Genome-Wide Identification of the B-BOX Genes that Respond to Multiple Ripening Related Signals in Sweet Cherry Fruit

B-BOX proteins are zinc finger transcription factors that play important roles in plant growth, development, and abiotic stress responses. In this study, we identified 15 PavBBX genes in the genome database of sweet cherry. We systematically analyzed the gene structures, clustering characteristics, and expression patterns of these genes during fruit development and in response to light and various hormones. The PavBBX genes were divided into five subgroups. The promoter regions of the PavBBX genes contain cis-acting elements related to plant development, hormones, and stress. qRT-PCR revealed five upregulated and eight downregulated PavBBX genes during fruit development. In addition, PavBBX6, PavBBX9, and PavBBX11 were upregulated in response to light induction. We also found that ABA, BR, and GA3 contents significantly increased in response to light induction. Furthermore, the expression of several PavBBX genes was highly correlated with the expression of anthocyanin biosynthesis genes, light-responsive genes, and genes that function in multiple hormone signaling pathways. Some PavBBX genes were strongly induced by ABA, GA, and BR treatment. Notably, PavBBX6 and PavBBX9 responded to all three hormones. Taken together, BBX proteins likely play major roles in regulating anthocyanin biosynthesis in sweet cherry fruit by integrating light, ABA, GA, and BR signaling pathways.

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Mungbean DIRIGENT Gene Subfamilies and Their Expression Profiles Under Salt and Drought Stresses

Frontiers in Genetics ◽

10.3389/fgene.2021.658148 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wenying Xu ◽

Tong Liu ◽

Huiying Zhang ◽

Hong Zhu

Keyword(s):

Stress Responses ◽

Expression Profiles ◽

Pfam Domain ◽

Vascular Plant ◽

Expression Patterns ◽

Promoter Regions ◽

Genome Wide ◽

A Genome ◽

Salt And Drought Stress ◽

Gene Structures

DIRIGENT (DIR) genes are key players in environmental stress responses that have been identified in many vascular plant species. However, few studies have examined the VrDIR genes in mungbean. In this study, we characterized 37 VrDIR genes in mungbean using a genome-wide identification method. VrDIRs were distributed on seven of the 11 mungbean chromosomes, and chromosome three contained the most VrDIR genes, with seven members. Thirty-two of the 37 VrDIRs contained a typical DIR gene structure, with one exon; the conserved DIR domain (i.e., Pfam domain) occupied most of the protein in 33 of the 37 VrDIRs. The gene structures of VrDIR genes were analyzed, and a total of 19 distinct motifs were detected. VrDIR genes were classified into five groups based on their phylogenetic relationships, and 13 duplicated gene pairs were identified. In addition, a total of 92 cis-acting elements were detected in all 37 VrDIR promoter regions, and VrDIR genes contained different numbers and types of cis-acting elements. As a result, VrDIR genes showed distinct expression patterns in different tissues and in response to salt and drought stress.

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Genome-wide in silico identification and expression analysis of beta-galactosidase family members in sweetpotato [Ipomoea batatas (L.) Lam]

BMC Genomics ◽

10.1186/s12864-021-07436-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Fuyun Hou ◽

Taifeng Du ◽

Zhen Qin ◽

Tao Xu ◽

Aixian Li ◽

...

Keyword(s):

Plant Development ◽

Stress Responses ◽

Ipomoea Batatas ◽

Expression Profiles ◽

Glycosyl Hydrolase ◽

Expression Patterns ◽

Human Beings ◽

Promoter Regions ◽

Cell Wall Modification ◽

Biotic Stresses

Abstract Background Sweetpotato (Ipomoea batatas (L.) Lam.) serves as an important food source for human beings. β-galactosidase (bgal) is a glycosyl hydrolase involved in cell wall modification, which plays essential roles in plant development and environmental stress adaptation. However, the function of bgal genes in sweetpotato remains unclear. Results In this study, 17 β-galactosidase genes (Ibbgal) were identified in sweetpotato, which were classified into seven subfamilies using interspecific phylogenetic and comparative analysis. The promoter regions of Ibbgals harbored several stress, hormone and light responsive cis-acting elements. Quantitative real-time PCR results displayed that Ibbgal genes had the distinct expression patterns across different tissues and varieties. Moreover, the expression profiles under various hormonal treatments, abiotic and biotic stresses were highly divergent in leaves and root. Conclusions Taken together, these findings suggested that Ibbgals might play an important role in plant development and stress responses, which provided evidences for further study of bgal function and sweetpotato breeding.

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Characterization of Mungbean CONSTANS-LIKE Genes and Functional Analysis of CONSTANS-LIKE 2 in the Regulation of Flowering Time in Arabidopsis

Frontiers in Plant Science ◽

10.3389/fpls.2021.608603 ◽

2021 ◽

Vol 12 ◽

Author(s):

Chenyang Liu ◽

Qianqian Zhang ◽

Hong Zhu ◽

Chunmei Cai ◽

Shuai Li

Keyword(s):

Flowering Time ◽

Expression Patterns ◽

Plant Growth And Development ◽

Promoter Regions ◽

Short Day ◽

Long Day ◽

Close Phylogenetic Relationship ◽

Gene Functions ◽

Gene Structures

CONSTANS-LIKE (COL) genes play important roles in the regulation of plant growth and development, and they have been analyzed in many plant species. However, few studies have examined COL genes in mungbean (Vigna radiata). In this study, we identified and characterized 31 mungbean genes whose proteins contained B-Box domains. Fourteen were designated as VrCOL genes and were distributed on 7 of the 11 mungbean chromosomes. Based on their phylogenetic relationships, VrCOLs were clustered into three groups (I, II, and III), which contained 4, 6, and 4 members, respectively. The gene structures and conserved motifs of the VrCOL genes were analyzed, and two duplicated gene pairs, VrCOL1/VrCOL2 and VrCOL8/VrCOL9, were identified. A total of 82 cis-acting elements were found in the VrCOL promoter regions, and the numbers and types of cis-acting elements in each VrCOL promoter region differed. As a result, the expression patterns of VrCOLs varied in different tissues and throughout the day under long-day and short-day conditions. Among these VrCOL genes, VrCOL2 showed a close phylogenetic relationship with Arabidopsis thaliana CO and displayed daily oscillations in expression under short-day conditions but not long-day conditions. In addition, overexpression of VrCOL2 accelerated flowering in Arabidopsis under short-day conditions by affecting the expression of the flowering time genes AtFT and AtTSF. Our study lays the foundation for further investigation of VrCOL gene functions.

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Genome-wide analysis of BBX gene family in Tartary buckwheat (Fagopyrum tataricum)

PeerJ ◽

10.7717/peerj.11939 ◽

2021 ◽

Vol 9 ◽

pp. e11939

Author(s):

Jiali Zhao ◽

Hongyou Li ◽

Juan Huang ◽

Taoxiong Shi ◽

Ziye Meng ◽

...

Keyword(s):

Growth And Development ◽

Environmental Changes ◽

Anthocyanin Biosynthesis ◽

Expression Patterns ◽

Tartary Buckwheat ◽

Chromosome 6 ◽

Fagopyrum Tataricum ◽

Conserved Motifs ◽

Genome Wide ◽

Gene Structures

BBX (B-box), a zinc finger transcription factor with one or two B-box domains, plays an important role in plant photomorphogenesis, growth, and development as well as response to environmental changes. In this study, 28 Tartary buckwheat BBX (FtBBX) genes were identified and screened using a comparison program. Their physicochemical properties, gene structures, conserved motifs, distribution in chromosomal, and phylogeny of the coding proteins, as well as their expression patterns, were analyzed. In addition, multiple collinearity analysis in three monocots and three dicot species illustrated that the BBX proteins identified from monocots clustered separately from those of dicots. Moreover, the expression of 11 candidate BBX genes with probable involvement in the regulation of anthocyanin biosynthesis was analyzed in the sprouts of Tartary buckwheat during light treatment. The results of gene structure analysis showed that all the 28 BBX genes contained B-box domain, three genes lacked introns, and these genes were unevenly distributed on the other seven chromosomes except for chromosome 6. The 28 proteins contained 10 conserved motifs and could be divided into five subfamilies. BBX genes of Tartary buckwheat showed varying expression under different conditions demonstrating that FtBBXs might play important roles in Tartary buckwheat growth and development. This study lays a foundation for further understanding of Tartary buckwheat BBX genes and their functions in growth and development as well as regulation of pigmentation in Tartary buckwheat.

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Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame

BMC Genomics ◽

10.1186/s12864-019-6091-5 ◽

2019 ◽

Vol 20 (1) ◽

Author(s):

Mengyuan Wei ◽

Aili Liu ◽

Yujuan Zhang ◽

Yong Zhou ◽

Donghua Li ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Leucine Zipper ◽

Expression Patterns ◽

Functional Characterization ◽

Genome Wide ◽

Gene Structures ◽

Relationship Of ◽

Zip Genes

Abstract Background The homeodomain-leucine zipper (HD-Zip) gene family is one of the plant-specific transcription factor families, involved in plant development, growth, and in the response to diverse stresses. However, comprehensive analysis of the HD-Zip genes, especially those involved in response to drought and salinity stresses is lacking in sesame (Sesamum indicum L.), an important oil crop in tropical and subtropical areas. Results In this study, 45 HD-Zip genes were identified in sesame, and denominated as SiHDZ01-SiHDZ45. Members of SiHDZ family were classified into four groups (HD-Zip I-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, which was further supported by the analysis of their conserved motifs and gene structures. Expression analyses of SiHDZ genes based on transcriptome data showed that the expression patterns of these genes were varied in different tissues. Additionally, we showed that at least 75% of the SiHDZ genes were differentially expressed in responses to drought and salinity treatments, and highlighted the important role of HD-Zip I and II genes in stress responses in sesame. Conclusions This study provides important information for functional characterization of stress-responsive HD-Zip genes and may contribute to the better understanding of the molecular basis of stress tolerance in sesame.

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In silico analysis and expression profiling of S-domain receptor-like kinases (SD-RLKs) under different abiotic stresses in Arabidopsis thaliana

BMC Genomics ◽

10.1186/s12864-021-08133-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Raju Mondal ◽

Subhankar Biswas ◽

Akanksha Srivastava ◽

Suvajit Basu ◽

Maitri Trivedi ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Abiotic Stress ◽

Signaling Pathways ◽

Differential Expression ◽

Stress Responses ◽

Abiotic Stresses ◽

Expression Patterns ◽

Light Stress ◽

Regulatory Elements ◽

Qrt Pcr

Abstract Background S-domain receptor-like kinases (SD-RLKs) are an important and multi-gene subfamily of plant receptor-like/pelle kinases (RLKs), which are known to play a significant role in the development and immune responses of Arabidopsis thaliana. The conserved cysteine residues in the extracellular domain of SD-RLKs make them interesting candidates for sensing reactive oxygen species (ROS), assisting oxidative stress mitigation and associated signaling pathways during abiotic stresses. However, how closely SD-RLKs are interrelated to abiotic stress mitigation and signaling remains unknown in A. thaliana. Results This study was initiated by examining the chromosomal localization, phylogeny, sequence and differential expression analyses of 37 SD-RLK genes using publicly accessible microarray datasets under cold, osmotic stress, genotoxic stress, drought, salt, UV-B, heat and wounding. Out of 37 SD-RLKs, 12 genes displayed differential expression patterns in both the root and the shoot tissues. Promoter structure analysis suggested that these 12 SD-RLK genes harbour several potential cis-regulatory elements (CREs), which are involved in regulating multiple abiotic stress responses. Based on these observations, we investigated the expression patterns of 12 selected SD-RLKs under ozone, wounding, oxidative (methyl viologen), UV-B, cold, and light stress at different time points using semi-qRT-PCR. Of these 12 SD-SRKs, the genes At1g61360, At1g61460, At1g61380, and At4g27300 emerged as potential candidates that maintain their expression in most of the stress treatments till exposure for 12 h. Expression patterns of these four genes were further verified under similar stress treatments using qRT-PCR. The expression analysis indicated that the gene At1g61360, At1g61380, and At1g61460 were mostly up-regulated, whereas the expression of At4g27300 either up- or down-regulated in these conditions. Conclusions To summarize, the computational analysis and differential transcript accumulation of SD-RLKs under various abiotic stresses suggested their association with abiotic stress tolerance and related signaling in A. thaliana. We believe that a further detailed study will decipher the specific role of these representative SD-RLKs in abiotic stress mitigation vis-a-vis signaling pathways in A. thaliana.

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088 Differential Expression of Expansin Genes Isolated from Sweet Cherry (Prunus avium L.) during Fruit Ripening

HortScience ◽

10.21273/hortsci.35.3.403f ◽

2000 ◽

Vol 35 (3) ◽

pp. 403F-404

Author(s):

Zhencai Wu ◽

Paul A. Wiersma

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Fruit Development ◽

Sweet Cherry ◽

Prunus Avium ◽

Expression Patterns ◽

Amino Acid Sequences ◽

Cdna Clones ◽

Low Level ◽

Expansin Gene

Expansins are a class of proteins that stimulate the extension of plant cell walls. Expansins have been found in nearly all growing plant tissues, such as hycopotyls, young seedlings, fibers, internodes, flower petals, and ripening fruits. We isolated two full-length expansin cDNA clones, Pruav-Exp1 and Pruav-Exp2, from sweet cherry (Prunus avium L.) fruit. Pruav-Exp1 has 1048 nucleotides encoding 254 amino acids, while Pruav-Exp2 has 1339 nucleotides encoding 250 amino acids. Deduced amino acid sequences of sweet cherry Pruav-Exp1 and Pruav-Exp2 share 72% identity. A Blast search of the GenBank database with the deduced amino acid sequences of Pruav-Exp1 and Pruav-Exp2 indicated a high sequence identity with other plant expansin genes. Interestingly, Pruav-Exp1 shares 99% identity of amino acid sequence with that of apricot expansin Pav-Exp1. Fragments from the 3' ends of Pruav-Exp1 and Pruav-Exp2 were cloned to generate gene-specific probes. These probes were used to study expansin gene expression in different tissues and during fruit development. Northern blot analysis showed different mRNA expression patterns for each gene. The mRNA of Pruav-Exp1 was expressed at the pink and ripe stages, but not at the early green and yellow stages of fruit development. The mRNA of Pruav-Exp2 was present earlier, from a low level in yellow expanding fruit, increasing to a high level at the pink stage and remaining at this level through the ripe stage. Both mRNAs were also expressed at a low level in flower, but not present in other tissues such as roots, leaves and peduncles. Our study indicates an expansin gene family is present in sweet cherry and suggests that two expansin genes may have different roles during fruit development and ripening.

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Genome-wide in silico identification and expression analysis of beta-galactosidase family members in sweetpotato [Ipomoea batatas (L.) Lam.]

10.21203/rs.3.rs-32133/v3 ◽

2020 ◽

Author(s):

Fuyun Hou ◽

Zhen Qin ◽

Taifeng Du ◽

Tao Xu ◽

Aixian Li ◽

...

Keyword(s):

Plant Development ◽

Stress Responses ◽

Ipomoea Batatas ◽

Expression Profiles ◽

Glycosyl Hydrolase ◽

Expression Patterns ◽

Human Beings ◽

Promoter Regions ◽

Cell Wall Modification ◽

Biotic Stresses

Abstract Background: Sweetpotato (Ipomoea batatas (L.) Lam.) serves as an important food source for human beings. β-galactosidase (bgal) is a glycosyl hydrolase involved in cell wall modification, which plays essential roles in plant development and environmental stress adaptation. However, the function of bgal genes in sweetpotato remains unclear.Results: In this study, 17 β-galactosidase genes (Ibbgal) were identified in sweetpotato, which were classified into seven subfamilies using interspecific phylogenetic and comparative analyses. The promoter regions of Ibbgals harbored several stress, hormone and light responsive cis-acting elements. Quantitative real-time PCR results displayed that Ibbgal genes had the distinct expression patterns across different tissues and varieties. Moreover, the expression profiles under various hormonal treatments, abiotic and biotic stresses were highly divergent in leaves and root. Conclusions: Taken together, these findings suggested that Ibbgals might play an important role in plant development and stress responses, which provided evidences for further study of bgal function and sweetpotato breeding.

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Comprehensive Genomic Characterization and Expression Analysis of the Lipoxygenase Gene Family in Watermelon under Hormonal Treatments

Agriculture ◽

10.3390/agriculture10100429 ◽

2020 ◽

Vol 10 (10) ◽

pp. 429

Author(s):

Jianping Liu ◽

Yong Zhou ◽

Jingwen Li ◽

Feng Wang ◽

Youxin Yang

Keyword(s):

Gene Family ◽

Expression Patterns ◽

Protein Structures ◽

Promoter Regions ◽

Element Analysis ◽

Cis Element ◽

Genome Wide ◽

Genomic Characterization ◽

Gene Structures ◽

Lipoxygenase Gene Family

Lipoxygenases (LOXs) are non-haem iron-containing dioxygenases and play vital roles in a variety of plant biological processes. Here, we first carried out the genome-wide identification of LOX genes in watermelon. A total of 16 LOX genes were identified, which could be classified into two categories according to phylogenetic analysis: the 9-LOXs (ClLOX1–4, 12, and 15) and 13-LOXs (ClLOX5–11, 13, 14, and 16). Furthermore, the protein structures, intrachromosomal distributions, and gene structures were thoroughly analyzed. Cis-element analysis of the promoter regions indicated that the expression of ClLOX genes may be influenced by stress and plant hormones. Bioinformatic and expression analyses revealed that the expression of ClLOX genes is tissue-specific and hormone-responsive. The detected LOX genes exhibited distinctive expression patterns in various tissues. Different ClLOX genes showed different responses to methyl jasmonate (MeJA), salicylic acid (SA), and ethylene (ET) treatments, particularly ClLOX7, which exhibited the most active response to the above treatments. This study provides valuable information for a better understanding of the functions of LOX genes and further exploration of the LOX gene family in watermelon.

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Transcriptome Co-Expression Network Analysis Identifies Key Genes and Regulators of Sweet Cherry Anthocyanin Biosynthesis

Horticulturae ◽

10.3390/horticulturae7060123 ◽

2021 ◽

Vol 7 (6) ◽

pp. 123

Author(s):

Haiying Yang ◽

Changping Tian ◽

Xiwen Li ◽

Hansheng Gong ◽

Aidi Zhang

Keyword(s):

Transcription Factors ◽

Network Analysis ◽

Sweet Cherry ◽

Anthocyanin Biosynthesis ◽

Expression Patterns ◽

Luciferase Assay ◽

Anthocyanin Synthesis ◽

Anthocyanin Content ◽

Sweet Cherries ◽

Key Factor

Anthocyanin is the key factor that results in the attractive color of sweet cherry fruits. However, information regarding sweet cherry coloration and the potential mechanisms underlying anthocyanin biosynthesis is limited. In this study, we found that the anthocyanin accumulation varied in sweet cherry flesh and peel, while the anthocyanin content increased sharply in the dark red (DR) stage. Correlations between anthocyanin concentrations and RNA sequencing (RNA-seq), constructed with Weighted Gene Co-Expression Network Analysis (WGCNA), indicated that two structural genes (Pac4CL2, PacANS) and 11 transcription factors (PacbHLH13/74, PacDIV, PacERF109/115, PacGATA8, PacGT2, PacGTE10, PacMYB308, PacPosF21, and PacWRKY7) had similar expression patterns with the changes in anthocyanin content. Additionally, real-time PCR verified all of these gene expression patterns and revealed that PacANS exhibited the highest transcription level. In order to search for potential regulators for anthocyanin biosynthesis, a dual-luciferase assay was performed to investigate the regulatory activities of 11 transcription factors on the PacANS promoter. The results revealed that two novelty bHLHs, PacbHLH13 and PacbHLH74, can trans-activate the PacANS promoter and they might be the candidate genes for regulating anthocyanin synthesis in sweet cherry fruits. The present findings provide a novel viewpoint with regard to anthocyanin biosynthesis mechanisms and the regulatory transcriptional network of fruit coloration in sweet cherries.

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