scholarly journals Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Jingjing Zhang ◽  
Aimin Wu ◽  
Hengling Wei ◽  
Pengbo Hao ◽  
Qi Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Histone Deacetylation ◽  
Systematic Research ◽  
Motif Analysis ◽  
Flower Bud ◽  
Early Maturity ◽  
Genome Wide ◽  
Flower Bud Differentiation

Abstract Background Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. Within the superfamily of HDACs, RPD3/HDA1-type HDACs are the most studied, and it is reported that RPD3 genes play crucial roles in plant growth and physiological processes. However, there is a lack of systematic research on the RPD3/HDA1 gene family in cotton. Results In this study, genome-wide analysis identified 9, 9, 18, and 18 RPD3 genes in Gossypium raimondii, G. arboreum, G. hirsutum, and G. barbadense, respectively. This gene family was divided into 4 subfamilies through phylogenetic analysis. The exon-intron structure and conserved motif analysis revealed high conservation in each branch of the cotton RPD3 genes. Collinearity analysis indicated that segmental duplication was the primary driving force during the expansion of the RPD3 gene family in cotton. There was at least one presumed cis-element related to plant hormones in the promoter regions of all GhRPD3 genes, especially MeJA- and ABA-responsive elements, which have more members than other hormone-relevant elements. The expression patterns showed that most GhRPD3 genes had relatively high expression levels in floral organs and performed higher expression in early-maturity cotton compared with late-maturity cotton during flower bud differentiation. In addition, the expression of GhRPD3 genes could be significantly induced by one or more abiotic stresses as well as exogenous application of MeJA or ABA. Conclusions Our findings reveal that GhRPD3 genes may be involved in flower bud differentiation and resistance to abiotic stresses, which provides a basis for further functional verification of GhRPD3 genes in cotton development and a foundation for breeding better early-maturity cotton cultivars in the future.

scholarly journals Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton

2020 ◽  
Author(s):  
Jingjing Zhang ◽  
Aimin Wu ◽  
Hengling Wei ◽  
Pengbo Hao ◽  
Qi Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Histone Deacetylation ◽  
Systematic Research ◽  
Motif Analysis ◽  
Flower Bud ◽  
Early Maturity ◽  
Genome Wide ◽  
Flower Bud Differentiation

Abstract Background: Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. Within the superfamily of HDACs, RPD3/HDA1-type HDACs are the most studied, and it is reported that RPD3 genes play crucial roles in plant growth and physiological processes. However, there is a lack of systematic research on the RPD3/HDA1 gene family in cotton.Results: In this study, genome-wide analysis identified 9, 9, 18, and 18 RPD3 genes in Gossypium raimondii, G. arboreum, G. hirsutum, and G. barbadense, respectively. This gene family was divided into 4 subfamilies through phylogenetic analysis. The exon-intron structure and conserved motif analysis revealed high conservation in each branch of the cotton RPD3 genes. Collinearity analysis indicated that segmental duplication was the primary driving force during the expansion of the RPD3 gene family in cotton. There was at least one presumed cis-element related to plant hormones in the promoter regions of all GhRPD3 genes, especially MeJA- and ABA-responsive elements, which have more members than other hormone-relevant elements. The expression patterns showed that most GhRPD3 genes had relatively high expression levels in floral organs and performed higher expression in early-maturity cotton compared with late-maturity cotton during flower bud differentiation. In addition, the expression of GhRPD3 genes could be significantly induced by one or more abiotic stresses as well as exogenous application of MeJA or ABA.Conclusions: Our findings reveal that GhRPD3 genes might be involved in flower bud differentiation and resistance to abiotic stresses, which provides a basis for further functional verification of GhRPD3 genes in cotton development and a foundation for breeding better early-maturity cotton cultivars in the future.

scholarly journals Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton

2019 ◽  
Author(s):  
Jingjing Zhang ◽  
Aimin Wu ◽  
Hengling Wei ◽  
Pengbo Hao ◽  
Qi Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Histone Deacetylation ◽  
Functional Verification ◽  
Systematic Research ◽  
Flower Bud ◽  
Early Maturity ◽  
Genome Wide ◽  
Flower Bud Differentiation

Abstract Background: Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. As the superfamily of HDACs, RPD3/HDA1-type HDACs were most studied and reported that RPD3 genes played crucial roles in plant growth and physiological processes. However, there is a lack of systematic research on RPD3/HDA1 gene family in cotton. Results: In this research, 9, 9, 18 and 18 RPD3 genes were determined by genome-wide analysis in Gossypium raimondii, G. arboreum, G. hirsutum and G. barbadense, respectively. This gene family was divided into 4 subfamilies through phylogenetic analysis. The exon-intron structure and conserved motifs analysis exhibited high conservation in each branch of cotton RPD3 genes. Collinearity analysis indicated that segmental duplication was the primary driving force during the expansion of the GhRPD3 gene family. There was at least one presumed cis-element related to plant hormone existing in the promoter regions of all the GhRPD3 genes, especially MeJA and ABA responsive elements, owning more members than other hormone-relevant elements. Characterizations of expression patterns showed that most GhRPD3 genes performed relative high expression in floral organs and possessed the higher expression in early-maturity cotton compared with the late-maturity cotton during flower bud differentiation period. In addition, the expression of GhRPD3 genes could be significantly induced by one or more abiotic stresses as well as exogenous application of MeJA and ABA. Conclusions: Our findings revealed that GhRPD3 genes might be involved in flower bud differentiation and resistance to abiotic stresses, which provided a basis for further functional verification of GhRPD3 genes in cotton development and a foundation for breeding better early-maturity cotton cultivars in the future.

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 Genome-Wide Identification of the TCP Gene Family in Broussonetia papyrifera and Functional Analysis of BpTCP8, 14 and 19 in Shoot Branching

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1301
Author(s):  
Meiling Zhao ◽  
Xianjun Peng ◽  
Naizhi Chen ◽  
Shihua Shen
Keyword(s):  
Gene Family ◽  
Transcriptional Activation ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Deciduous Tree ◽  
Shoot Branching ◽  
Coding Region ◽  
Motif Analysis ◽  
Broussonetia Papyrifera ◽  
Genome Wide

The plant-specific TCP family proteins play an important role in the processes of plant growth and development. Broussonetia papyrifera is a versatile perennial deciduous tree, and its genome data have been published. However, no comprehensive analysis of the TCP gene family in B. papyrifera has been undertaken. In this study, 20 BpTCP genes (BpTCPs) were identified in the B. papyrifera genome. Phylogenetic analysis divided BpTCPs into three subclades, the PCF subclade, the CIN subclade and the CYC/TB1 subclade. Gene structure analysis displayed that all BpTCPs except BpTCP19 contained one coding region. Conserved motif analysis showed that BpTCP proteins in the same subclade possessed similar motif structures. Segmental duplication was the primary driving force for the expansion of BpTCPs. Expression patterns showed that BpTCPs may play diverse biological functions in organ or tissue development. Transcriptional activation activity analysis of BpTCP8, BpTCP14 and BpTCP19 showed that they possessed transcriptional activation ability. The ectopic expression analysis in Arabidopsis wild-type and AtBRC1 ortholog mutant showed that BpTCP8, BpTCP14 and BpTCP19 could prevent rosette branch outgrowth. Collectively, our study not only established the first genome-wide analysis of the B. papyrifera TCP gene family, but also provided valuable information for understanding the function of BpTCPs in shoot branching.

Genome-wide Analysis of the Rice Mate Gene Family: Identification, Genomic Organization and Expression Profiles in Response to Abiotic Stresses

2020 ◽  
Author(s):  
Zhixuan Du ◽  
Qitao Su ◽  
Zheng Wu ◽  
Zhou Huang ◽  
Jianzhong Bao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Chemical Properties ◽  
Motif Analysis ◽  
Functional Homology ◽  
Exogenous Compounds

Abstract Background: Multidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice.Results: In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. In addition, physical and chemical properties of the encoded proteins, subcellular localization, chromosome localization, stress-related cis-elements in abiotic stresses were determined, and a phylogenetic analysis and conserved motif analysis were performed. The rice MATE family can be divided into four subfamilies. It is speculated that members of the rice MATE family have many potential functions, such as the transport and accumulation of flavonoids and alkaloids, the extrusion of plant or exogenous compounds, the regulation of disease resistance and the response to abiotic stress, based on the proteins and cis-acting elements with known functions in the same subfamily. Analysis of gene expression showed that most of the genes were constitutively expressed. Furthermore, eight MATE genes were chosen for qRT-PCR-based analysis and showed differential expression patterns in response to salt and drought stress. Conclusions: Phylogenetic analysis, element prediction, expression data and homology with other species provided strong evidence for functional homology of MATE gene in rice. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

scholarly journals Genome-Wide Analysis of the β-Amylase Gene Family in Brassica L. Crops and Expression Profiles of BnaBAM Genes in Response to Abiotic Stresses

Agronomy ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1855
Author(s):  
Dan Luo ◽  
Ziqi Jia ◽  
Yong Cheng ◽  
Xiling Zou ◽  
Yan Lv
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Sequence Similarity ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Chromosomal Distribution ◽  
Brassica Napus L ◽  
Oil Crops ◽  
Genome Wide ◽  
Gene Structures

The β-amylase (BAM) gene family, known for their property of catalytic ability to hydrolyze starch to maltose units, has been recognized to play critical roles in metabolism and gene regulation. To date, BAM genes have not been characterized in oil crops. In this study, the genome-wide survey revealed the identification of 30 BnaBAM genes in Brassica napus L. (B. napus L.), 11 BraBAM genes in Brassica rapa L. (B. rapa L.), and 20 BoBAM genes in Brassica oleracea L. (B. oleracea L.), which were divided into four subfamilies according to the sequence similarity and phylogenetic relationships. All the BAM genes identified in the allotetraploid genome of B. napus, as well as two parental-related species (B. rapa and B. oleracea), were analyzed for the gene structures, chromosomal distribution and collinearity. The sequence alignment of the core glucosyl-hydrolase domains was further applied, demonstrating six candidate β-amylase (BnaBAM1, BnaBAM3.1-3.4 and BnaBAM5) and 25 β-amylase-like proteins. The current results also showed that 30 BnaBAMs, 11 BraBAMs and 17 BoBAMs exhibited uneven distribution on chromosomes of Brassica L. crops. The similar structural compositions of BAM genes in the same subfamily suggested that they were relatively conserved. Abiotic stresses pose one of the significant constraints to plant growth and productivity worldwide. Thus, the responsiveness of BnaBAM genes under abiotic stresses was analyzed in B. napus. The expression patterns revealed a stress-responsive behaviour of all members, of which BnaBAM3s were more prominent. These differential expression patterns suggested an intricate regulation of BnaBAMs elicited by environmental stimuli. Altogether, the present study provides first insights into the BAM gene family of Brassica crops, which lays the foundation for investigating the roles of stress-responsive BnaBAM candidates in B. napus.

scholarly journals Genome-Wide Identification and Characterization of Soybean GmLOR Gene Family and Expression Analysis in Response to Abiotic Stresses

2021 ◽  
Vol 22 (22) ◽  
pp. 12515
Author(s):  
Yisheng Fang ◽  
Dong Cao ◽  
Hongli Yang ◽  
Wei Guo ◽  
Wenqi Ouyang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Plant Tolerance ◽  
Promoter Regions ◽  
Real Time Quantitative Pcr ◽  
Related Family ◽  
Genome Wide ◽  
A Genome

The LOR (LURP-one related) family genes encode proteins containing a conserved LOR domain. Several members of the LOR family genes are required for defense against Hyaloperonospora parasitica (Hpa) in Arabidopsis. However, there are few reports of LOR genes in response to abiotic stresses in plants. In this study, a genome-wide survey and expression levels in response to abiotic stresses of 36 LOR genes from Glycine max were conducted. The results indicated that the GmLOR gene family was divided into eight subgroups, distributed on 14 chromosomes. A majority of members contained three extremely conservative motifs. There were four pairs of tandem duplicated GmLORs and nineteen pairs of segmental duplicated genes identified, which led to the expansion of the number of GmLOR genes. The expansion patterns of the GmLOR family were mainly segmental duplication. A heatmap of soybean LOR family genes showed that 36 GmLOR genes exhibited various expression patterns in different tissues. The cis-acting elements in promoter regions of GmLORs include abiotic stress-responsive elements, such as dehydration-responsive elements and drought-inducible elements. Real-time quantitative PCR was used to detect the expression level of GmLOR genes, and most of them were expressed in the leaf or root except that GmLOR6 was induced by osmotic and salt stresses. Moreover, GmLOR4/10/14/19 were significantly upregulated after PEG and salt treatments, indicating important roles in the improvement of plant tolerance to abiotic stress. Overall, our study provides a foundation for future investigations of GmLOR gene functions in soybean.

scholarly journals Genome-wide characterization and expression profiling analysis of the xyloglucan endotransglycosylase/hydrolase gene family in Brachypodium distachyon

2020 ◽  
Author(s):  
Hongyan Shen ◽  
Qiuping Tan ◽  
Wei Xiao ◽  
Wenpeng Deng ◽  
Xiaoyan Yu ◽  
...  
Keyword(s):  
Gene Family ◽  
Plant Hormones ◽  
Stress Responses ◽  
Brachypodium Distachyon ◽  
Expression Patterns ◽  
Growth Stages ◽  
Xyloglucan Endotransglycosylase ◽  
Motif Analysis ◽  
Group I ◽  
Genome Wide

Abstract Background: Xyloglucan endotransglucosylase/hydrolases (XTHs) are a class of cell wall-associated enzymes involved in the construction and remodeling of cellulose/xyloglucan crosslinks. However, knowledge of this gene family in the model monocot Brachypodium distachyon is limited. Results: A total of 29 BdXTH genes were identified from the reference genome, and these were further divided into three main groups (Group I/II, Group III, and the Ancestral Group) through comparative phylogenetic analysis. Gene structure and protein motif analysis indicate that closely clustered BdXTH genes are relatively conserved within each group. A highly conserved amino acid domain (DEIDFEFLG) responsible for catalytic activity was identified in all BdXTH proteins. We detected three pairs of segmentally duplicated BdXTH genes and five groups of tandemly duplicated BdXTH genes, which have played important roles in the expansion of the BdXTH gene family. Cis -elements related to hormones, growth, and abiotic stress responses were identified in the promoters of each BdXTH gene. Most BdXTH genes have distinct expression patterns in different tissues and growth stages. Furthermore, when roots were treated with two abiotic stresses (salinity and drought) and four plant hormones (IAA, auxin; GA3, gibberellin; ABA, abscisic acid and BR, brassinolide), the expression levels of many BdXTH genes changed significantly, suggesting possible roles in response to various environmental stimuli and plant hormones. Conclusion: In this study, we performed genome-wide identification, characterization, and expression pattern analysis of the XTH gene family in Brachypodium, which provide valuable information for further elucidation of the biological functions of BdXTH genes in the model grass B. distachyon.

Identification of stress repressive zinc finger gene family and its expression analysis in rice under abiotic constraints

2020 ◽  
Author(s):  
Chao Zhang ◽  
Yanning Tan ◽  
Jemaa Essemine ◽  
Ni Li ◽  
Zhongxiao Hu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Zinc Finger ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Rt Pcr ◽  
Conserved Domains ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Survey

Abstract Background: Stress repressive zinc finger (SRZ) gene family in rice is one of the plant defense gene families that play a pivotal role in plant growth regulation and development, particularly under stressful conditions. However, there is no genome-wide survey regarding SRZ gene family in rice (OsSRZ) till date. Results: We studied, herein, this gene family by performing a genome-wide screening and we identified 25 OsSRZ gene members using Japonica cultivar as an investigating material. Their chromosome localizations, phylogenetic relationships, genomic structures, conserved domains and promoter cis-regulatory elements were analyzed. Besides, their spatio-temporal expression profiles and expression patterns under various hormones and stress treatments were also assessed. Based on the phylogeny and domain constitution, the OsSRZ gene family was classified into five groups (I-V). Conserved domains analysis demonstrates that OsSRZ proteins contain at least one highly conserved SRZ domain. The analysis of expression patterns of the SRZ gene family reveal that OsSRZ genes display tissue-specific expression patterns at various rice developmental stages and exhibit differential responses to both phytohormones and abiotic stresses. Furthermore, q-RT-PCR analysis reveals that Os SRZ genes exhibit different expression patterns under various abiotic stresses. We notice the presence of a single specific gene considerably or strongly up-regulated for each kind of abiotic stress. Over 12 OsSRZ genes analyzed with q-RT-PCR, solely 4 genes (OsSRZ 1, 2, 10 and 11) were found to be substantially or strongly up-regulated following abiotic stress. Notably, OsSRZ 10 and 11 were up-regulated under heat stress by 7 and 5 times, respectively. However, OsSRZ2 was up-regulated by 7 and 3.5 folds under salt and cold stresses, respectively. Interestingly, OsSRZ1 was up-regulated by about 3~11 times in 24 h following artificial oxidative stress application using 1 mM H2O2 . Conclusions: We deduce that some members of OsSRZ gene family function as abiotic stress marker in rice. At the genomic level and expression pattern, our genome-wide survey could provide promising and valuable insights to widen and strengthen further future investigation by leading a cutting edge research regarding the biological and molecular functions of this gene family.

scholarly journals Comprehensive Identification and Expression Analysis of the Members of the B-Box Gene Family of Cotton Involved in Flower bud Differentiation and Responses to Multiple Stresses

2021 ◽  
Author(s):  
Zhen Feng ◽  
Mengyu Li ◽  
Yi Li ◽  
Xu Yang ◽  
Hengling Wei ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Selection Process ◽  
Biological Functions ◽  
Flower Bud ◽  
Protein Motifs ◽  
Genome Wide ◽  
Flower Bud Differentiation

Abstract Background: B-BOX (BBX) proteins are zinc-finger transcription factors with one or two BBX domains and sometimes a CCT domain. These proteins play an essential role in regulating plant growth and development, as well as in resisting abiotic stress. So far, the BBX gene family has been widely studied in other crops. However, no one has systematically studied the BBX gene in cotton. Results: In the present study, 17, 18, 37 and 33 BBX genes were detected in Gossypium arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively, via genome-wide identification. Phylogenetic analysis showed that all BBX genes were divided into 5 main categories. The protein motifs and exon/intron structures indicated that each group of BBX genes was highly conserved. Collinearity analysis revealed that the amplification of BBX gene family in Gossypium spp. was mainly through segmental replication. Nonsynonymous (Ka)/ synonymous (Ks) substitution ratios indicated that the BBX gene family had undergone purification selection throughout the long-term natural selection process. Moreover, transcriptomic data showed that some GhBBX genes were highly expressed in floral organs. Transcriptome data analysis and qRT-PCR verification showed that different GhBBX genes had different biological functions in flower bud differentiation, abiotic stress and stress response. Conclusions: Our comprehensive analysis of BBX in G. hirsutum provides a basis for further study on the molecular role of GhBBXs in regulating flowering and cotton resistance to abiotic stress.

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