Genome-wide identification and expression analysis of the SPL gene family in woodland strawberry Fragaria vesca

Genome ◽  
2018 ◽  
Vol 61 (9) ◽  
pp. 675-683 ◽  
Author(s):  
Jin-Song Xiong ◽  
Dan Zheng ◽  
Hong-Yu Zhu ◽  
Jian-Qiu Chen ◽  
Ran Na ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Growth And Development ◽  
Expression Patterns ◽  
Systematic Research ◽  
Fragaria Vesca ◽  
Woodland Strawberry ◽  
Genome Wide ◽  
Squamosa Promoter Binding Protein ◽  
Spl Genes ◽  
Localization Analysis

SQUAMOSA promoter-binding protein-like (SPL) is a class of plant-specific transcription factors that play critical roles in regulating plant growth and development. However, little systematic research on SPL genes has been conducted in strawberry. In this study, 14 SPL genes were identified in the genome of woodland strawberry (Fragaria vesca), one of the model plants of the family Rosaceae. Chromosome localization analysis indicated that the 14 FvSPL genes were unevenly distributed on six chromosomes. Phylogenetic analysis indicated that the FvSPL proteins could be clustered into six groups (G1 to G6). Genes with similar structure were classified into the same group, implying their functional redundancy. In addition, nine out of the 14 FvSPL genes, belonging to G1, G2, and G5, were found to be the putative targets of FvmiR156 genes. Expression analysis indicated FvSPL genes exhibited highly diverse expression patterns in the tissues and organs examined. The transcript levels of most FvmiR156-targeted FvSPL genes in fruit were lower than those non-miR156-targeted genes. In addition, the expression of the FvmiR156-targeted FvSPL genes decreased during fruit ripening, whereas the expression of FvmiR156 genes increased in fruit during this process. The results provide a foundation for future functional analysis of FvSPL genes in strawberry growth and development.

Cloning, Characterization, and Overexpression in Arabidopsis to Determine the Function of SPL Genes from Woodland Strawberry (Fragaria Vesca)

2021 ◽  
Author(s):  
Yibo Bai ◽  
Morong Liang ◽  
Chuangju Ma ◽  
Zongming Cheng ◽  
Jinsong Xiong
Keyword(s):  
Untranslated Region ◽  
Transcriptional Activity ◽  
Biochemical Analysis ◽  
Activity Analysis ◽  
Fragaria Vesca ◽  
Mobility Shift ◽  
Woodland Strawberry ◽  
Squamosa Promoter Binding Protein ◽  
Spl Genes ◽  
Mobility Shift Assay

Abstract SQUAMOSA promoter binding protein-like (SPL) proteins is a class of plant specific transcription factors that play important roles during plant development. However, the majority of SPL genes in strawberry are functionally uncharacterized. In this study, three SPL genes, i.e. FvSPL1, FvSPL2, and FvSPL11 (FvSPL1/2/11), from woodland strawberry were cloned and characterized. Phylogenetic analysis with SPL genes from Arabidopsis, tomato and chrysanthemum indicated that FvSPL1/2/11 were clustered into the same group with those of miR156 target site located at the 3’-untranslated region (UTR). Further biochemical analysis indicated that FvSPL1 was exclusively localized in the nucleus. Electrophoretic mobility shift assay demonstrated FvSPL1 could specifically recognized the GTAC motif. Transcriptional activity analysis showed FvSPL1 was a transcriptional activator that could activate the expression of FvAP1 gene. Finally, all of the transgenic Arabidopsis that overexpression the three FvSPL genes were exhibited significantly early flowering phenotype. Taken together, our study indicated that FvSPL1/2/11 similar to their orthologs in Arabidopsis mainly functions in regulating plant flowering. These results enriched our understanding to the functions of SPL genes in strawberry and might be utilized for strawberry flowering time manipulation in the future.

scholarly journals Molecular Cloning and Characterization of SQUAMOSA-Promoter Binding Protein-Like Gene FvSPL10 from Woodland Strawberry (Fragaria vesca)

Plants ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 342 ◽  
Author(s):  
Jinsong Xiong ◽  
Yibo Bai ◽  
Chuangju Ma ◽  
Hongyu Zhu ◽  
Dan Zheng ◽  
...  
Keyword(s):  
Plant Growth ◽  
Growth And Development ◽  
Binding Protein ◽  
Ectopic Expression ◽  
Plant Growth And Development ◽  
Woodland Strawberry ◽  
Squamosa Promoter Binding Protein ◽  
Spl Genes

SQUAMOSA-promoter binding protein-like (SPL) proteins are plant-specific transcript factors that play essential roles in plant growth and development. Although many SPL genes have been well characterized in model plants like Arabidopsis, rice and tomato, the functions of SPLs in strawberry are still largely elusive. In the present study, we cloned and characterized FvSPL10, the ortholog of AtSPL9, from woodland strawberry. Subcellular localization shows FvSPL10 localizes in the cell nucleus. The luciferase system assay indicates FvSPL10 is a transcriptional activator, and both in vitro and in vivo assays indicate FvSPL10 could bind to the promoter of FvAP1 and activate its expression. Ectopic expression of FvSPL10 in Arabidopsis promotes early flowering and increases organs size. These results demonstrate the multiple regulatory roles of FvSPL10 in plant growth and development and lay a foundation for investigating the biological functions of FvSPL10 in strawberry.

scholarly journals Genome-Wide Analysis of Poplar SQUAMOSA-Promoter-Binding Protein (SBP) Family under Salt Stress

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 413
Author(s):  
Qing Guo ◽  
Li Li ◽  
Kai Zhao ◽  
Wenjing Yao ◽  
Zihan Cheng ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Growth And Development ◽  
Binding Protein ◽  
Gene Segment ◽  
Gene Expression Pattern ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Squamosa Promoter Binding Protein

SQUAMOSA promoter binding protein (SBP) is a kind of plant-specific transcription factor, which plays a crucial role in stress responses and plant growth and development by activating and inhibiting the transcription of multiple target genes. In this study, a total of 30 SBP genes were identified from Populus trichocarpa genome and randomly distributed on 16 chromosomes in poplar. According to phylogenetic analysis, the PtSBPs can be divided into six categories, and 14 out of the genes belong to VI. Furthermore, the SBP genes in VI were proved to have a targeting relationship with miR156. The homeopathic element analysis showed that the promoters of poplar SBP genes mainly contain the elements involved in growth and development, abiotic stress and hormone response. In addition, there existed 10 gene segment duplication events in the SBP gene duplication analysis. Furthermore, there were four poplar and Arabidopsis orthologous gene pairs among the poplar SBP members. What is more, poplar SBP gene family has diverse gene expression pattern under salt stress. As many as nine SBP members were responding to high salt stress and six members possibly participated in growth development and abiotic stress. Yeast two-hybrid experiments indicated that PtSBPs can form heterodimers to interact in the transcriptional regulatory networks. The genome-wide analysis of poplar SBP family will contribute to function characterization of SBP genes in woody plants.

scholarly journals Genome-Wide Identification and Expression Profiling Analysis of the Galactinol Synthase Gene Family in Cassava (Manihot esculenta Crantz)

Agronomy ◽  
2018 ◽  
Vol 8 (11) ◽  
pp. 250 ◽  
Author(s):  
Ruimei Li ◽  
Shuai Yuan ◽  
Yingdui He ◽  
Jie Fan ◽  
Yangjiao Zhou ◽  
...  
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Manihot Esculenta ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Systematic Research ◽  
Raffinose Family Oligosaccharides ◽  
Manihot Esculenta Crantz ◽  
Galactinol Synthase ◽  
Genome Wide

Galactinol synthases (GolSs) are the key enzymes that participate in raffinose family oligosaccharides (RFO) biosynthesis, which perform a big role in modulating plant growth and response to biotic or abiotic stresses. To date, no systematic study of this gene family has been conducted in cassava (Manihot esculenta Crantz). Here, eight MeGolS genes are isolated from the cassava genome. Based on phylogenetic background, the MeGolSs are clustered into four groups. Through predicting the cis-elements in their promoters, it was discovered that all MeGolS members act as hormone-, stress-, and tissue-specific related elements to different degrees. MeGolS genes exhibit incongruous expression patterns in various tissues, indicating that different MeGolS proteins might have diverse functions. MeGolS1 and MeGolS3–6 are highly expressed in leaves and midveins. MeGolS3–6 are highly expressed in fibrous roots. Quantitative real-time Polymerase Chain Reaction (qRT-PCR) analysis indicates that several MeGolSs, including MeGolS1, 2, 5, 6, and 7, are induced by abiotic stresses. microRNA prediction analysis indicates that several abiotic stress-related miRNAs target the MeGolS genes, such as mes-miR156, 159, and 169, which also respond to abiotic stresses. The current study is the first systematic research of GolS genes in cassava, and the results of this study provide a basis for further exploration the functional mechanism of GolS genes in cassava.

scholarly journals Roles of the GA-mediated SPL Gene Family and miR156 in the Floral Development of Chinese Chestnut (Castanea mollissima)

2019 ◽  
Vol 20 (7) ◽  
pp. 1577 ◽  
Author(s):  
Guosong Chen ◽  
Jingtong Li ◽  
Yang Liu ◽  
Qing Zhang ◽  
Yuerong Gao ◽  
...  
Keyword(s):  
Target Genes ◽  
Floral Development ◽  
Binding Protein ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Deciduous Tree ◽  
Main Function ◽  
Squamosa Promoter Binding Protein ◽  
Spl Genes ◽  
Castanea Mollissima

Chestnut (Castanea mollissima) is a deciduous tree species with major economic and ecological value that is widely used in the study of floral development in woody plants due its monoecious and out-of-proportion characteristics. Squamosa promoter-binding protein-like (SPL) is a plant-specific transcription factor that plays an important role in floral development. In this study, a total of 18 SPL genes were identified in the chestnut genome, of which 10 SPL genes have complementary regions of CmmiR156. An analysis of the phylogenetic tree of the squamosa promoter-binding protein (SBP) domains of the SPL genes of Arabidopsis thaliana, Populus trichocarpa, and C. mollissima divided these SPL genes into eight groups. The evolutionary relationship between poplar and chestnut in the same group was similar. A structural analysis of the protein-coding regions (CDSs) showed that the domains have the main function of SBP domains and that other domains also play an important role in determining gene function. The expression patterns of CmmiR156 and CmSPLs in different floral organs of chestnut were analyzed by real-time quantitative PCR. Some CmSPLs with similar structural patterns showed similar expression patterns, indicating that the gene structures determine the synergy of the gene functions. The application of gibberellin (GA) and its inhibitor (Paclobutrazol, PP333) to chestnut trees revealed that these exert a significant effect on the number and length of the male and female chestnut flowers. GA treatment significantly increased CmmiR156 expression and thus significantly decreased the expression of its target gene, CmSPL6/CmSPL9/CmSPL16, during floral bud development. This finding indicates that GA might indirectly affect the expression of some of the SPL target genes through miR156. In addition, RNA ligase-mediated rapid amplification of the 5′ cDNA ends (RLM-RACE) experiments revealed that CmmiR156 cleaves CmSPL9 and CmSPL16 at the 10th and 12th bases of the complementary region. These results laid an important foundation for further study of the biological function of CmSPLs in the floral development of C. mollissima.

Identification and expression analysis of chloroplast ribonucleoproteins (cpRNPs) in Arabidopsis and rice

Genome ◽  
2020 ◽  
Author(s):  
Jiawen Wu ◽  
Huimin Liu ◽  
Shan Lu ◽  
Jian Hua ◽  
Baohong Zou
Keyword(s):  
Expression Analysis ◽  
Stress Responses ◽  
Expression Patterns ◽  
Tissue Expression ◽  
Stability Control ◽  
Rna Recognition Motif ◽  
Chloroplast Targeting ◽  
Genome Wide ◽  
A Genome ◽  
Targeting Signal

Chloroplast ribonucleoproteins (cpRNPs) are implicated in splicing, editing and stability control of chloroplast RNAs as well as in regulating development and stress tolerance. To facilitate a comprehensive understanding of their functions, we carried out a genome-wide identification, curation, and phylogenetic analysis of cpRNP genes in Oryza sativa (rice) and Arabidopsis thaliana (Arabidopsis). Ten cpRNP genes were identified in each of Arabidopsis and rice genomes based on the presence of two RRM (RNA recognition motif) domains and an N-terminal chloroplast targeting signal peptide in the predicted proteins. These proteins are localized to chloroplasts. Gene expression analysis revealed that cpRNPs have differential tissue expression patterns and some cpRNPs are induced by abiotic stresses such as cold, heat and drought. Taken together, our study provides a comprehensive annotation of the cpRNP gene family and their expression patterns in Arabidopsis and rice which will facilitate further studies on their roles in plant growth and stress responses.

scholarly journals The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Hui Liu ◽  
Wei Qu ◽  
Kaikai Zhu ◽  
Zong-Ming Cheng
Keyword(s):  
Protein Kinases ◽  
Evolutionary Dynamics ◽  
Expression Patterns ◽  
Gene Families ◽  
Gray Mold ◽  
Fragaria Vesca ◽  
Woodland Strawberry ◽  
Go Enrichment ◽  
Potential Link ◽  
Wild Strawberry

Abstract Background Protein kinases (PKs) play an important role in signaling cascades and are one of the largest and most conserved protein super families in plants. Despite their importance, the woodland strawberry (Fragaria vesca) kinome and expression patterns of PK genes remain to be characterized. Results Here, we report on the identification and classification of 954 Fragaria vesca PK genes, which were classified into nine groups and 124 gene families. These genes were distributed unevenly among the seven chromosomes, and the number of introns per gene varied from 0 to 47. Almost half of the putative PKs were predicted to localize to the nucleus and 24.6% were predicted to localize to the cell membrane. The expansion of the woodland strawberry PK gene family occurred via different duplication mechanisms and tandem duplicates occurred relatively late as compared to other duplication types. Moreover, we found that tandem and transposed duplicated PK gene pairs had undergone stronger diversifying selection and evolved relatively faster than WGD genes. The GO enrichment and transcriptome analysis implicates the involvement of strawberry PK genes in multiple biological processes and molecular functions in differential tissues, especially in pollens. Finally, 109 PKs, mostly the receptor-like kinases (RLKs), were found transcriptionally responsive to Botrytis cinerea infection. Conclusions The findings of this research expand the understanding of the evolutionary dynamics of PK genes in plant species and provide a potential link between cell signaling pathways and pathogen attack.

scholarly journals Genome-Wide Identification and Comparison of Cysteine Proteases in the Pollen Coat and Other Tissues in Maize

2021 ◽  
Vol 12 ◽  
Author(s):  
Yanhua Li ◽  
Liangjie Niu ◽  
Xiaolin Wu ◽  
Claudia Faleri ◽  
Fuju Tai ◽  
...  
Keyword(s):  
Growth And Development ◽  
Cellular Localization ◽  
Expression Patterns ◽  
Sodium Dodecyl ◽  
Cysteine Proteases ◽  
Immunogold Electron Microscopy ◽  
Upstream Sequence ◽  
Maize Pollen ◽  
Genome Wide ◽  
Pollen Coat

Cysteine proteases, belonging to the C1-papain family, play a major role in plant growth and development, senescence, and immunity. There is evidence to suggest that pollen cysteine protease (CP) (ZmCP03) is involved in regulating the anther development and pollen formation in maize. However, there is no report on the genome-wide identification and comparison of CPs in the pollen coat and other tissues in maize. In this study, a total of 38 homologous genes of ZmCP03 in maize were identified. Subsequently, protein motifs, conserved domains, gene structures, and duplication patterns of 39 CPs are analyzed to explore their evolutionary relationship and potential functions. The cis-elements were identified in the upstream sequence of 39 CPs, especially those that are related to regulating growth and development and responding to environmental stresses and hormones. The expression patterns of these genes displayed remarked difference at a tissue or organ level in maize based on the available transcriptome data in the public database. Quantitative reverse transcription PCR (RT-qPCR) analysis showed that ZmCP03 was preferably expressed at a high level in maize pollen. Analyses by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblot, immunofluorescence and immunogold electron microscopy all validated the cellular localization of ZmCP03 in both the pollen coat and pollen cytoplasm. In addition, 142 CP genes from Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and cotton (Gossypium hirsutum), together with 39 maize CPs, were retrieved to analyze their evolution by comparing with orthologous genes. The results suggested that ZmCP03 was relatively conservative and stable during evolution. This study may provide a referential evidence on the function of ZmCP03 in pollen development and germination in maize.

scholarly journals Title: Genome-Wide Survey and Expression Analysis of NIN-Like Protein (NLP) Genes Reveals Its Potential Roles in the Response to Nutrition Deficiency in Tomato

2021 ◽  
Author(s):  
Mengyuan Liu ◽  
Xiaona Zhi ◽  
Yi Wang ◽  
Yang Wang
Keyword(s):  
Expression Analysis ◽  
Nitrate Uptake ◽  
Molecular Mechanisms ◽  
Inorganic Nitrogen ◽  
Expression Patterns ◽  
Potassium Deficiency ◽  
Comparative Genomic ◽  
Tomato Genome ◽  
Inorganic Nitrogen Source ◽  
Genome Wide

Abstract Background: Tomato (Solanum lycopersicum) is one of the most important horticultural crops, with a marked preference of nitrate as inorganic nitrogen source. The molecular mechanisms of nitrate uptake and assimilation are poorly understood in tomato. NIN-Like Proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in nitrate signaling. Results: In this study, genome-wide analysis revealed six NLP members in tomato genome. They were clustered into three clades in a phylogenic tree. Comparative genomic analysis showed that SlNLP genes had collinear relationships to NLPs in Arabidopsis, canola, maize and rice, and that the expansion of the SlNLP family mainly resulted from segmental duplications in tomato genome. Tissue-specific expression analysis showed that the close homologues of AtNLP6/7, SlNLP3, was strongly expressed in roots during both seedling and flowering stages; SlNLP4 and SlNLP6 exhibited preferential expression in stems and leaves; and SlNLP6 were expressed in high levels in fruits. Further, the nitrate uptake in tomato roots and expression patterns of SlNLP genes were measured under nitrogen/phosphate/potassium deficiency and nitrate resupply conditions. The transcript abundance of SlNLP3 decreased to 70% under phosphate/potassium deficiency. Most of SlNLPs were up-regulated after nitrogen starvation. SlNLP1 and SlNLP5 were induced rapidly and temporally by nitrate. Conclusions: These results provided significant insights into the potential diverse functions of SlNLPs to regulate nitrate uptake.

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