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Sequence alignment of petunia miR156/157 complementary sequences with the target sites in PhSPL genes. The target sites are located in the coding regions with the exception of PhSPL3, PhSPL4a, PhSPL4b and PhSPL4c where they are located in the 3'-UTR. RC, reverse complementary sequence of the mature petunia miR156/157
Source publication
Background:
SQUAMOSA PROMOTER BINDING PROTEIN (SBP)-box genes encode a family of plant-specific transcription factors (TFs) that play important roles in many growth and development processes including phase transition, leaf initiation, shoot and inflorescence branching, fruit development and ripening etc. The SBP-box gene family has been identifie...
Contexts in source publication
Context 1
... genome, which produced three kinds of mature miRNA sequences (miR0156a-g, miR0156j-l and miR0157a-e) [50]. A com- parison of the mature PhmiR156/157 sequences to PhSPLs transcript sequences showed that 14 out of 21 PhSPL genes contained sequences complementary to the PhmiR156 or PhmiR157 mature sequences with one to two mismatches as maximum (Fig. 6), which suggests that PhmiR156/157 may specifically target these gene in petunia. These putative miR156/157 response elements (MREs) of PhSPL genes were located downstream of the SBP-box in the coding region of genes in groups IV (PhSPL6a-e), V (PhSPL2), VII (PhSPL13) and VIII (PhSPL9a/b/c), while in the case of members in Group VI ...
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... faster loss of some members in other Solanaceae species. For instance, there are two orthologs in petunia corresponding to one gene in tomato for several members, such as PhSPL4a and PhSPL4b vs. SlySBP4, PhSPL6a and PhSPL6b vs. SlySBP6b, PhSPL12a and PhSPL12c vs. SlySBP12a, PhSPL12b and PhSPL12d vs. SlySBP12b, and PhSPL9a and PhSPL9b vs. SlySBP15 (Fig. 6). The PhSPL12b and PhSPL12d gene pair was evidently produced by a more recent additional duplication in Petunia, but for other mem- bers it also could be resulted from the loss of dupli- cated genes in tomato. In addition, tomato has no counterparts of PhSPL4c and PhSPL9c, suggesting they may also had lost. The duplicated genes are ...
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... PhSPL genes were potential targets of PhmiR156/157. All the putative PhmiR156-targeted PhSPL genes were clustered into groups IV to VIII, and miR156/157-targeting sites in 10 PhSPLs belonging to groups IV, V, VII and VIII locate in the coding region, while the target sites for other 4 PhSPLs belonging to group VI locate in the 3' UTRs (Fig. 6), which is consistent with the results from other plants [58], suggesting miR156/157-mediated post- transcriptional regulation of SPLs is a highly conserved mechanism in plants. In animals, miRNAs are prone to act by repressing translation and their target sites are mostly found in 3' UTRs, however, plant miRNAs were believed to exert ...
Citations
... The analysis of the conserved motifs and gene structure could help in understanding the evolution of the SPL family genes [41,42]. The analysis results show that the peanut SPL members within the same group have a similar motif arrangement and gene structure (Figure 2), supporting the reliability of the phylogenetic analysis and the evolutionarily conserved features of the peanut SPL family. ...
SPL (SQUAMOSA promoter binding protein-like), as one family of plant transcription factors, plays an important function in plant growth and development and in response to environmental stresses. Despite SPL gene families having been identified in various plant species, the understanding of this gene family in peanuts remains insufficient. In this study, thirty-eight genes (AhSPL1-AhSPL38) were identified and classified into seven groups based on a phylogenetic analysis. In addition, a thorough analysis indicated that the AhSPL genes experienced segmental duplications. The analysis of the gene structure and protein motif patterns revealed similarities in the structure of exons and introns, as well as the organization of the motifs within the same group, thereby providing additional support to the conclusions drawn from the phylogenetic analysis. The analysis of the regulatory elements and RNA-seq data suggested that the AhSPL genes might be widely involved in peanut growth and development, as well as in response to environmental stresses. Furthermore, the expression of some AhSPL genes, including AhSPL5, AhSPL16, AhSPL25, and AhSPL36, were induced by drought and salt stresses. Notably, the expression of the AhSPL genes might potentially be regulated by regulatory factors with distinct functionalities, such as transcription factors ERF, WRKY, MYB, and Dof, and microRNAs, like ahy-miR156. Notably, the overexpression of AhSPL5 can enhance salt tolerance in transgenic Arabidopsis by enhancing its ROS-scavenging capability and positively regulating the expression of stress-responsive genes. These results provide insight into the evolutionary origin of plant SPL genes and how they enhance plant tolerance to salt stress.
... For example, in CcaSBP2, in the first zinc-binding site, C3H, histidine was replaced by cysteine and in second zincbinding site, C2HC, serine is replaced by glycine. Such amino acid substitutions are also found in other species like cotton (Ali et al., 2017), Arabidopsis (Yang et al., 2008), and Petunia (Zhou et al., 2018). ...
Background: Worldwide, Pigeonpea (Cajanus cajan L.) is a protein source. SBP-box transcription factors are crucial for plant development and regulation of stress resistance. The SBP genes in Pigeonpea were examined utilizing genomic information. Methods: Using databases, PlantTFDB and NCBI, SBP-box family genes of Pigeonpea were identified and then characterized in silico using bioinformatics tools. Results: In this study, 5 major chromosomes out of 11 and an unplaced scaffold of the Pigeonpea were found to have 24 SBP genes. Significant differences in CcaSBPs protein length, molecular weight, GRAVY value (grand average of hydropathicity), and theoretical isoelectric point were observed. It was shown by Gene Structure Display Server (GSDS) that all CcaSBP genes contain one or more introns. CcaSBP proteins and SBP proteins from other species (A. thaliana and O. sativa) were analyzed phylogenetically and grouped into seven major groups (I–VII). Through this, an effort has been made to present unique information on CcaSBP genes to study Pigeonpea growth and stress mechanisms.
... The transition of plants from the juvenile to adult phases is mostly facilitated by the miR156-SPL module [19,33]. Several prior research have shown the collaborative role of microRNA 156 (miR156) and its target SPL transcription factor in the regulation of the blooming transition process in plants [19,25,34]. ...
... The findings of the phylogenetic tree analysis were categorised into five groups, consistent with earlier studies on SPL genes in Arabidopsis and tartary buckwheat [33,40]. The similarity in structural characteristics and motif composition within the same group provides additional evidence for their placement in the phylogenetic tree ( Figure 1B), suggesting a correlation between the functional evolution of SPL genes and their varied structures and conserved motifs [38,39]. ...
SPL transcription factors affect plant growth and development, including blooming and photoperiod control. The investigation began with transcriptome data screening of 28 JrSPL genes in walnut (Junglans regia L.) ‘Wen185’. These genes were discovered on all chromosomes except 6 and 15. Phylogenetic study divides the 28 JrSPL genes into five groupings. The biggest cluster, cluster IV, has 12 JrSPL genes. The expression of JrSPL genes in different tissues was investigated by qRT-PCR. JrSPL02 gene expression was greater in walnut female and male flower tissues than other genes. Subcellular localization has shown the JrSPL02 gene resides in the nucleus. Jre-miR156 may target JrSPL02’s 3′-UTR region, according to miRNA sequencing, RACE, and BiFC studies. Arabidopsis plants expressing the JrSPL02 gene flowered 3 days faster than the wild type, according to phenotypic observation. Transgenic lines had more stem branches and siliques than the control group but fewer rosette leaves. In summary, this study functionally analyses the metamorphosis of the miR156-SPL module during the blooming stage and the underlying mechanisms that govern early fruiting in early-fruiting walnuts in Xinjiang.
... Compared with those of the WT plants, the MiSPL3a/b-OE lines promoted early flowering, the number of rosette leaves was lower, and the expression of AtSOC1, AtAP1, and AtFUL was upregulated. Most of the SPL-like genes had similar functions, such as PhSPL9a/b [42], AfSPL14 [43], TaSPL16 [44] and FmSPL2 [45], suggesting the MiSPL family might have conserved functions in promoting the transition from vegetative to reproductive growth. ...
... In organisms, gene expression is often a prerequisite for gene function, and gene expression patterns are usually related to gene function [55]. The SPL gene is widely involved in plant growth and development and plays a vital role in promoting the transition of plants from the seedling stage to the mature stage [56,57]. ...
Background
SPL transcription factors play vital roles in regulating plant growth, development, and abiotic stress responses. Sugar beet (Beta vulgaris L.), one of the world’s main sugar-producing crops, is a major source of edible and industrial sugars for humans. Although the SPL gene family has been extensively identified in other species, no reports on the SPL gene family in sugar beet are available.
Results
Eight BvSPL genes were identified at the whole-genome level and were renamed based on their positions on the chromosome. The gene structure, SBP domain sequences, and phylogenetic relationship with Arabidopsis were analyzed for the sugar beet SPL gene family. The eight BvSPL genes were divided into six groups (II, IV, V, VI, VII, and VIII). Of the BvSPL genes, no tandem duplication events were found, but one pair of segmental duplications was present. Multiple cis-regulatory elements related to growth and development were identified in the 2000-bp region upstream of the BvSPL gene start codon (ATG). Using quantitative real-time polymerase chain reaction (qRT-PCR), the expression profiles of the eight BvSPL genes were examined under eight types of abiotic stress and during the maturation stage. BvSPL transcription factors played a vital role in abiotic stress, with BvSPL3 and BvSPL6 being particularly noteworthy.
Conclusion
Eight sugar beet SPL genes were identified at the whole-genome level. Phylogenetic trees, gene structures, gene duplication events, and expression profiles were investigated. The qRT-PCR analysis indicated that BvSPLs play a substantial role in the growth and development of sugar beet, potentially participating in the regulation of root expansion and sugar accumulation.
... Many studies have revealed that SBP genes are TFs with multiple functions involved in leaf, flower, and fruit development, vegetative phase change, and the signal transduction of plants [4][5][6][7][8][9][10]39]. The SBP-box gene family has been identified and investigated in numerous plants, such as A. thaliana [3], rice [3], tomato [40], tobacco [41], soybean [42], pepper [43], apple [44], castor bean [45], Populus [46], and Petunia [47]. However, the SBP-box gene family has not been characterized in the loquat, a subtropical fruit tree with delicious fruit. ...
The loquat (Eriobotrya japonica L.) is a special evergreen tree, and its fruit is of high medical and health value as well as having stable market demand around the world. In recent years, research on the accumulation of nutrients in loquat fruit, such as carotenoids, flavonoids, and terpenoids, has become a hotspot. The SBP-box gene family encodes transcription factors involved in plant growth and development. However, there has been no report on the SBP-box gene family in the loquat genome and their functions in carotenoid biosynthesis and fruit ripening. In this study, we identified 28 EjSBP genes in the loquat genome, which were unevenly distributed on 12 chromosomes. We also systematically investigated the phylogenetic relationship, collinearity, gene structure, conserved motifs, and cis-elements of EjSBP proteins. Most EjSBP genes showed high expression in the root, stem, leaf, and inflorescence, while only five EjSBP genes were highly expressed in the fruit. Gene expression analysis revealed eight differentially expressed EjSBP genes between yellow- and white-fleshed fruits, suggesting that the EjSBP genes play important roles in loquat fruit development at the breaker stage. Notably, EjSBP01 and EjSBP19 exhibited completely opposite expression patterns between white- and yellow-fleshed fruits during fruit development, and showed a close relationship with SlCnr involved in carotenoid biosynthesis and fruit ripening, indicating that these two genes may participate in the synthesis and accumulation of carotenoids in loquat fruit. In summary, this study provides comprehensive information about the SBP-box gene family in the loquat, and identified two EjSBP genes as candidates involved in carotenoid synthesis and accumulation during loquat fruit development.
... To reveal the association of TaAAO genes with biotic and abiotic stresses, their expression study is carried out using diverse sets of data for various treatments. The modulated could be associated with the development (Wang et al. 2018;Masiero et al. 2011;Zhou et al. 2018). Similarly, the hormone-responsive cis-elements and TFs such as ARR-B, EIL, ERF, and ARF indicate the probable role of AAO genes in hormone-mediated signaling (Yokoyama et al. 2007;Wu et al. 2022;Tiwari et al. 2003). ...
Ascorbate oxidases (AAOs) are apoplastic enzymes of the multi-copper oxidase family and have a significant role in redox homeostasis. Herein, we identified 14 TaAAO genes consisting of two to five exons in the bread wheat genome. These genes are present on the A, B, and D subgenomes of chromosomes 5 and 7. Analyses of gene regulatory networks revealed the occurrence of growth and development, phytohormones, light, and stress-responsive cis-regulatory elements, which interact with a diverse range of transcription factors in the promoter region of these genes. Additionally, a few TaAAO genes showed miRNA-mediated regulation. The TaAAO proteins consisted of three conserved domains; Cu_oxidase1, Cu_oxidase2, and Cu_oxidase3, and clustered into two phylogenetic groups. The majority of TaAAOs showed higher expression in roots, and mostly upregulated at 6 h of salt stress. Further, a few genes also showed modulated expression in other vegetative and reproductive tissues, and in heat stress, drought stress and fungal infestations. The interaction of TaAAO proteins with antioxidant enzymes such as dehydroascorbate reductases, ascorbate peroxidases, monodehydroascorbate reductases, etc., and related molecules like ascorbic acid and dehydroascorbate exposed their synchronized functioning in redox homeostasis. These results revealed the varied functions of TaAAOs from development to the stress response. The current study will lay the groundwork to find out the detailed function of each gene in upcoming investigations.
... Gene amplification is the main driver for generating new functional genes during evolution and can be divided into segmental duplications and tandem replication [55]. Compared to segmental replication, tandem duplication events occupy a larger proportion of plant genomes, with an approximately 10% incidence in Arabidopsis and rice [56,57]. We found more bZIP proteins in pea compared with V. vinifera (55), A. thaliana (75), and S. lycopersic (69), indicating that there are likely more gene duplication events in pea. ...
Background
Basic leucine zipper (bZIP) protein is a plant-specific transcription factor involved in various biological processes, including light signaling, seed maturation, flower development, cell elongation, seed accumulation protein, and abiotic and biological stress responses. However, little is known about the pea bZIP family.
Results
In this study, we identified 87 bZIP genes in pea, named PsbZIP1 ~ PsbZIP87, via homology analysis using Arabidopsis. The genes were divided into 12 subfamilies and distributed unevenly in 7 pea chromosomes. PsbZIPs in the same subfamily contained similar intron/exon organization and motif composition. 1 tandem repeat event and 12 segmental duplication events regulated the expansion of the PsbZIP gene family. To better understand the evolution of the PsbZIP gene family, we conducted collinearity analysis using Arabidopsis thaliana, Oryza sativa Japonica, Fagopyrum tataricum, Solanum lycopersicum, Vitis vinifera, and Brachypodium distachyon as the related species of pea. In addition, interactions between PsbZIP proteins and promoters containing hormone- and stress-responsive cis-acting elements suggest that the regulation of PsbZIP expression was complex. We also evaluated the expression patterns of bZIP genes in different tissues and at different fruit development stages, all while subjecting them to five hormonal treatments.
Conclusion
These results provide a deeper understanding of PsbZIP gene family evolution and resources for the molecular breeding of pea. The findings suggested that PsbZIP genes, specifically PSbZIP49, play key roles in the development of peas and their response to various hormones.
... The SBP (SQUAMOSA PROMOTER-BINDING PRO-TEIN), also known as SPL (SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE), is a plant-specific transcription factor. SBP transcription factors contain a highly conserved amino acid sequence, referred to as the SBPconserved structural domain, consisting of two zinc finger structures and a nuclear localization signal [24][25][26][27]. SBP transcription factor contains two zinc finger motifs, the first zinc finger structure located at the N-terminal end and usually contains two types of C3H (Cys-Cys-Cys-His, CysHis) or C4 (Cys-Cys-Cys-Cys-Cys, Cys4). ...
... Since the first SBP gene was identified in Antirrhinum majus, the SBP gene family has been identified and studied in numerous plants [29].In addition, the grouping of SBP gene family members varied among plants. SBP genes could be classified into eight branches in most plants, such as tomato [30], Arabidopsis [31], Petunia [24], apple [32], Gossypium [33], tobacco [34], oilseed rape [29], and moso bamboo [35]. However, there are seven branches in grapes [36], and six branches in poplar [37] and pepper [38]. ...
Background
Chimonanthus praecox and Chimonanthus salicifolius are closely related species that diverged approximately six million years ago. While both C. praecox and C. salicifolius could withstand brief periods of low temperatures of – 15 °C. Their flowering times are different, C. praecox blooms in early spring, whereas C. salicifolius blooms in autumn. The SBP-box (SQUAMOSA promoter-binding protein) is a plant-specific gene family that plays a crucial vital role in regulating plant flowering. Although extensively studied in various plants, the SBP gene family remains uncharacterized in Calycanthaceae.
Methods and results
We conducted genome-wide identification of SBP genes in both C. praecox and C. salicifolius and comprehensively characterized the chromosomal localization, gene structure, conserved motifs, and domains of the identified SBP genes. In total, 15 and 18 SBP genes were identified in C. praecox and C. salicifolius, respectively. According to phylogenetic analysis, the SBP genes from Arabidopsis, C. praecox, and C. salicifolius were clustered into eight groups. Analysis of the gene structure and conserved protein motifs showed that SBP proteins of the same subfamily have similar motif structures. The expression patterns of SBP genes were analyzed using transcriptome data. The results revealed that more than half of the genes exhibited lower expression levels in leaves than in flowers, suggesting their potential involvement in the flower development process and may be linked to the winter and autumn flowering of C. praecox and C. salicifolius.
Conclusion
Thirty-three SBPs were identified in C. praecox and C. salicifolius. The evolutionary characteristics and expression patterns were examined in this study. These results provide valuable information to elucidate the evolutionary relationships of the SBP family and help determine the functional characteristics of the SBP genes in subsequent studies.
... Gene amplification is the main driver for the generation of new functional genes during evolution, which is divided into two types: segmental duplications and tandem replication. Compared to segmental replication [48], tandem duplication events reprensent a larger proportion of plant genomes, with an approximately 10% incidence in Arabidopsis and rice [49,50]. We found more HSF proteins in Rye compared with A. tauschii Coss (19), A. thaliana (21), Z. mays (25), and O. sativa (26). ...
... Based on the fact that homologous genes with similar structures may have similar functions, it is speculated that ScHSF23 may be related to root growth and development. Overexpression of AtHSFA2 in A. thaliana increases stress tolerance, and enhanced callus growth [49,54]. The ScHSF1, ScHSF 2, ScHSF 14, ScHSF 15, ScHSF 16, ScHSF 25, and ScHSF 31 belong to A2 subfamily, which had high similarity to AtHSFA2.. ...
Background
Heat shock factor (HSF), a typical class of transcription factors in plants, has played an essential role in plant growth and developmental stages, signal transduction, and response to biotic and abiotic stresses. The HSF genes families has been identified and characterized in many species through leveraging whole genome sequencing (WGS). However, the identification and systematic analysis of HSF family genes in Rye is limited.
Results
In this study, 31 HSF genes were identified in Rye , which were unevenly distributed on seven chromosomes. Based on the homology of A. thaliana , we analyzed the number of conserved domains and gene structures of ScHSF genes that were classified into seven subfamilies. To better understand the developmental mechanisms of ScHSF family during evolution, we selected one monocotyledon ( Arabidopsis thaliana ) and five ( Triticum aestivum L., Hordeum vulgare L . , Oryza sativa L . , Zea mays L., and Aegilops tauschii Coss.) specific representative dicotyledons associated with Rye for comparative homology mapping. The results showed that fragment replication events modulated the expansion of the ScHSF genes family. In addition, interactions between ScHSF proteins and promoters containing hormone- and stress-responsive cis-acting elements suggest that the regulation of ScHSF expression was complex. A total of 15 representative genes were targeted from seven subfamilies to characterize their gene expression responses in different tissues, fruit developmental stages, three hormones, and six different abiotic stresses.
Conclusions
This study demonstrated that ScHSF genes, especially ScHSF1 and ScHSF3 , played a key role in Rye development and its response to various hormones and abiotic stresses. These results provided new insights into the evolution of HSF genes in Rye , which could help the success of molecular breeding in Rye .
