stress. We found 20 out of 23 MsTCPs were up-regulated in 200 mM NaCl treatment, and MsTCP3/14/15/18 were significantly induced by 10 μM KCl, a K⁺ deficiency treatment. Fourteen non-redundant MsTCPs contained miR319 target site, 11 of them were upregulated in MIM319 transgenic alfalfa, and among them four (MsTCP3/4/10A/B) genes were directly degraded by miR319. MIM319 transgene alfalfa plants showed a salt sensitive phenotype, which caused by a lower content of potassium in alfalfa at least partly. The expression of potassium transported related genes showed significantly higher expression in MIM319 plants.

CONCLUSIONS

We systematically analyzes the MsTCP gene family at a genome-wide level and reported that miR319-TCPs model played a function in K⁺ up-taking and/ or transportation especially in salt stress. The study provide valuable information for future study of TCP genes in alfalfa and supplies candidate genes for salt-tolerance alfalfa molecular-assisted breeding.

Genome-wide analysis of TCP transcription factor family in sunflower and identification of HaTCP1 involved in the regulation of shoot branching

BACKGROUND

Sunflower is an important ornamental plant, which can be used for fresh cut flowers and potted plants. Plant architecture regulation is an important agronomic operation in its cultivation and production. As an important aspect of plant architecture formation, shoot branching has become an important research direction of sunflower.

RESULTS

TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors are essential in regulating various development process. However, the role of TCPs in sunflowers has not yet been studied. This study, 34 HaTCP genes were identified and classified into three subfamilies based on the conservative domain and phylogenetic analysis. Most of the HaTCPs in the same subfamily displayed similar gene and motif structures. Promoter sequence analysis has demonstrated the presence of multiple stress and hormone-related cis-elements in the HaTCP family. Expression patterns of HaTCPs revealed several HaTCP genes expressed highest in buds and could respond to decapitation. Subcellular localization analysis showed that HaTCP1 was located in the nucleus. Paclobutrazol (PAC) and 1-naphthylphthalamic acid (NPA) administration significantly delayed the formation of axillary buds after decapitation, and this suppression was partially accomplished by enhancing the expression of HaTCP1. Furthermore, HaTCP1 overexpressed in Arabidopsis caused a significant decrease in branch number, indicating that HaTCP1 played a key role in negatively regulating sunflower branching.

CONCLUSIONS

This study not only provided the systematic analysis for the HaTCP members, including classification, conserved domain and gene structure, expansion pattern of different tissues or after decapitation. But also studied the expression, subcellular localization and function of HaTCP1. These findings could lay a critical foundation for further exploring the functions of HaTCPs.

Genome-Wide Identification, Characterization, and Expression of TCP Genes Family in Orchardgrass

Plant-specific TCP transcription factors regulate several plant growth and development processes. Nevertheless, little information is available about the TCP family in orchardgrass (Dactylis glomerata L.). This study identified 22 DgTCP transcription factors in orchardgrass and determined their structure, phylogeny, and expression in different tissues and developmental stages. The phylogenetic tree classified the DgTCP gene family into two main subfamilies, including class I and II supported by the exon-intron structure and conserved motifs. The DgTCP promoter regions contained various cis-elements associated with hormones, growth and development, and stress responses, including MBS (drought inducibility), circadian (circadian rhythms), and TCA-element (salicylic acid responsiveness). Moreover, DgTCP9 possibly regulates tillering and flowering time. Additionally, several stress treatments upregulated DgTCP1, DgTCP2, DgTCP6, DgTCP12, and DgTCP17, indicting their potential effects regarding regulating responses to the respective stress. This research offers a valuable basis for further studies of the TCP gene family in other Gramineae and reveals new ideas for increasing gene utilization.

Physiological Roles and Mechanisms of Action of Class I TCP Transcription Factors

TEOSINTE BRANCHED1, CYCLOIDEA, PROLIFERATING CELL FACTOR 1 and 2 (TCP) proteins constitute a plant-specific transcription factors family exerting effects on multiple aspects of plant development, such as germination, embryogenesis, leaf and flower morphogenesis, and pollen development, through the recruitment of other factors and the modulation of different hormonal pathways. They are divided into two main classes, I and II. This review focuses on the function and regulation of class I TCP proteins (TCPs). We describe the role of class I TCPs in cell growth and proliferation and summarize recent progresses in understanding the function of class I TCPs in diverse developmental processes, defense, and abiotic stress responses. In addition, their function in redox signaling and the interplay between class I TCPs and proteins involved in immunity and transcriptional and posttranslational regulation is discussed.

Genome-wide identification and expression pattern analysis of the TCP transcription factor family in Ginkgo biloba

Plant-specific TCP transcription factors play an essential role in plant growth and development. They can regulate leaf curvature, flower symmetry and the synthesis of secondary metabolites. The flavonoids in Ginkgo biloba leaf are one of the main medicinally bioactivate compounds, which have pharmacological and beneficial health effects for humans. In this study, a total of 13 TCP genes were identified in G. biloba, and 5 of them belonged to PCF subclades (GbTCP03, GbTCP07, GbTCP05, GbTCP13, GbTCP02) while others belonged to CIN (GbTCP01, GbTCP04, GbTCP06, GbTCP08, GbTCP09, GbTCP10, GbTCP11, GbTCP12) subclades according to phylogenetic analysis. Numerous cis-acting elements related to various biotic and abiotic signals were predicted on the promoters by cis-element analysis, suggesting that the expression of GbTCPs might be co-regulated by multiple signals. Transcript abundance analysis exhibited that most of GbTCPs responded to multiple phytohormones. Among them, the relative expression levels of GbTCP06, GbTCP11, and GbTCP13 were found to be significantly influenced by exogenous ABA, SA and MeJA application. In addition, a total of 126 miRNAs were predicted to target 9 TCPs (including GbTCP01, GbTCP02, GbTCP04, GbTCP05, GbTCP06, GbTCP08, GbTCP11, GbTCP12, GbTCP13). The correlation analysis between the expression level of GbTCPs and the flavonoid contents showed that GbTCP03, GbTCP04, GbTCP07 might involve in flavonoid biosynthesis in G. biloba. In short, this study mainly provided a theoretical foundation for better understanding the potential function of TCPs in G. biloba.

Genome-Wide Identification and Characterization of TCP Gene Family Members in Melastoma candidum

It has been confirmed that the plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) gene family plays a pivotal role during plant growth and development. M. candidum is a native ornamental species and has a wide range of pharmacodynamic effects. However, there is still a lack of research on TCP’s role in controlling M. candidum’s development, abiotic stress responses and hormone metabolism. A comprehensive description of the TCP gene family in M. candidum is urgently needed. In this study, we used the HMMER search method in conjunction with the BLASTp method to identify the members of the TCP gene family, and a total of 35 TCP genes were identified. A domain analysis further confirmed that all 35 TCPs contained a TCP superfamily, a characteristic involved in dimerization and DNA binding that can be found in most genes from this gene family, suggesting that our identification was effective. As a result of the domain conservation analysis, the 35 TCP genes could be classified into two classes, TCP-P and TCP-C, based on the conservative regions of 55 and 59 amino acids, respectively. Gene-duplication analysis revealed that most TCP genes were present in duplication events that eventually led to TCP gene expansion in M. candidum. All the detected gene pairs had a Ka/Ks value of less than one, suggesting that purification selection is the most important factor that influences the evolution of TCP genes. Phylogenetic analysis of three species displayed the evolutionary relationship of TCP genes across different species and further confirmed our results. The real-time quantitative PCR (qRT-PCR) results showed that McTCP2a, McTCP7a, McTCP10, McTCP11, McTCP12a, McTCP13, McTCP16, McTCP17, McTCP18, McTCP20 and McTCP21 may be involved in leaf development; McTCP4a, McTCP1, McTCP14, McTCP17, McTCP18, McTCP20, McTCP22 and McTCP24 may be involved in flower development; and McTCP2a, McTCP3, McTCP5a, McTCP6, McTCP7a, McTCP9, McTCP11, McTCP14 and McTCP16 may be involved in seed development. Our results dissect the TCP gene family across the genome of M. candidum and provide valuable information for exploring TCP genes to promote molecular breeding and property improvement of M. candidum in the future.

Comparative genomic investigation of TCP gene family in eggplant (Solanum melongena L.) and expression analysis under divergent treatments

The putative TCP genes and their responses to abiotic stress in eggplant were comprehensively characterized, and SmTCP genes (Smechr0202855.1 and Smechr0602431.1) may be involved in anthocyanin synthesis. The Teosinte branched1/Cycloidea/Proliferating cell factors (TCPs), a family of plant-specific transcription factors, plays paramount roles in a plethora of developmental and physiological processes. We here systematically characterized putative TCP genes and their response to abiotic stress in eggplant. In total, 30 SmTCP genes were categorized into two subfamilies based on the classical TCP conserved domains. Chromosomal location analysis illustrated the random distribution of putative SmTCP genes along 12 eggplant chromosomes. Cis-acting elements and miRNA target prediction suggested that versatile and complicated regulatory mechanisms that control SmTCPs gene expression, and 3 miRNAs (miR319a, miR319b, and miR319c-3p) might act as major regulators targeting SmTCPs. Tissue expression profiles indicated divergent spatiotemporal expression patterns of SmTCPs. qRT-PCR assays demonstrated different expression profiles of SmTCP under 4 °C, drought and ABA treatment conditions, suggesting the possible participation of SmTCP genes in multiple signaling pathways. Furthermore, RNA-seq data of eggplant anthocyanin synthesis coupled with yeast one-hybrid and dual-luciferase assays suggested the involvement of SmTCP genes (Smechr0202855.1 and Smechr0602431.1) in the mediation of anthocyanin synthesis. Our study will facilitate further investigation on the putative functional characterization of eggplant TCP genes and lay a solid foundation for the in-depth study of the involvement of SmTCP genes in the regulation of anthocyanin synthesis.

Insights into transcription factors controlling strawberry fruit development and ripening

Fruit ripening is a highly regulated and complex process involving a series of physiological and biochemical changes aiming to maximize fruit organoleptic traits to attract herbivores, maximizing therefore seed dispersal. Furthermore, this process is of key importance for fruit quality and therefore consumer acceptance. In fleshy fruits, ripening involves an alteration in color, in the content of sugars, organic acids and secondary metabolites, such as volatile compounds, which influence flavor and aroma, and the remodeling of cell walls, resulting in the softening of the fruit. The mechanisms underlying these processes rely on the action of phytohormones, transcription factors and epigenetic modifications. Strawberry fruit is considered a model of non-climacteric species, as its ripening is mainly controlled by abscisic acid. Besides the role of phytohormones in the regulation of strawberry fruit ripening, a number of transcription factors have been identified as important regulators of these processes to date. In this review, we present a comprehensive overview of the current knowledge on the role of transcription factors in the regulation of strawberry fruit ripening, as well as in compiling candidate regulators that might play an important role but that have not been functionally studied to date.

Optimization of an Efficient Protoplast Transformation System for Transient Expression Analysis Using Leaves of Torenia fournieri

Torenia fournieri (T. fournieri) is one of the most widely used horticultural flowers and is considered a potential model plant for the genetic investigation of ornamental traits. In this study, we optimized an efficient protocol for high efficiency preparation and transformation of T. fournieri protoplast. The transformation rate reached ~75% when a 35S:GFP construct was used for the transformation. Using this system, we characterized the subcellular localization of several TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors (TFs), and found a distinct localization pattern between the CIN and CYC classes of TCP TFs. Furthermore, we also demonstrated the feasibility of the expression of dual luciferase assay system in T. fournieri protoplasts for the measurement of the activity of cis-regulatory elements. Taken together, a well-optimized transient expression system in T. fournieri protoplasts would be crucial for rapid exploration of the gene function or cis-regulatory elements.

Identification and characterization of auxin response factor (ARF) family members involved in fig (Ficus carica L.) fruit development

The auxin response factor (ARF) combines with AuxREs cis-acting elements in response to auxin to regulate plant development. To date, no comprehensive analysis of ARF genes expressed during fruit development has been conducted for common fig (Ficus carica L.). In this study, members of the FcARF gene family were screened, identified in the fig genome database and their features characterized using bioinformatics. Twenty FcARF genes were clustered into three classes, with almost similar highly conserved DBD (B3-like DNA binding domain), AUX/IAA (auxin/indole-3-acetic acid gene family) and MR domain structure among class members. Analysis of amino acid species in MR domain revealed 10 potential transcription activators and 10 transcription inhibitors, and 17 FcARF members were predicted to be located in the nucleus. DNA sequence analysis showed that the ARF gene family consisted of 4-25 exons, and the promoter region contained 16 cis-acting elements involved in stress response, hormone response and flavonoid biosynthesis. ARF genes were expressed in most tissues of fig, especially flower and peel. Transcriptomics analysis results showed that FcARF2, FcARF11 and FcARF12, belonging to class-Ia, were stably and highly expressed in the early development stage of flower and peel of 'Purple peel' fig. However, their expression levels decreased after maturity. Expression of class-Ic member FcARF3 conformed to the regularity of fig fruit development. These four potential transcription inhibitors may regulate fruit growth and development of 'Purple Peel' fig. This study provides comprehensive information on the fig ARF gene family, including gene structure, chromosome position, phylogenetic relationship and expression pattern. Our work provides a foundation for further research on auxin-mediated fig fruit development.

Identification of TCP family in moso bamboo (Phyllostachys edulis) and salt tolerance analysis of PheTCP9 in transgenic Arabidopsis

Bioinformatic analysis of moso bamboo TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (TCP) transcription factors reveals their conservation and variation as well as the probable biological functions in abiotic stress response. Overexpressing PheTCP9 in Arabidopsis thaliana illustrates it may exhibit a new vision in different aspects of response to salt stress. Plant specific TCPs play important roles in plant growth, development and stress response, but studies of TCP in moso bamboo are limited. Therefore, in this study, a total of 40 TCP genes (PheTCP1 ~ 40) were identified and characterized from moso bamboo genome and divided into three different subfamilies, namely, 7 in TEOSINTE BRANCHED 1 / CYCLOIDEA (TB1/CYC), 14 in CINCINNATA (CIN) and 19 in PROLIFERATING CELL FACTOR (PCF). Subsequently, we analyzed the gene structures and conserved domain of these genes and found that the members from the same subfamilies exhibited similar exon/intron distribution patterns. Selection pressure and gene duplication analysis results indicated that PheTCP genes underwent strong purification selection during evolution. There were many cis-elements related to phytohermone and stress responsive existing in the upstream promoter regions of PheTCP genes, such as ABRE, CGTCA-motif and ARE. Subcellular localization experiments showed that PheTCP9 was a nuclear localized protein. As shown by β-glucuronidase (GUS) activity, the promoter of PheTCP9 was significantly indicated by salt stress. PheTCP9 was significantly induced in the roots, stems and leaves of moso bamboo. It was also significantly induced by NaCl solution. Overexpressing PheTCP9 increased the salt tolerance of transgenic Arabidopsis. Meanwhile, H₂O₂ and malondialdehyde (MDA) contents were significantly lower in PheTCP9 over expression (OE) transgenic Arabidopsis than WT. Catalase (CAT) activity, K⁺/Na⁺ ratio as well as CAT2 expression level was also much improved in transgenic Arabidopsis than WT under salt conditions. In addition, PheTCP9 OE transgenic Arabidopsis held higher survival rates of seedlings than WT under NaCl conditions. These results showed the positive regulation functions of PheTCP9 in plants under salt conditions.

Genome-Wide Identification and Characterization of TCP Family Genes in Pak-Choi [Brassica campestris (syn. Brassica rapa) ssp. chinensis var. communis]

The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) gene family, a kind of plant specific transcription factor, is essential for stress response, cell growth, and cell proliferation. However, the characterization of TCP family is still not clear in Pak-choi [Brassica campestris (syn. Brassica rapa) ssp. chinensis var. communis]. In this study, genome-wide analysis of TCP gene family was performed and 26 TCP genes were identified in Pak-choi. Phylogenetic analysis demonstrated that the 26 BcTCPs were divided into two classes: Class I and Class II. Class II was further classified into two subclasses, CIN and CYC/TB1. The qPCR results suggested that most BcTCPs respond to abiotic stresses. The expressions of BcTCP3, BcTCP12, BcTCP21, and BcTCP22 were significantly changed under ABA and cold treatment. BcTCP3 and BcTCP12 were also up-regulated under osmotic treatment. Subcellular localization showed that BcTCP3 and BcTCP21 were located in the nucleus. Our results will facilitate revealing the functions and regulatory mechanisms of BcTCPs.

Priming-induced alterations in histone modifications modulate transcriptional responses in soybean under salt stress

Plants that have experienced certain abiotic stress may gain tolerance to a similar stress in subsequent exposure. This phenomenon, called priming, was observed here in soybean (Glycine max) seedlings exposed to salt stress. Time-course transcriptomic profiles revealed distinctively different transcriptional responses in the primed seedlings from those in the non-primed seedlings under high salinity stress, indicating a stress response strategy of repressing unhelpful biotic stress responses and focusing on the promotion of those responses important for salt tolerance. To identify histone marks altered by the priming salinity treatment, a genome-wide profiling of histone 3 lysine 4 dimethylation (H3K4me2), H3K4me3, and histone 3 lysine 9 acetylation (H3K9ac) was performed. Our integrative analyses revealed that priming induced drastic alterations in these histone marks, which coordinately modified the stress response, ion homeostasis, and cell wall modification. Furthermore, transcriptional network analyses unveiled epigenetically modified networks which mediate the strategic downregulation of defense responses. Altering the histone acetylation status using a chemical inhibitor could elicit the priming-like transcriptional responses in non-primed seedlings, confirming the importance of histone marks in forming the priming response.

Transcriptomic Analysis Suggests Auxin Regulation in Dorsal-Ventral Petal Asymmetry of Wild Progenitor Sinningia speciosa

The establishment of dorsal-ventral (DV) petal asymmetry is accompanied by differential growth of DV petal size, shape, and color differences, which enhance ornamental values. Genes involved in flower symmetry in Sinningia speciosa have been identified as CYCLOIDEA (SsCYC), but which gene regulatory network (GRN) is associated with SsCYC to establish DV petal asymmetry is still unknown. To uncover the GRN of DV petal asymmetry, we identified 630 DV differentially expressed genes (DV-DEGs) from the RNA-Seq of dorsal and ventral petals in the wild progenitor, S. speciosa 'ES'. Validated by qRT-PCR, genes in the auxin signaling transduction pathway, SsCYC, and a major regulator of anthocyanin biosynthesis were upregulated in dorsal petals. These genes correlated with a higher endogenous auxin level in dorsal petals, with longer tube length growth through cell expansion and a purple dorsal color. Over-expression of SsCYC in Nicotiana reduced petal size by regulating cell growth, suggesting that SsCYC also controls cell expansion. This suggests that auxin and SsCYC both regulate DV petal asymmetry. Transiently over-expressed SsCYC, however, could not activate most major auxin signaling genes, suggesting that SsCYC may not trigger auxin regulation. Whether auxin can activate SsCYC or whether they act independently to regulate DV petal asymmetry remains to be explored in the future.

Genome-Wide Identification and Comparative Analysis of the Teosinte Branched 1/Cycloidea/Proliferating Cell Factors 1/2 Transcription Factors Related to Anti-cancer Drug Camptothecin Biosynthesis in Ophiorrhiza pumila

Ophiorrhiza pumila (O. pumila; Op) is a medicinal herbaceous plant, which can accumulate camptothecin (CPT). CPT and its derivatives are widely used as chemotherapeutic drugs for treating malignant tumors. Its biosynthesis pathway has been attracted significant attention. Teosinte branched 1/cycloidea/proliferating cell factors 1/2 (TCP) transcription factors (TFs) regulate a variety of physiological processes, while TCP TFs are involved in the regulation of CPT biosynthesis remain unclear. In this study, a systematic analysis of the TCP TFs family in O. pumila was performed. A total of 16 O. pumila TCP (OpTCP) genes were identified and categorized into two subgroups based on their phylogenetic relationships with those in Arabidopsis thaliana. Tissue-specific expression patterns revealed that nine OpTCP genes showed the highest expression levels in leaves, while the other seven OpTCPs showed a higher expression level in the stems. Co-expression, phylogeny analysis, and dual-luciferase (Dual-LUC) assay revealed that OpTCP15 potentially plays important role in CPT and its precursor biosynthesis. In addition, the subcellular localization experiment of candidate OpTCP genes showed that they are all localized in the nucleus. Our study lays a foundation for further functional characterization of the candidate OpTCP genes involved in CPT biosynthesis regulation and provides new strategies for increasing CPT production.

Analysis of Evolution, Expression and Genetic Transformation of TCP Transcription Factors in Blueberry Reveal That VcTCP18 Negatively Regulates the Release of Flower Bud Dormancy

Plant-specific TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTORS (TCP) transcription factors have versatile functions in plant growth, development and response to environmental stress. Despite blueberry's value as an important fruit crop, the TCP gene family has not been systematically studied in this plant. The current study identified blueberry TCP genes (VcTCPs) using genomic data from the tetraploid blueberry variety 'Draper'; a total of 62 genes were obtained. Using multiple sequence alignment, conserved motif, and gene structure analyses, family members were divided into two subfamilies, of which class II was further divided into two subclasses, CIN and TB1. Synteny analysis showed that genome-wide or segment-based replication played an important role in the expansion of the blueberry TCP gene family. The expression patterns of VcTCP genes during fruit development, flower bud dormancy release, hormone treatment, and tissue-specific expression were analyzed using RNA-seq and qRT-PCR. The results showed that the TB1 subclass members exhibited a certain level of expression in the shoot, leaf, and bud; these genes were not expressed during fruit development, but transcript levels decreased uniformly during the release of flower bud dormancy by low-temperature accumulation. The further transgenic experiments showed the overexpression of VcTCP18 in Arabidopsis significantly decreased the seed germination rate in contrast to the wild type. The bud dormancy phenomena as late-flowering, fewer rosettes and main branches were also observed in transgenic plants. Overall, this study provides the first insight into the evolution, expression, and function of VcTCP genes, including the discovery that VcTCP18 negatively regulated bud dormancy release in blueberry. The results will deepen our understanding of the function of TCPs in plant growth and development.

Abscisic acid crosstalk with auxin and ethylene in biosynthesis and degradation of inulin-type fructans in chicory

The effect of different hormones on fructan accumulation and the genes regulating biosynthesis and degradation is known; however, information on hormonal interaction mechanisms for fructan content and mean degree of polymerization (mDP) is limited. Cell suspension cultures of chicory were prepared and treated with abscisic acid (ABA), auxin (AUX), ethylene (ETH), ABA + AUX or ABA + ETH, then inulin concentration, mDP of inulin and expression of FAZY genes was determined. A low concentration of AUX and ETH increased fructan content, while a high concentration of AUX and ETH decreased it. Exogenous ABA increased mDP of inulin and this coincided with the low expression of 1-FEHII. In hormone interactions, ABA changed and adjusted the effect of both AUX and ETH. ABA, together with a low level of AUX and ETH, resulted in a decrease in inulin content and increase in mDP, which coincided with low expression of FEHII. ABA together with a high level of AUX and ETH caused an increase in inulin content with a lower mDP, which coincided with high expression of biosynthesis (1-FFT) and degradation (1-FEHII) genes. The effect of both AUX and ETH was almost the same, although the effect of ETH was more severe. ABA had a modulating role in combinations with AUX and ETH. Among biosynthesis and degradation genes, the expression of 1-FEHII was more affected by these hormones.

Genome-Wide Identification and Transcript Analysis of TCP Gene Family in Banana (Musa acuminata L.)

Plant-specific TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1 (TCP) gene family has versatile functions in diverse aspects of plants. However, less research on banana TCPs was done comprehensively. Accordingly, 48 banana TCP genes were characterized on aspects of gene structure, conserved motifs, phylogenetic relationship, and expression patterns. Members of the MaTCP gene family were unevenly distributed among 11 chromosomes and purification selection was the driving force of the MaTCP gene family. Gene duplication analysis indicated that segmental duplication is the major contributor to family expansion. Promoter analysis showed that MaTCPs might be involved in banana growth, development, and abiotic stress responses. Further, the expression of 12 MaTCPs was analyzed by real-time quantitative RT-PCR, and the protein interaction analysis showed that MaPCF10 and MaPCF13 may have an important function in banana fruit development and ripening. These results lay the foundation for further study of the functions of TCP genes in banana.

Integration of Metabolome and Transcriptome Reveals the Relationship of Benzenoid-Phenylpropanoid Pigment and Aroma in Purple Tea Flowers

Tea (Camellia sinensis) flowers are normally white, even though the leaves could be purple. We previously discovered a specific variety with purple leaves and flowers. In the face of such a phenomenon, researchers usually focus on the mechanism of color formation but ignore the change of aroma. The purple tea flowers contain more anthocyanins, which belong to flavonoids. Meanwhile, phenylalanine (Phe), derived from the shikimate pathway, is a precursor for both flavonoids and volatile benzenoid-phenylpropanoids (BPs). Thus, it is not clear whether the BP aroma was attenuated for the appearance of purple color. In this study, we integrated metabolome and transcriptome of petals of two tea varieties, namely, Zijuan (ZJ) with white flowers and Baitang (BT) with purple flowers, to reveal the relationship between color (anthocyanins) and aroma (volatile BPs). The results indicated that in purple petals, the upstream shikimate pathway promoted for 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS) was elevated. Among the increased anthocyanins, delphinidin-3-O-glucoside (DpG) was extremely higher; volatile BPs, including benzyl aldehyde, benzyl alcohol, acetophenone (AP), 1-phenylethanol, and 2-phenylethanol, were also enhanced, and AP was largely elevated. The structural genes related to the biosynthesis of volatile BPs were induced, while the whole flavonoid biosynthesis pathway was downregulated, except for the genes flavonoid 3'-hydroxylase (F3'H) and flavonoid 3',5'-hydroxylase (F3'5'H), which were highly expressed to shift the carbon flux to delphinidin, which was then conjugated to glucoside by increased bronze-1 (BZ1) (UDP-glucose: flavonoid 3-O-glucosyltransferase) to form DpG. Transcription factors (TFs) highly related to AP and DpG were selected to investigate their correlation with the differentially expressed structural genes. TFs, such as MYB, AP2/ERF, bZIP, TCP, and GATA, were dramatically expressed and focused on the regulation of genes in the upstream synthesis of Phe (DAHPS; arogenate dehydratase/prephenate dehydratase) and the synthesis of AP (phenylacetaldehyde reductase; short-chain dehydrogenase/reductase), Dp (F3'H; F3'5'H), and DpG (BZ1), but inhibited the formation of flavones (flavonol synthase) and catechins (leucoanthocyanidin reductase). These results discovered an unexpected promotion of volatile BPs in purple tea flowers and extended our understanding of the relationship between the BP-type color and aroma in the tea plant.

Genome-wide analysis of PmTCP4 transcription factor binding sites by ChIP-Seq during pistil abortion in Japanese apricot

The TCP4 transcription factor plays an important role in plant growth and development, especially in flower development. PmTCP4 is involved in the process of pistil abortion in Japanese apricot, but its molecular mechanism, particularly the DNA binding sites and co-regulatory genes, are quite unknown. Therefore, to identify the genome-wide binding sites of PmTCP4 transcription factors and their co-regulatory genes, chromatin immunoprecipitation sequencing (ChIP-Seq) was carried out. ChIP-Seq data produced the maximum enriched peaks in two Japanese apricot cultivars 'Daqiandi' (DQD) and 'Longyan' (LY), which showed that the majority of DNA-protein interactions are relevant and have a significant function in binding sites. Moreover, 720 and 251 peak-associated genes regulated by PmTCP4 were identified in DQD and LY, respectively, and most of them were involved in the flower and pistil development process. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that photosynthesis and oxidative phosphorylation were the most enriched pathways in both cultivars and all identified genes related to these pathways were down-regulated. This study will provide a reference for a better understanding of the PmTCP4 regulatory mechanism during pistil abortion in Japanese apricot.

Comparative phenotypic and transcriptomic analysis of Victoria and flame seedless grape cultivars during berry ripening

Grape berry development is a highly coordinated and intricate process. Herein, we analyzed the phenotypic and transcriptomic patterns of Victoria (VT) and Flame Seedless (FS) grape varieties during berry development. Physiological analysis and transcriptomic sequencing were performed at four berry developmental phases. VT berry size was comparatively larger to the FS variety. At maturity, 80 days postanthesis (DPA), the FS soluble solids were 61.8% higher than VT. Further, 4889 and 2802 differentially expressed genes were identified from VT and FS 40 DPA to 80 DPA development stages, respectively. VvSWEET15, VvHXK, and MYB44 genes were up‐regulated during the postanthesis period, while bHLH14, linked to glucose metabolism, was gradually down‐regulated during berry development. These genes may have significant roles in berry development, ripening, and sugar accumulation.

Genome-Wide Identification of the TCP Gene Family in Broussonetia papyrifera and Functional Analysis of BpTCP8, 14 and 19 in Shoot Branching

The plant-specific TCP family proteins play an important role in the processes of plant growth and development. Broussonetia papyrifera is a versatile perennial deciduous tree, and its genome data have been published. However, no comprehensive analysis of the TCP gene family in B. papyrifera has been undertaken. In this study, 20 BpTCP genes (BpTCPs) were identified in the B. papyrifera genome. Phylogenetic analysis divided BpTCPs into three subclades, the PCF subclade, the CIN subclade and the CYC/TB1 subclade. Gene structure analysis displayed that all BpTCPs except BpTCP19 contained one coding region. Conserved motif analysis showed that BpTCP proteins in the same subclade possessed similar motif structures. Segmental duplication was the primary driving force for the expansion of BpTCPs. Expression patterns showed that BpTCPs may play diverse biological functions in organ or tissue development. Transcriptional activation activity analysis of BpTCP8, BpTCP14 and BpTCP19 showed that they possessed transcriptional activation ability. The ectopic expression analysis in Arabidopsis wild-type and AtBRC1 ortholog mutant showed that BpTCP8, BpTCP14 and BpTCP19 could prevent rosette branch outgrowth. Collectively, our study not only established the first genome-wide analysis of the B. papyrifera TCP gene family, but also provided valuable information for understanding the function of BpTCPs in shoot branching.

Genome-Wide Identification, Characterization and Expression Analysis of TCP Transcription Factors in Petunia

The plant-specific TCP transcription factors are well-characterized in both monocots and dicots, which have been implicated in multiple aspects of plant biological processes such as leaf morphogenesis and senescence, lateral branching, flower development and hormone crosstalk. However, no systematic analysis of the petunia TCP gene family has been described. In this work, a total of 66 petunia TCP genes (32 PaTCP genes in P. axillaris and 34 PiTCP genes in P. inflata) were identified. Subsequently, a systematic analysis of 32 PaTCP genes was performed. The phylogenetic analysis combined with structural analysis clearly distinguished the 32 PaTCP proteins into two classes—class Ι and class Ⅱ. Class Ⅱ was further divided into two subclades, namely, the CIN-TCP subclade and the CYC/TB1 subclade. Plenty of cis-acting elements responsible for plant growth and development, phytohormone and/or stress responses were identified in the promoter of PaTCPs. Distinct spatial expression patterns were determined among PaTCP genes, suggesting that these genes may have diverse regulatory roles in plant growth development. Furthermore, differential temporal expression patterns were observed between the large- and small-flowered petunia lines for most PaTCP genes, suggesting that these genes are likely to be related to petal development and/or petal size in petunia. The spatiotemporal expression profiles and promoter analysis of PaTCPs indicated that these genes play important roles in petunia diverse developmental processes that may work via multiple hormone pathways. Moreover, three PaTCP-YFP fusion proteins were detected in nuclei through subcellular localization analysis. This is the first comprehensive analysis of the petunia TCP gene family on a genome-wide scale, which provides the basis for further functional characterization of this gene family in petunia.

Inhibition of FvMYB10 transcriptional activity promotes color loss in strawberry fruit

FvMYB10 protein has been proved to be a transcriptional switch for anthocyanin biosynthesis in strawberry. A single nucleotide mutation in R2 domain of FvMYB10, named as FvmMYB10, is found to be responsible for the white color in strawberry variety 'Yellow Wonder'. However, the mechanism of FvmMYB10 suppresses anthocyanin biosynthesis in strawberry is largely unknown. Here, we show that the transcriptional level of FvMYB10 and key enzyme genes involved in anthocyanin biosynthesis in 'Yellow Wonder' were lower than that in red color variety 'Ruegen', especially at turning to ripening stage. The low expression level of FvmMYB10 may due to his inability to bind to its promoter region and activate its own expression. We found FvMYB10-overexpressing, but not FvmMYB10-overexpressing, promote anthocyanin accumulation in Arabidopsis and strawberry fruit despite of their similar expression levels. In addition, subcellular localization assay indicated that FvMYB10-YFP, but not FvmMYB10-YFP, localized to sub-nucleus foci (speckles) in the nucleus, implying the mutation of FvMYB10 might inhibit its transcription factor activity and eventually interfere with its function. Subsequently, we confirmed that FvMYB10 bind to the promoter region of some specific key enzyme genes, including FvCHS2 and FvDFR1 and activated their expression. While FvmMYB10 failed to binding and transcriptional activating these genes. Our findings provide insights into molecular mechanism of anthocyanin biosynthesis regulated by MYB10 in strawberry fruits.

Genome-wide analysis of the TCP transcription factor genes in five legume genomes and their response to salt and drought stresses

The teosinte branched1, cycloidea, and proliferating cell factor family (TCP) proteins, plant-specific transcription factors, are involved in the regulation of plant development; however, the TCP gene family of legumes has been based primarily on a single crop. Here, a total of 55, 22, 26, 21, and 25 genes containing the VQ motif were identified from the genomes of Glycine max, Cicer arietinum, Phaseolus vulgaris, Medicago truncatula, and Lotus japonicus, respectively. Based on the phylogenetic analysis, we divided these TCP genes into three distinct subfamilies: PCF, CYC/TB1, and CIN. The conserved domain analysis indicated that the TCP gene family members contain the bHLH and R domains. The TCP genes from the same evolutionary branches of legumes shared similar motifs and structures. The promoter analysis revealed that cis-elements were related to stress responses, phytohormone responses, and physical and reproductive growth regulation. In addition, the TCP genes presented different expression patterns in the five legumes. Most of them showed specific expression patterns during development. The results of qRT-PCR indicated that the TCP genes played regulatory roles in both salt and drought stresses. The present study provides novel and detailed information regarding the legume TCP gene family, which aids in functional characterisation of the TCP genes in other plants.

Molecular characterization of teosinte branched1 gene governing branching architecture in cultivated maize and wild relatives

We sequenced the entire tb1 gene in six maize inbreds and its wild relatives (parviglumis, mexicana, perennis and luxurians) to characterize it at molecular level. Hopscotch and Tourist transposable elements were observed in the upstream of tb1 in all maize inbreds, while they were absent in wild relatives. In maize, tb1 consisted of 431-443 bp 5'UTR, 1101 bp coding sequence and 211-219 bp 3'UTR. In promoter region, mutations in the light response element in mexicana (~ 35 bp and ~ 55 bp upstream of TSS) and perennis (at ~ 35 bp upstream of TSS) were found. A 6 bp insertion at 420 bp downstream of the polyA signal site was present among teosinte accessions, while it was not observed in maize. A codominant marker flanking the 6 bp InDel was developed, and it differentiated the teosintes from maize. In Tb1 protein, alanine (12.7-14.6%) was the most abundant amino acid with tryptophan as the rarest (0.5-0.9%). The molecular weight of Tb1 protein was 38757.15 g/mol except 'Palomero Toluqueno' and HKI1128. R and TCP motifs in Tb1 protein were highly conserved across maize, teosinte and orthologues, while TCP domain differed for tb1 paralogue. Tb1 possessed important role in light-, auxin-, stress-response and meristem identity maintenance. Presence of molecular signal suggested its localization in mitochondria, nucleus and nucleolus. Parviglumis and mexicana shared closer relationship with maize than perennis and luxurians. A highly conserved 59-60 amino acids long bHLH region was observed across genotypes. Information generated here assumes significance in evolution of tb1 gene and breeding for enhancement of prolificacy in maize.

SRNAome and transcriptome analysis provide insight into strawberry fruit ripening

Strawberry fruit ripening is a complex process affected by multiple factors at different regulation levels. To elucidate the regulation mechanisms, the combined analysis of sRNAome and transcriptome were used. A total of 124 known and 190 novel miRNAs were found, 62 of them were significantly differentially expressed (DE). The targets of the DE miRNAs were parsed and several TFs, such as SPL, ARF, WRKY, and TCP, were found to be involved in ripening. Elevated CO₂ can significantly postpone ripening and miR156, miR166f, miR171a, and miR171d were the DE miRNAs. Transcriptome analysis found 313 DE genes related to fruit ripening, including cell wall metabolism-related genes, color-related genes, ethylene-related genes, and genes encoding TFs such as MYB, SPL, NAC, TCP, and ARF. Based on above, a combined regulatory model involved in fruit ripening was created. These results provide valuable information for understanding the complicated coordinated regulatory network of strawberry fruit ripening.

The crystal structure of the TCP domain of PCF6 in Oryza sativa L. reveals an RHH-like fold

The Teosinte branched 1/Cycloidea/Proliferating cell factor (TCP) domain is an evolutionarily conserved DNA binding domain unique to the plant kingdom. To date, the functions of TCPs have been well studied, but the three-dimensional structure of the TCP domain is lacking. Here, we have determined the crystal structure of the TCP domain from OsPCF6. The structure reveals that the TCP domain adopts three short β-strands followed by a helix-loop-helix structure, distinct from the canonical basic helix-loop-helix structure. This folded domain shows high structural similarity to the ribbon-helix-helix (RHH) transcriptional repressors, a family of DNA binding proteins with a conserved 3D structural motif (RHH fold), indicating that TCPs could be reclassified as RHH proteins. Our work will provide insight toward a better understanding of the mechanisms underlying TCP protein function.

Transcription factor FvTCP9 promotes strawberry fruit ripening by regulating the biosynthesis of abscisic acid and anthocyanins

The plant-specific transcription factor TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING4 CELL FACTORS (TCP) plays a crucial role in plant growth and development. However, there have been no studies reporting on the function of strawberry TCP in regulating fruit development. In this study, FvTCP9, a woodland strawberry (Fragaria vesca) TCP gene, was isolated to explore its function in fruit ripening. The transcript accumulation levels of FvTCP9 were high in fruits, specifically in red fruits compared with other tissues or organs. Transient expression of the FvTCP9 gene in cultivated strawberry fruits revealed that over-expression of FvTCP9 promoted fruit ripening. Meanwhile, silencing FvTCP9, using tobacco rattle virus-induced gene silencing (VIGS), inhibited fruit ripening. The changes in ripening-related physiological conditions in transient fruits, such as the accumulation of anthocyanins and abscisic acid (ABA), and fruit firmness confirmed above results. Results suggested that FvTCP9 was involved in the biosynthesis of ABA and anthocyanins to regulate fruit ripening. Transcription analysis showed that the expression levels of ABA signaling-related genes (FaNCED1, FaPYR1, FaSnRK2, and FaABI5) were affected by FvTCP9. A yeast two-hybrid assay revealed that FvTCP9 interacted physically with FaMYC1 to modulate the biosynthesis process of anthocyanins. Taken together, this study demonstrated that FvTCP9 promoted fruit ripening by regulating the biosynthesis of ABA and anthocyanins.

Genome-Wide Identification, Characterization, and Transcript Analysis of the TCP Transcription Factors in Vitis vinifera

The TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTORS (TCP) protein, belonging to a plant-specific transcription factors (TFs) family, participates in the control of plant growth and development by regulating cell proliferation. Until now, a comprehensive study of concerning the TCP gene family and their roles in grapevine (Vitis vinifera L.) has not been completed. Using bioinformatics approaches, 17 VvTCP genes were identified and further classified into two classes, designated class I (PCF subclass) and class II (CIN and CYC/TB1 subclass), which was further supported by exon-intron organizations and conserved motif analysis. Promoter analysis demonstrated that VvTCPs have numerous cis-acting elements related to plant growth and development, phytohormone, and abiotic/biotic stress responses. The singleton duplication of grapevine TCP genes contributed to this gene family expansion. The syntenic analyses among Vitis vinifera, Arabidopsis, and Oryza sativa showed that these genes located in corresponding syntenic blocks arose before the divergence of V. vinifera, Arabidopsis, and O. sativa. The expression levels of 17 VvTCPs were determined in different tissues and fruit developmental stages, and abscisic acid (ABA) treatment. Seventeen VvTCPs exhibited distinct tissue-specific expression patterns, potentially illustrating the functional divergence of VvTCPs in all tested tissues. Eleven VvTCPs were down-regulated in five berry developmental stages, while three VvTCPs were up-regulated. Additionally, many members were strongly modulated by ABA treatment, suggesting these VvTCPs have important and diverse regulatory roles in ABA treatment. Our results provide valuable information on the evolution and functions of the VvTCPs, pave the way for further functional verification of these VvTCPs in grapevine.

Genome-wide identification and transcript analysis of TCP transcription factors in grapevine

BACKGROUND

The plant-specific TCP transcription factors play different functions in multiple processes of plant growth and development. TCP family genes have been identified in several plant species, but no comprehensive analysis of the TCP family in grapevine has been undertaken to date, especially their roles in fruit development.

RESULTS

A total of 18 non-redundant grapevine TCP (VvTCP) genes distributing on 11 chromosomes were identified. Phylogenetic and structural analysis showed that VvTCP genes were divided into two main classes - class I and class II. The Class II genes were further classified into two subclasses, the CIN subclass and the CYC/TB1 subclass. Segmental duplication was a predominant duplication event which caused the expansion of VvTCP genes. The cis-acting elements analysis and tissue-specific expression patterns of VvTCP genes demonstrated that these VvTCP genes might play important roles in plant growth and development. Expression patterns of VvTCP genes during fruit development and ripening were analyzed by RNA-Seq and qRT-PCR. Among them, 11 VvTCP genes were down-regulated during different fruit developmental stages, while only one VvTCP genes were up-regulated, suggesting that most VvTCP genes were probably related to early development in grapevine fruit. Futhermore, the expression of most VvTCP genes can be inhibited by drought and waterlogging stresses.

CONCLUSIONS

Our study establishes the first genome-wide analysis of the grapevine TCP gene family and provides valuable information for understanding the classification and functions of the TCP genes in grapevine.

Sweet cherry fruit miRNAs and effect of high CO2 on the profile associated with ripening

157 known and 55 novel miRNAs were found in sweet cherry fruit. MiRNA target genes involved in fruit ripening and the differentially expressed miRNAs under CO₂ treatment were identified. MicroRNAs (miRNAs) are short non-coding RNAs and play important functions in many biological processes, including fruit ripening and senescence. In the current study, the high-throughput sequencing and bioinformatics methods were implemented to decipher the miRNAs landscape in sweet cherry fruit. A total of 157 known miRNAs belonging to 50 families and 55 putative novel miRNAs were found. Target genes of the miRNAs were predicted and genes involved in fruit ripening were found, including F-box proteins and TFs such as SPL, TCP, NAC, MYB, ARF and AP2/ERF. And these target genes were further confirmed by degradome sequencing. A regulatory network model was constructed to uncover the miRNAs and their targets involved in fruit ripening and senescence. Importantly, elevated carbon dioxide can significantly postpone the ripening and senescence of sweet cherry fruit and the differentially expressed miRNAs exposed to CO₂ were identified. These miRNAs included miR482j, miR6275, miR164, miR166, miR171, miR393, miR858, miR3627a, miR6284, miR6289 and miR7122b, and some of their functions were linked to fruit ripening. This study was the first report to profile miRNAs in sweet cherry fruit and it would provide more information for further study of miRNA roles in the ripening processes and their regulation mechanism underlying the effects of high carbon dioxide treatment on fruit ripening.

Transcriptome Profile Analysis Reveals that CsTCP14 Induces Susceptibility to Foliage Diseases in Cucumber

Foliage diseases are prevalent in cucumber production and cause serious yield reduction across the world. Identifying resistance or susceptible genes under foliage-disease stress is essential for breeding resistant varieties, of which leaf-specific expressed susceptible genes are extremely important but rarely studied in crops. This study performed an in-depth mining of public transcriptome data both in different cucumber tissues and under downy mildew (DM) inoculation, and found that the expression of leaf-specific expressed transcription factor CsTCP14 was significantly increased after treatment with DM, as well as being upregulated under stress from another foliage disease, watermelon mosaic virus (WMV), in susceptible cucumbers. Furthermore, the Pearson correlation analysis identified genome-wide co-expressed defense genes with CsTCP14. A potential target CsNBS-LRR gene, Csa6M344280.1, was obtained as obviously reduced and was negatively correlated with the expression of the susceptible gene CsTCP14. Moreover, the interaction experiments of electrophoretic mobility shift assay (EMSA) and yeast one-hybrid assay (Y1H) were successfully executed to prove that CsTCP14 could transcriptionally repress the expression of the CsNBS-LRR gene, Csa6M344280.1, which resulted in inducing susceptibility to foliage diseases in cucumber. As such, we constructed a draft model showing that the leaf-specific expressed gene CsTCP14 was negatively regulating the defense gene Csa6M344280.1 to induce susceptibility to foliage diseases in cucumber. Therefore, this study explored key susceptible genes in response to foliage diseases based on a comprehensive analysis of public transcriptome data and provided an opportunity to breed new varieties that can resist foliage diseases in cucumber, as well as in other crops.

The regulatory effects of MeTCP4 on cold stress tolerance in Arabidopsis thaliana: A transcriptome analysis

Cassava (Manihot esculenta), an important food crop in tropical areas, is well-adapted to drought conditions, but is sensitive to cold. The expression of MeTCP4, a transcription factor involved in the regulation of plant development and abiotic stresses responses, was altered under cold stress. However, its biological function under abiotic stress responses is still unclear. Here, we show that increased MeTCP4 expression enhances cold stress tolerance in Arabidopsis (Arabidopsis thaliana). To better understand the biological role of MeTCP4, the mRNA from overexpression and wild-type (WT) plants was isolated for whole genome sequencing to identify MeTCP4-mediated cold-responsive genes. Our results identify 1341 and 797 differentially expressed genes (DEGs) affected by MeTCP4 overexpression under normal and cold conditions, respectively. Gene ontology analysis revealed that a portion of the DEGs were involved in reactive oxygen species (ROS) metabolism process after cold treatment. qRT-PCR analysis revealed that the expression of cold-responsive genes and ROS-scavenging-related genes were increased in MeTCP4 overexpression plant, which could be responsible for the reduced ROS levels and enhanced cold resistance observed in transgenic plant. The findings provide insight into mechanisms of MeTCP4-mediated cold stress response, and provide clues for development of low temperature-tolerant cassava cultivars.

The trihelix family of transcription factors: functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis)

BACKGROUND

Trihelix transcription factors (TTFs) are photoresponsive proteins that have a representative three-helix structure (helix-loop-helix-loop-helix). Members of this gene family have been reported to play roles in many plant processes.

RESULTS

In this study, we performed a functional and evolutionary analysis of the TTFs in Moso bamboo (Phyllostachys edulis). A total of 35 genes were identified and grouped into five subfamilies (GT-1, GT-γ, GT-2, SIP1 and SH4) according to their structural properties. Gene structure analysis showed that most genes in the PeTTF family had fewer introns. A unique motif (Motif 16) to the GT-γ subfamily was identified by conserved motif analysis. Promoter analysis revealed various cis-acting elements related to plant growth and development, abiotic and biotic stresses, and phytohormone responses. Data for the 35 Moso bamboo TTF genes were used to generate heat maps, which indicated that these genes were expressed in different tissues or developmental stages. Most of the TTF genes identified here had high expression in leaves and panicles according to the expression profile analysis. The expression levels of the TTF members in young leaves were studied using quantitative real-time PCR to determine their tissue specificity and stress-related expression patterns to help functionally characterize individual members.

CONCLUSIONS

The results indicated that members of the TTF gene family may be involved in plant responses to stress conditions. Additionally, PeTTF29 was shown to be located in the nucleus by subcellular localization analysis and to have transcriptional activity in a transcriptional activity assay. Our research provides a comprehensive summary of the PeTTF gene family, including functional and evolutionary perspectives, and provides a basis for functionally characterizing these genes.

Evolution of RADIALIS and DIVARICATA gene lineages in flowering plants with an expanded sampling in non-core eudicots

PREMISE OF THE STUDY

Bilateral symmetry in core eudicot flowers is established by the differential expression of CYCLOIDEA (CYC), DICHOTOMA (DICH), and RADIALIS (RAD), which are restricted to the dorsal portion of the flower, and DIVARICATA (DIV), restricted to the ventral and lateral petals. Little is known regarding the evolution of these gene lineages in non-core eudicots, and there are no reports on gene expression that can be used to assess whether the network predates the diversification of core eudicots.

METHODS

Homologs of the RAD and DIV lineages were isolated from available genomes and transcriptomes, including those of three selected non-core eudicot species, the magnoliid Aristolochia fimbriata and the monocots Cattleya trianae and Hypoxis decumbens. Phylogenetic analyses for each gene lineage were performed. RT-PCR was used to evaluate the expression and putative contribution to floral symmetry in dissected floral organs of the selected species.

KEY RESULTS

RAD-like genes have undergone at least two duplication events before eudicot diversification, three before monocots and at least four in Orchidaceae. DIV-like genes also duplicated twice before eudicot diversification and underwent independent duplications specific to Orchidaceae. RAD-like and DIV-like genes have differential dorsiventral expression only in C. trianae, which contrasts with the homogeneous expression in the perianth of A. fimbriata.

CONCLUSIONS

Our results point to a common genetic regulatory network for floral symmetry in monocots and core eudicots, while alternative genetic mechanisms are likely driving the bilateral perianth symmetry in the early-diverging angiosperm Aristolochia.

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

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.

Ectopic expression of FvWRKY42, a WRKY transcription factor from the diploid woodland strawberry (Fragaria vesca), enhances resistance to powdery mildew, improves osmotic stress resistance, and increases abscisic acid sensitivity in Arabidopsis

WRKY transcription factors play a critical role in biotic and abiotic stress responses in plants, but very few WRKYs have been reported in strawberry plants. Here, a multiple stress-inducible gene, FvWRKY42, was isolated from the wild diploid woodland strawberry (accession Heilongjiang-3). FvWRKY42 expression was induced by treatment with powdery mildew, salt, drought, salicylic acid (SA), methyl jasmonate (MeJA), abscisic acid (ABA), and ethylene. The protein interaction network analysis showed that the FvWRKY42 protein interacts with various stress-related proteins. Overexpression of FvWRKY42 in Arabidopsis resulted in cell death, sporulation, slow hypha growth, and enhanced resistance to powdery mildew that was concomitant with increased expression of PR1 genes in Arabidopsis. Overexpression also led to enhanced salt and drought stress tolerance, increased primary root length and germination rate, decreased water loss rate, reduced relative electrolyte leakage, and malondialdehyde accumulation, and upregulation of superoxide dismutase and catalase activity. Additionally, FvWRKY42-overexpressing Arabidopsis plants showed increased ABA sensitivity during seed germination and seedling growth, increased stomatal closure after ABA and drought treatment, and altered expression of ABA-responsive genes. Collectively, our data demonstrate that FvWRKY42 may play an important role in powdery mildew infection and the regulation of salt and drought stress responses in plants.

Genetic diversity of strawberry germplasm using metabolomic biomarkers

High-throughput metabolomics technologies can provide the quantification of metabolites levels across various biological processes in different tissues, organs and species, allowing the identification of genes underpinning these complex traits. Information about changes of metabolites during strawberry development and ripening processes is key to aiding the development of new approaches to improve fruit attributes. We used network-based methods and multivariate statistical approaches to characterize and investigate variation in the primary and secondary metabolism of seven domesticated and seven wild strawberry fruit accessions at three different fruit development and ripening stages. Our results demonstrated that Fragaria sub-species can be identified solely based on the gathered metabolic profiles. We also showed that domesticated accessions displayed highly similar metabolic changes due to shared domestication history. Differences between domesticated and wild accessions were detected at the level of metabolite associations which served to rank metabolites whose regulation was mostly altered in the process of domestication. The discovery of comprehensive metabolic variation among strawberry accessions offers opportunities to probe into the genetic basis of variation, providing insights into the pathways to relate metabolic variation with important traits.

Heterodimerization of MaTCP proteins modulates the transcription of MaXTH10/11 genes during banana fruit ripening

The biological processes involved in banana fruit ripening are extremely complex and modulated by a number of genes such as transcription factors (TFs). Although TFs like MADS, ERF and NAC are implicated in controlling banana ripening, little is known about other TFs such as TCP in this process. In this work, 25 MaTCPs named MaTCP1 to MaTCP25 were characterized from our previously reported transcriptomes related to banana ripening. Expression analysis revealed that these MaTCPs displayed differential expression patterns during the progression of banana ripening. Particularly, MaTCP5, MaTCP19 and MaTCP20 were ethylene-inducible and nuclear-localized, with MaTCP5 and MaTCP20 acting as transcriptional activators while MaTCP19 being a transcriptional inhibitor. Moreover, MaTCP5 and MaTCP20 promoted the transcription of MaXTH10/11 that may play a role in fruit softening during banana ripening, whereas MaTCP19 repressed their transcription, by directly binding to their promoters. Importantly, protein-protein interaction assays demonstrated that MaTCP20 physically interacts with MaTCP5 and MaTCP19 to form heterodimers in vitro and in vivo, and these protein complexes affects their transcriptional activities in regulating the target genes. Taken together, our results provide an overview of the interactions between MaTCPs in controlling the ripening-associated genes and lay a foundation for further investigation of MaTCP gene family in regulating banana fruit ripening.

Genome-Wide Identification of TCP Family Transcription Factors in Medicago truncatula Reveals Significant Roles of miR319-Targeted TCPs in Nodule Development

TCP proteins, the plant-specific transcription factors, are involved in the regulation of multiple aspects of plant development among different species, such as leaf development, branching, and flower symmetry. However, thus far, the roles of TCPs in legume, especially in nodulation are still not clear. In this study, a genome-wide analysis of TCP genes was carried out to discover their evolution and function in Medicago truncatula. In total, 21 MtTCPs were identified and classified into class I and class II, and the class II MtTCPs were further divided into two subclasses, CIN and CYC/TB1. The expression profiles of MtTCPs are dramatically different. The universal expression of class I MtTCPs was detected in all organs. However, the MtTCPs in CIN subclass were highly expressed in leaf and most of the members in CYC/TB1 subclass were highly expressed in flower. Such organ-specific expression patterns of MtTCPs suggest their different roles in plant development. In addition, most MtTCPs were down-regulated during the nodule development, except for the putative MtmiR319 targets, MtTCP3, MtTCP4, and MtTCP10A. Overexpression of MtmiR319A significantly reduced the expression level of MtTCP3/4/10A/10B and resulted in the decreased nodule number, indicating the important roles of MtmiR319-targeted MtTCPs in nodulation. Taken together, this study systematically analyzes the MtTCP gene family at a genome-wide level and their possible functions in nodulation, which lay the basis for further explorations of MtmiR319/MtTCPs module in association with nodule development in M. truncatula.