scholarly journals Genome-Wide Characterization and Expression Analysis of the SBP-Box Gene Family in Sweet Orange (Citrus sinensis)

2021 ◽  
Vol 22 (16) ◽  
pp. 8918
Author(s):  
Na Song ◽  
Yulin Cheng ◽  
Weiye Peng ◽  
ErPing Peng ◽  
Zengling Zhao ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Citrus Sinensis ◽  
Sweet Orange ◽  
Expression Profiles ◽  
Protein Structures ◽  
Evolutionary Relationship ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Variable Expression

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.

scholarly journals Genome-wide identification of small heat shock protein (HSP20) gene family in grape and expression profile during berry development

2019 ◽  
Author(s):  
Xiao-Ru Ji ◽  
Yi-He Yu ◽  
Pei-Yi Ni ◽  
Guo-Hai Zhang ◽  
Da-Long Guo
Keyword(s):  
Heat Shock ◽  
Heat Shock Protein ◽  
Gene Family ◽  
Expression Profiles ◽  
Evolutionary Relationship ◽  
Functional Differentiation ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Berry Development ◽  
Hsp20 Gene Family

Abstract Background : Studies have shown that HSP20 (heat-shock protein 20) genes play important roles in regulating plant growth, development, and stress response. However, the grape HSP20 gene family has not been well studied. Results : A total of 48 VvHsp20 genes were identified from the grape genome, which were divided into 11 subfamilies (CI, CII, CIII, CV, CVI, CVII, MI, MII, ER, CP and PX/Po) based on a phylogenetic analysis and subcellular localization. Further structural analysis showed that most of the VvHsp20 genes (93.8%) had no intron or only one intron, while genes that clustered together based on a phylogenetic tree had similar motifs and evolutionarily conserved structures. The HSP20s share a conservedα-crystalline domain (ACD) and the different components of the ACD domain suggest the functional diversity of VvHSP20s. In addition, the 48 VvHSP20 genes were distributed on 12 grape chromosomes and the majority of VvHSP20 genes were located at the proximal or distal ends of chromosomes. Chromosome mapping indicated that four groups of VvHSP20 genes were identified as tandem duplication genes. Phytohormone responsive, abiotic and biotic stress-responsive, and plant development-related cis-elements were identified from the cis-regulatory elements analysis of VvHSP20s. The expression profiles of VvHSP20s genes (VvHsp20-1, 11, 14, 17, 18, 19, 20, 24, 25, 28, 31, 39, 42, and 43) were largely similar between RNA-Seq and qRT-PCR analysis after hydrogen peroxide (H 2 O 2 ) treatment. The results showed that most VvHSP20s were down-regulated by H 2 O 2 treatment during fruit development. VvHSP20s genes were indeed found to be involved in the grape berry development and differences in their transcriptional levels may be the result of functional differentiation during evolution. Conclusions : Our results provide valuable information on the evolutionary relationship of genes in the VvHSP20 family, which is useful for future studies on the functional characteristics of VvHSP20 genes in grape.

scholarly journals Genome-wide identification of small heat shock protein (HSP20) gene family in grape and expression profile during berry development

2019 ◽  
Author(s):  
Xiao-Ru Ji ◽  
Yi-He Yu ◽  
Pei-Yi Ni ◽  
Guo-Hai Zhang ◽  
Da-Long Guo
Keyword(s):  
Heat Shock ◽  
Heat Shock Protein ◽  
Gene Family ◽  
Expression Profiles ◽  
Evolutionary Relationship ◽  
Functional Differentiation ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Berry Development ◽  
Hsp20 Gene Family

Abstract Background : Studies have shown that HSP20 (heat-shock protein 20) genes play important roles in regulating plant growth, development, and stress response. However, the grape HSP20 gene family has not been well studied. Results : A total of 48 VvHsp20 genes were identified from the grape genome, which were divided into 11 subfamilies (CI, CII, CIII, CV, CVI, CVII, MI, MII, ER, CP and PX/Po) based on a phylogenetic analysis and subcellular localization. Further structural analysis showed that most of the VvHsp20 genes (93.8%) had no intron or only one intron, while genes that clustered together based on a phylogenetic tree had similar motifs and evolutionarily conserved structures. The HSP20s share a conservedα-crystalline domain (ACD) and the different components of the ACD domain suggest the functional diversity of VvHSP20s. In addition, the 48 VvHSP20 genes were distributed on 12 grape chromosomes and the majority of VvHSP20 genes were located at the proximal or distal ends of chromosomes. Chromosome mapping indicated that four groups of VvHSP20 genes were identified as tandem duplication genes. Phytohormone responsive, abiotic and biotic stress-responsive, and plant development-related cis-elements were identified from the cis-regulatory elements analysis of VvHSP20s. The expression profiles of VvHSP20s genes (VvHsp20-1, 11, 14, 17, 18, 19, 20, 24, 25, 28, 31, 39, 42, and 43) were largely similar between RNA-Seq and qRT-PCR analysis after hydrogen peroxide (H 2 O 2 ) treatment. The results showed that most VvHSP20s were down-regulated by H 2 O 2 treatment during fruit development. VvHSP20s genes were indeed found to be involved in the grape berry development and differences in their transcriptional levels may be the result of functional differentiation during evolution. Conclusions : Our results provide valuable information on the evolutionary relationship of genes in the VvHSP20 family, which is useful for future studies on the functional characteristics of VvHSP20 genes in grape.

scholarly journals Genome-wide identification of small heat shock protein (HSP20) gene family in grape and expression profile during berry development

2019 ◽  
Author(s):  
Xiao-Ru Ji ◽  
Yi-He Yu ◽  
Pei-Yi Ni ◽  
Guo-Hai Zhang ◽  
Da-Long Guo
Keyword(s):  
Heat Shock ◽  
Heat Shock Protein ◽  
Gene Family ◽  
Expression Profiles ◽  
Evolutionary Relationship ◽  
Functional Differentiation ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Berry Development ◽  
Hsp20 Gene Family

Abstract Background : Studies have shown that HSP20 (heat-shock protein 20) genes play important roles in regulating plant growth, development, and stress response. However, the grape HSP20 gene family has not been well studied. Results : A total of 48 VvHsp20 genes were identified from the grape genome, which were divided into 11 subfamilies (CI, CII, CIII, CV, CVI, CVII, MI, MII, ER, CP and PX/Po) based on a phylogenetic analysis and subcellular localization. Further structural analysis showed that most of the VvHsp20 genes (93.8%) had no intron or only one intron, while genes that clustered together based on a phylogenetic tree had similar motifs and evolutionarily conserved structures. The HSP20s share a conservedα-crystalline domain (ACD) and the different components of the ACD domain suggest the functional diversity of VvHSP20s. In addition, the 48 VvHSP20 genes were distributed on 12 grape chromosomes and the majority of VvHSP20 genes were located at the proximal or distal ends of chromosomes. Chromosome mapping indicated that four groups of VvHSP20 genes were identified as tandem duplication genes. Phytohormone responsive, abiotic and biotic stress-responsive, and plant development-related cis-elements were identified from the cis-regulatory elements analysis of VvHSP20s. The expression profiles of VvHSP20s genes (VvHsp20-1, 11, 14, 17, 18, 19, 20, 24, 25, 28, 31, 39, 42, and 43) were largely similar between RNA-Seq and qRT-PCR analysis after hydrogen peroxide (H 2 O 2 ) treatment. The results showed that most VvHSP20s were down-regulated by H 2 O 2 treatment during fruit development. VvHSP20s genes were indeed found to be involved in the grape berry development and differences in their transcriptional levels may be the result of functional differentiation during evolution. Conclusions : Our results provide valuable information on the evolutionary relationship of genes in the VvHSP20 family, which is useful for future studies on the functional characteristics of VvHSP20 genes in grape.

scholarly journals Genome-wide identification of small heat-shock protein (HSP20) gene family in grape and expression profile during berry development

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Xiao-Ru Ji ◽  
Yi-He Yu ◽  
Pei-Yi Ni ◽  
Guo-Hai Zhang ◽  
Da-Long Guo
Keyword(s):  
Heat Shock ◽  
Heat Shock Protein ◽  
Gene Family ◽  
Expression Profiles ◽  
Evolutionary Relationship ◽  
Chromosome Mapping ◽  
Functional Differentiation ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Berry Development

Abstract Background Studies have shown that HSP20 (heat-shock protein 20) genes play important roles in regulating plant growth, development, and stress response. However, the grape HSP20 gene family has not been well studied. Results A total of 48 VvHSP20 genes were identified from the grape genome, which were divided into 11 subfamilies (CI, CII, CIII, CV, CVI, CVII, MI, MII, ER, CP and PX/Po) based on a phylogenetic analysis and subcellular localization. Further structural analysis showed that most of the VvHSP20 genes (93.8%) had no intron or only one intron, while genes that clustered together based on a phylogenetic tree had similar motifs and evolutionarily conserved structures. The HSP20s share a conservedα-crystalline domain (ACD) and the different components of the ACD domain suggest the functional diversity of VvHSP20s. In addition, the 48 VvHSP20 genes were distributed on 12 grape chromosomes and the majority of VvHSP20 genes were located at the proximal or distal ends of chromosomes. Chromosome mapping indicated that four groups of VvHSP20 genes were identified as tandem duplication genes. Phytohormone responsive, abiotic and biotic stress-responsive, and plant development-related cis-elements were identified from the cis-regulatory elements analysis of VvHSP20s. The expression profiles of VvHSP20s genes (VvHSP20–1, 11, 14, 17, 18, 19, 20, 24, 25, 28, 31, 39, 42, and 43) were largely similar between RNA-Seq and qRT-PCR analysis after hydrogen peroxide (H2O2) treatment. The results showed that most VvHSP20s were down-regulated by H2O2 treatment during fruit development. VvHSP20s genes were indeed found to be involved in the grape berry development and differences in their transcriptional levels may be the result of functional differentiation during evolution. Conclusions Our results provide valuable information on the evolutionary relationship of genes in the VvHSP20 family, which is useful for future studies on the functional characteristics of VvHSP20 genes in grape.

scholarly journals Genome-wide identification of small heat shock protein (HSP20) gene family in grape and expression profile during berry development

2019 ◽  
Author(s):  
Xiao-Ru Ji ◽  
Yi-He Yu ◽  
Pei-Yi Ni ◽  
Guo-Hai Zhang ◽  
Da-Long Guo
Keyword(s):  
Heat Shock ◽  
Heat Shock Protein ◽  
Gene Family ◽  
Expression Profiles ◽  
Evolutionary Relationship ◽  
Functional Differentiation ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Berry Development ◽  
Hsp20 Gene Family

Abstract Background : Studies have shown that HSP20 (heat-shock protein 20) genes play important roles in regulating plant growth, development, and stress response. However, the grape HSP20 gene family has not been well studied. Results : A total of 48 VvHsp20 genes were identified from the grape genome, which were divided into 11 subfamilies (CI, CII, CIII, CV, CVI, CVII, MI, MII, ER, CP and PX/Po) based on a phylogenetic analysis and subcellular localization. Further structural analysis showed that most of the VvHsp20 genes (93.8%) had no intron or only one intron, while genes that clustered together based on a phylogenetic tree had similar motifs and evolutionarily conserved structures. The HSP20s share a conservedα-crystalline domain (ACD) and the different components of the ACD domain suggest the functional diversity of VvHSP20s. In addition, the 48 VvHSP20 genes were distributed on 12 grape chromosomes and the majority of VvHSP20 genes were located at the proximal or distal ends of chromosomes. Chromosome mapping indicated that four groups of VvHSP20 genes were identified as tandem duplication genes. Phytohormone responsive, abiotic and biotic stress-responsive, and plant development-related cis-elements were identified from the cis-regulatory elements analysis of VvHSP20s. The expression profiles of VvHSP20s genes (VvHsp20-1, 11, 14, 17, 18, 19, 20, 24, 25, 28, 31, 39, 42, and 43) were largely similar between RNA-Seq and qRT-PCR analysis after hydrogen peroxide (H 2 O 2 ) treatment. The results showed that most VvHSP20s were down-regulated by H 2 O 2 treatment during fruit development. VvHSP20s genes were indeed found to be involved in the grape berry development and differences in their transcriptional levels may be the result of functional differentiation during evolution. Conclusions : Our results provide valuable information on the evolutionary relationship of genes in the VvHSP20 family, which is useful for future studies on the functional characteristics of VvHSP20 genes in grape.

Genome-Wide Characterization of PDI Gene Family in Medicago truncatula and their Roles in Response to ER stress

Genome ◽  
2020 ◽  
Author(s):  
Zhe Meng ◽  
Yuwei Zhao ◽  
Lijie Liu ◽  
Xihua Du
Keyword(s):  
Protein Folding ◽  
Er Stress ◽  
Gene Family ◽  
Medicago Truncatula ◽  
Environmental Changes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Structures ◽  
Pcr Analysis ◽  
Model Legume

Protein disulfide isomerases (PDIs) are pivotal protein folding catalysts in the endoplasmic reticulum (ER) through formation of disulfide bond, isomerization, and inhibition of misfolded protein aggregation. When protein folding capacity is overwhelmed by the demands during transitions between growth phases or under environmental changes, the accumulation of unfolded or misfolded proteins in the ER triggers ER stress. However, little is known about PDI gene family in the model legume, Medicago truncatula, especially the responses to ER stress. Therefore, we identified 17 putative PDIs from the genome of M. truncatula and presented their gene and protein structures, phylogenetic relationships, chromosomal distributions, and synteny analysis with the orthologs in other four eudicot species inculding A. thaliana, G. max, B. rapa, and V. vinifera. Moreover, expression profiles derived from transcriptome data showed distinct expression patterns of MtPDI genes among plant organs, while real-time quantitative PCR analysis and data from the proteome revealed the potential roles of MtPDIs in response to ER stress. Our study provides a foundation for further investigations of the biological roles of PDIs in Medicago, especially their roles in response to ER stress.

scholarly journals Evolutionary Understanding of Metacaspase Genes in Cultivated and Wild Oryza Species and Its Role in Disease Resistance Mechanism in Rice

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1412
Author(s):  
Ruchi Bansal ◽  
Nitika Rana ◽  
Akshay Singh ◽  
Pallavi Dhiman ◽  
Rushil Mandlik ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Wild Rice ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Resistance Mechanism ◽  
Regulatory Elements ◽  
Stress Conditions ◽  
Pcr Analysis ◽  
North East ◽  
Wild Rice Species

Metacaspases (MCs), a class of cysteine-dependent proteases found in plants, fungi, and protozoa, are predominately involved in programmed cell death processes. In this study, we identified metacaspase genes in cultivated and wild rice species. Characterization of metacaspase genes identified both in cultivated subspecies of Oryza sativa, japonica, and indica and in nine wild rice species was performed. Extensive computational analysis was conducted to understand gene structures, phylogenetic relationships, cis-regulatory elements, expression patterns, and haplotypic variations. Further, the haplotyping study of metacaspase genes was conducted using the whole-genome resequencing data publicly available for 4726 diverse genotype and in-house resequencing data generated for north-east Indian rice lines. Sequence variations observed among wild and cultivated rice species for metacaspase genes were used to understand the duplication and neofunctionalization events. The expression profiles of metacaspase genes were analyzed using RNA-seq transcriptome profiling in rice during different developmental stages and stress conditions. Real-time quantitative PCR analysis of candidate metacaspase genes in rice cultivars Pusa Basmati-1 in response to Magnaporthe oryzae infection indicated a significant role in the disease resistance mechanism. The information provided here will help to understand the evolution of metacaspases and their role under stress conditions in rice.

Gene isolation and expression analysis of two distinct sweet orange [Citrus sinensis L. (Osbeck)] tau-type glutathione transferases

Gene ◽  
2009 ◽  
Vol 443 (1-2) ◽  
pp. 143-150 ◽  
Author(s):  
Angela Roberta Lo Piero ◽  
Valeria Mercurio ◽  
Ivana Puglisi ◽  
Goffredo Petrone
Keyword(s):  
Expression Analysis ◽  
Citrus Sinensis ◽  
Sweet Orange ◽  
Gene Isolation ◽  
Glutathione Transferases

scholarly journals In Silico and Transcription Analysis of Trehalose-6-Phosphate Phosphatase Gene Family of Wheat: Trehalose Synthesis Genes Contribute to Salinity, Drought Stress and Leaf Senescence

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1652
Author(s):  
Md Ashraful Islam ◽  
Md Mustafizur Rahman ◽  
Md Mizanor Rahman ◽  
Xiujuan Jin ◽  
Lili Sun ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Tolerance ◽  
Leaf Senescence ◽  
Brachypodium Distachyon ◽  
Protein Structures ◽  
Regulatory Elements ◽  
Transcriptional Analysis ◽  
Pcr Analysis ◽  
Evolutionary Status ◽  
Transcription Analysis

Trehalose-6-phosphate phosphatase (TPP) genes take part in trehalose metabolism and also in stress tolerance, which has been well documented in many species but poorly understood in wheat. The present research has identified a family of 31 TPP genes in Triticum aestivum L. through homology searches and classified them into five clades by phylogenetic tree analysis, providing evidence of an evolutionary status with Hordeum vulgare, Brachypodium distachyon and Oryza sativa. The exon-intron distribution revealed a discrete evolutionary history and projected possible gene duplication occurrences. Furthermore, different computational approaches were used to analyze the physical and chemical properties, conserved domains and motifs, subcellular and chromosomal localization, and three-dimensional (3-D) protein structures. Cis-regulatory elements (CREs) analysis predicted that TaTPP promoters consist of CREs related to plant growth and development, hormones, and stress. Transcriptional analysis revealed that the transcription levels of TaTPPs were variable in different developmental stages and organs. In addition, qRT-PCR analysis showed that different TaTPPs were induced under salt and drought stresses and during leaf senescence. Therefore, the findings of the present study give fundamental genomic information and possible biological functions of the TaTPP gene family in wheat and will provide the path for a better understanding of TaTPPs involvement in wheat developmental processes, stress tolerance, and leaf senescence.

Sign in / Sign up

Export Citation Format

Share Document