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-Sequence alignments of maize miR156 with their complementary sequence in the coding sequences and 3' UTRs of ZmSPLs.
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SPLs are plant-specific transcription factors that play important regulatory roles in plant growth and development. Systematic analysis of the SPL family has been performed in numerous plants, such as Arabidopsis, rice, and Populus. However, no comparative analysis has been performed across different species to examine evolutionary features. In thi...
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... also found that the targeting sites of miR156 were located in coding regions for 11 ZmSPLs, and only two complementary sites were located in the 3' UTRs ( ZmSPL7 and ZmSPL26). Consistent with previous studies, the targeting sites of maize SPLs were highly conserved in the evolution by the alignments of miR156 with their complementary sequence of maize SPLs ( Figure 6). ...
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Citations
... SBP was first successfully cloned from a Antirrhinum majus cDNA library [9]. Subsequently, SPL genes have been found in multiple species, including rice (Oryza sativa) [10], maize (Zea mays) [11], sweet cherry (Prunus avium) [12], quinoa (Chenopodium quinoa) [13], millet (Setaria italica) [8], and Arabidopsis [10]. ...
... In the present study, segmental duplication events were the main sources of the SPL family expansion in the peanut, rather than tandem duplication events ( Figure 4B). Comparable results have also been obtained in other plant SPL gene groups, including maize [11], potato [38], and rice [10]. In addition, the twenty-four pairs of AhSPL genes all exhibited Ka/Ks values less than one (Supplementary Table S2), suggesting that purifying selection may have influenced the evolution of these AhSPL genes in the peanut. ...
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.
... These Arabidopsis SPL family members have been shown to play important roles in the development of Arabidopsis stems, leaves, and flowers [29][30]. To date, whole-genome identification and analysis of SPL transcription factors in many plants have been completed, including Arabidopsis [24,28], rice [31,32], millet [33], quinoa [34], corn [35], tomato [36], buckwheat [37], barley [38], and wheat [39]. ...
... In the evolution of the sugar beet SPL transcription factor family, three monocotyledonous plants (O. sativa [31][32], Z. mays [35], and S. bicolor [35]) and three dicotyledonous plants (A. thaliana [24][25][26][27][28], S. lycopersicum [36], and F. titanium [37]) were selected for a comparative analysis of the SPL transcription factor families (Fig. 4). ...
... In the evolution of the sugar beet SPL transcription factor family, three monocotyledonous plants (O. sativa [31][32], Z. mays [35], and S. bicolor [35]) and three dicotyledonous plants (A. thaliana [24][25][26][27][28], S. lycopersicum [36], and F. titanium [37]) were selected for a comparative analysis of the SPL transcription factor families (Fig. 4). ...
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.
... LG1 is a member of the SBP family, which are special transcription factors in plants that contribute to growth and development as well as various physiological and biochemical processes (Klein et al., 1996;Cardon et al., 1999;Birkenbihl et al., 2005;Xie et al., 2006;Guo et al., 2008;Chen et al., 2010;Preston and Hileman, 2013;Zhang et al., 2016;Peng et al., 2019). SBP family proteins comprise 80 conserved amino acids, two conserved zinc finger domains (Zn1 and Zn2) and a C-terminal nuclear localization signal. ...
Plant architecture is a culmination of the features necessary for capturing light energy and adapting to the environment. An ideal architecture can promote an increase in planting density, light penetration to the lower canopy, airflow as well as heat distribution to achieve an increase in crop yield. A number of plant architecture-related genes have been identified by map cloning, quantitative trait locus (QTL) and genome-wide association study (GWAS) analysis. LIGULELESS1 (LG1) belongs to the squamosa promoter-binding protein (SBP) family of transcription factors (TFs) that are key regulators for plant growth and development, especially leaf angle (LA) and flower development. The DRL1/2-LG1-RAVL pathway is involved in brassinosteroid (BR) signaling to regulate the LA in maize, which has facilitated the regulation of plant architecture. Therefore, exploring the gene regulatory functions of LG1, especially its relationship with LA genes, can help achieve the precise regulation of plant phenotypes adapted to varied environments, thereby increasing the yield. This review comprehensively summarizes the advances in LG1 research, including its effect on LA and flower development. Finally, we discuss the current challenges and future research goals associate with LG1.
... MiR156 and its target SPL genes play vital roles in regulating plant growth and development (Ferreirae Silva et al., 2014;Gandikota et al., 2007;Manning et al., 2006). The SPL gene family has been identified in many green plants, such as Arabidopsis (Xu et al., 2016), wheat , maize (Peng et al., 2019), rice (Xie et al., 2006), and M. truncatula (Wang et al., 2019a). We identified 26 MsSPL genes in the M. sativa genome using a genome-wide screening. ...
To improve alfalfa (Medicago sativa) biomass yield and abiotic stress resistance is a challenge due to its autotetraploidy and self-incompatibility. Previously we have generated transgenic alfalfa lines overexpressing miR156 and showing excellent plant architecture. In this study, we investigated the regulation network of miR156 in these transgenic alfalfa lines. Based on 83,202 non-redundant full-length transcripts in a pool of roots, stems, leaves, flowers, pods, and apical buds, we identified 154 candidate genes as potential downstream targets of miR156, especially for M. sativa SQUAMOSA promoter binding protein-like genes (MsSPLs), and then identified 26 MsSPL gene family members in alfalfa genome. The expressions of MsSPL5B and MsSPL3 were downregulated in root and leaf respectively, whereas that of MsSPL4 was significantly downregulated in stem, leaf, root, and apical bud tissues due to miR156 overexpression. We revealed the key role of MsSPL4-mediated regulatory pathways in the substantial correlations between agronomic traits and gene expression, and further found several involved hub genes showing significant correlation with MsSPL4. In addition, MsSPL4 overexpression in tobacco enhanced salinity tolerance but inhibited bud induction. Our results provide strong evidence for understanding the roles of miR156 and MsSPLs in regulating plant architecture and abiotic stress responses in alfalfa.
... For instance, we found that all SPL genes were significantly up-regulated in stems and leaves in response to cold and UV treatments. This finding suggests that it may be possible to adapt quinoa for growth at high altitudes due to its potential cold tolerance and UV resistance [58]. We also found that the expression of SPL genes was significantly up-regulated in leaves and stems in response to all six abiotic stress treatments. ...
Background
Squamous promoter binding protein-like (SPL) proteins are a class of transcription factors that play essential roles in plant growth and development, signal transduction, and responses to biotic and abiotic stresses. The rapid development of whole genome sequencing has enabled the identification and characterization of SPL gene families in many plant species, but to date this has not been performed in quinoa ( Chenopodium quinoa ).
Results
This study identified 23 SPL genes in quinoa, which were unevenly distributed on 18 quinoa chromosomes. Quinoa SPL genes were then classified into eight subfamilies based on homology to Arabidopsis thaliana SPL genes. We selected three dicotyledonous and monocotyledonous representative species, each associated with C. quinoa , for comparative sympatric mapping to better understand the evolution of the developmental mechanisms of the CqSPL family. Furthermore, we also used 15 representative genes from eight subfamilies to characterize CqSPL s gene expression in different tissues and at different fruit developmental stages under six different abiotic stress conditions.
Conclusions
This study, the first to identify and characterize SPL genes in quinoa, reported that CqSPL genes, especially CqSPL1 , play a critical role in quinoa development and in its response to various abiotic stresses.
... AthmiR156targeted SPL13 downregulated to enhance the tolerance of drought (Beveridge & Kyozuka, 2010). Besides, miR156 -targeted SPL2/9/11 genes neutralized negative effects of upregulated miR156 under heat stress in plant growth and TcSPLs in tamarisk showed a critical post-transcription regulation at 1 h under salt stress (Stief et al., 2014;Wang et al., 2019). ...
... In this study, we identified 21 CnSBP family genes from C. nankingense genome and provided new insights for comprehensive understanding of the SBP-box genes in non-model plants (Fig. 1). Compared with crops, cotton (83 GhSBPs), maize (42 ZmSBPs), oilseed rape (58 BnaSBP) and wheat (50 TaSBPs), C. nankingense contained much less SBP-box genes (Zhang et al., 2015;Cheng et al., 2016;Peng et al., 2019;Li et al., 2020), but resembled the model plant Arabidopsis (17 AtSPLs), flowering plants petunia (21 PhSPLs), Prunus persica (17 PpSPLs), Prunus mume (17 PmSPLs) and Rosa rugosa (17 RcSPLs), indicating that the SBP-box family genes endowed with more diversified and complicated functions with species specificity. It could be a consequence of the divergence of flowering responsive functions in SBP-box genes. ...
SQUAMOSA promoter-binding-protein (SBP)-box family proteins are a class of plant-specific transcription factors, and widely regulate the development of floral and leaf morphology in plant growth and involve in environment and hormone signal response. In this study, we isolated and identified 21 non-redundant SBP-box genes in Chrysanthemum nankingense with bioinformatics analysis. Sequence alignments of 21 CnSBP proteins discovered a highly conserved SBP domain including two zinc finger-like structures and a nuclear localization signal region. According to the amino acid sequence alignments, 67 SBP-box genes from Arabidopsis thaliana , rice, Artemisia annua and C. nankingense were clustered into eight groups, and the motif and gene structure analysis also sustained this classification. The gene evolution analysis indicated the CnSBP genes experienced a duplication event about 10 million years ago (Mya), and the CnSBP and AtSPL genes occurred a divergence at 24 Mya. Transcriptome data provided valuable information for tissue-specific expression profiles of the CnSBPs , which highly expressed in floral tissues and differentially expressed in leaf, root and stem organs. Quantitative Real-time Polymerase Chain Reaction data showed expression patterns of the CnSBPs under exogenous hormone and abiotic stress treatments, separately abscisic acid, salicylic acid, gibberellin A3, methyl jasmonate and ethylene spraying as well as salt and drought stresses, indicating that the candidate CnSBP genes showed differentiated spatiotemporal expression patterns in response to hormone and abiotic stresses. Our study provides a systematic genome-wide analysis of the SBP-box gene family in C. nankingense . In general, it provides a fundamental theoretical basis that SBP-box genes may regulate the resistance of stress physiology in chrysanthemum via exogenous hormone pathways.
... In fact, many gene families in foxtail millet have been fully identified and analyzed, including bHLH [24], NAC [25], GRAS [26] and AP2/ ERF [27]. At present, the SPL gene families of several species have been extensively studied, including dicotyledons (Arabidopsis [18,28], tomato [22], Tartary buckwheat [23], grape [29], and cotton [30]), monocotyledons (rice [31,32], wheat [33], and barley [34]), and C4 crops (maize and Sorghum bicolor [35]). ...
... In addition, OsSPL3 can improve the cold resistance of plants [45]. Some of the wheat SPL genes have been found to be down regulated under NaCl and PEG treatments [33], while 13 ZmSPLs in maize were found to be involved in the drought stress response [35]. Since the SPL transcription factor family was found to be targeted by miR156 [18,46], the gene function of SPL has been more widely studied. ...
Background
Among the major transcription factors, SPL plays a crucial role in plant growth, development, and stress response. Foxtail millet (Setaria italica), as a C4 crop, is rich in nutrients and is beneficial to human health. However, research on the foxtail millet SPL (SQUAMOSA PROMOTER BINDING-LIKE) gene family is limited.
Results
In this study, a total of 18 SPL genes were identified for the comprehensive analysis of the whole genome of foxtail millet. These SiSPL genes were divided into seven subfamilies (I, II, III, V, VI, VII, and VIII) according to the classification of the Arabidopsis thaliana SPL gene family. Structural analysis of the SiSPL genes showed that the number of introns in subfamilies I and II were much larger than others, and the promoter regions of SiSPL genes were rich in different cis-acting elements. Among the 18 SiSPL genes, nine genes had putative binding sites with foxtail millet miR156. No tandem duplication events were found between the SiSPL genes, but four pairs of segmental duplications were detected. The SiSPL genes expression were detected in different tissues, which was generally highly expressed in seeds development process, especially SiSPL6 and SiSPL16, which deserve further study. The results of the expression levels of SiSPL genes under eight types of abiotic stresses showed that many stress responsive genes, especially SiSPL9, SiSPL10, and SiSPL16, were highly expressed under multiple stresses, which deserves further attention.
Conclusions
In this research, 18 SPL genes were identified in foxtail millet, and their phylogenetic relationships, gene structural features, duplication events, gene expression and potential roles in foxtail millet development were studied. The findings provide a new perspective for the mining of the excellent SiSPL gene and the molecular breeding of foxtail millet.
... To date, the genome-wide SPL gene family has been identified in several plants, such as rice (Xie et al. 2006), maize (Peng et al. 2019), Arabidopsis (Birkenbihl et al. 2005), wheat (Li et al. 2020), citrus (Zeng et al. 2019), oilseed rape (Cheng et al. 2016), cotton (Cai et al. 2018) and Populus trichocarpa (Li and Lu, 2014). Sugarcane (Saccharum spp.) is the largest crop by production quantity and the sixth in economic value; it is grown in over 100 tropical and subtropical countries worldwide. ...
Sugarcane is an important sugar and energy crop that is widely grown in tropical and subtropical regions worldwide. SPL genes are a type of plant-specific transcription factor and play key roles in plant growth and development. Here, 17 SPL genes were identified from Saccharum spontaneum. A phylogenetic analysis of 72 SPLs from four species showed that the SPL family was divided into six groups and may have originated from at least two different last common ancestors. Comparative gene structure analysis revealed that the SPL family underwent exon gain or loss during evolution. Synteny analysis indicated that segmental duplication mainly contributed to the expansion of the SPL family in sugarcane. Eleven SsSPLs were predicted to have potential miR156 binding sites. Expression pattern analysis showed that the SsSPL gene family was functionally differentiated, besides, there also may be functional redundancy among paralogous SPL genes. SsSPL genes in clade I may be involved mainly in the development of reproductive organs, while SsSPL genes in clade VI, including SsSPL13, SsSPL1 and SsSPL16, participate predominantly in the development of various tissues during the vegetative growth stage. These results lay a foundation for further functional analysis of SPL in sugarcane.
... In the past few years, we have witnessed an exponential growth of studies that aimed at characterizing a wide variety of gene families that are somehow related to important agronomic traits such as acquisition of tolerance to biotic and abiotic stresses, plant architecture and development, grain quality and yield, flowering, floral induction, photoperiodic regulation, and phytohormone responses. This is especially true for crop species, such as Castor bean (Ricinus communis L.), sweet orange (Citrus sinensis L.), maize (Zea mays L.), rice (Oryza sativa L.), barley (Hordeum vulgare L.), and soybean [Glycine max (L.) Merr.] (Brito et al., 2020;Jiang et al., 2021;Khan et al., 2021;Neto et al., 2020;Peng et al., 2019;Tripathi et al., 2021;H. Zhang et al., 2019). ...
... SQUAMOSA promoter-binding-protein (SBP) gene family is exclusively found in plants, and the members of this family all share a highly conserved DNA-binding domain, which is composed of approximately 80 amino acid residues and contains C3H or C2HC zinc-finger structure [4]. Conserved domain structural analysis of SBP revealed that a highly conserved nuclear localization signal partially overlapped with the zinc-finger structure at the C-terminal region [5]. SPB genes are known to be associated with the transcriptional regulation of various physiological processes related to growth and development and can regulate multiple plant adaptational responses to biotic and abiotic stresses [6]. ...
SBP-box is an important plant-specific transcription factor family and is involved in diverse biological processes. Here, we identified a total of 15 SBP-BOX genes in the important fruit crop sweet orange (Citrus sinensis) and characterized their gene structures, conserved domain and motif, chromosomal location, and cis-acting regulatory elements. SBP genes were classified into four subfamilies based on the amino acid sequence homology, and the classification is equally strongly supported by the gene and protein structures. Our analysis revealed that segmental duplication events were the main driving force in the evolution of CsSBP genes, and gene pairs might undergo extensive purifying selection. Further synteny analysis of the SBP members among sweet orange and other plant species provides valuable information for clarifying the CsSBP family evolutionary relationship. According to publicly available RNA-seq data and qRT-PCR analysis from various sweet orange tissues, CsSBP genes may be expressed in different tissues and developmental stages. Gene expression analysis showed variable expression profiles of CsSBP genes under various abiotic stresses, such as high and low-temperature, salt, and wound treatments, demonstrating the potential role of SBP members in sweet orange response to abiotic stress. Noticeably, all CsSBP genes were also downregulated in sweet orange upon the infection of an important fungal pathogen Diaporthe citri. Our results provide valuable information for exploring the role of SBP-Box in sweet orange.
