scholarly journals Genome-wide identification and expression pattern of SnRK gene family under several hormone treatments and its role in floral scent emission in Hedychium coronarium

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10883
Author(s):  
Chutian Wang ◽  
Farhat Abbas ◽  
Yiwei Zhou ◽  
Yanguo Ke ◽  
Xinyue Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Floral Scent ◽  
Regulatory Elements ◽  
Terpene Synthase ◽  
Segmental Duplications ◽  
Plant Signaling ◽  
Transcriptome Data ◽  
Virus Induced Gene Silencing ◽  
Kinase Gene ◽  
Hedychium Coronarium

The SnRK (Snf1-Related protein Kinase) gene family plays crucial roles in various plant signaling pathways and stress-adaptive responses including biotic and abiotic stresses via activating protein phosphorylation pathways. However, there is no information available on the role of the SnRK gene family in Hedychium coronarium. H. coronarium is an important crop widely cultivated as an ornamental plant, herb, spice, or condiment. In this study, 60 HcSnRK genes were identified from the H. coronarium genomic and transcriptome data. Phylogenetic and gene structure analysis showed that the HcSnRK genes were divided into three groups (HcSnRK1, HcSnRK2 and HcSnRK3) and among them HcSnRK3 subfamily was further subdivided into two clades according to the number of introns. Chromosome localization analysis showed that HcSnRK genes were unevenly mapped onto all chromosomes, and the Ka/Ks ratio of 24 paralogues includes four tandems and 20 segmental duplications indicated that the HcSnRK gene family underwent a purifying selection. Cis-regulatory elements analysis suggested that the HcSnRK genes respond to multiple hormones and other stresses. The responsiveness of HcSnRK genes to several hormones was analyzed by quantitative real-time PCR. Based on the different transcriptome data, two candidates HcSnRK genes (HcSnRK2.2 and HcSnRK2.9) were screened out for further characterization . The subcellular localization experiment revealed that both genes were located in the nucleus and cytoplasm. Moreover, virus-induced gene silencing (VIGS) of HcSnRK2.2 and HcSnRK2.9 significantly reduced the floral volatile contents by suppressing the expression of terpene synthase genes (HcTPS1, HcTPS3, and HcTPS5), indicating that HcSnRK2.2 and HcSnRK2.9 genes play an important role in the regulatory mechanism of floral aroma. These results will provide novel insights into the functional dissection of H. coronarium SnRK gene family.

scholarly journals Genome-Wide Analysis and Characterization of the Aux/IAA Family Genes Related to Floral Scent Formation in Hedychium coronarium

2019 ◽  
Vol 20 (13) ◽  
pp. 3235 ◽  
Author(s):  
Yanguo Ke ◽  
Farhat Abbas ◽  
Yiwei Zhou ◽  
Rangcai Yu ◽  
Yuechong Yue ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Floral Scent ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Virus Induced Gene Silencing ◽  
Cut Flowers ◽  
Flower Opening ◽  
Hedychium Coronarium

Auxin plays a key role in different plant growth and development processes, including flower opening and development. The perception and signaling of auxin depend on the cooperative action of various components, among which auxin/indole-3-acetic acid (Aux/IAA) proteins play an imperative role. In a recent study, the entire Aux/IAA gene family was identified and comprehensively analyzed in Hedychium coronarium, a scented species used as an ornamental plant for cut flowers. Phylogenetic analysis showed that the Aux/IAA gene family in H. coronarium is slightly contracted compared to Arabidopsis, with low levels of non-canonical proteins. Sequence analysis of promoters showed numerous cis-regulatory elements related to various phytohormones. HcIAA genes showed distinct expression patterns in different tissues and flower developmental stages, and some HcIAA genes showed significant responses to auxin and ethylene, indicating that Aux/IAAs may play an important role in linking hormone signaling pathways. Based on the expression profiles, HcIAA2, HcIAA4, HcIAA6 and HcIAA12, were selected as candidate genes and HcIAA2 and HcIAA4 were screened for further characterization. Downregulation of HcIAA2 and HcIAA4 by virus-induced gene silencing in H. coronarium flowers modified the total volatile compound content, suggesting that HcIAA2 and HcIAA4 play important roles in H. coronarium floral scent formation. The results presented here will provide insights into the putative roles of HcIAA genes and will assist the elucidation of their precise roles during floral scent formation.

scholarly journals Genome-Wide Analysis Reveals the Potential Role of MYB Transcription Factors in Floral Scent Formation in Hedychium coronarium

2021 ◽  
Vol 12 ◽  
Author(s):  
Farhat Abbas ◽  
Yanguo Ke ◽  
Yiwei Zhou ◽  
Yunyi Yu ◽  
Muhammad Waseem ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Family ◽  
Floral Scent ◽  
Expression Patterns ◽  
Acid Methyl Ester ◽  
Regulatory Elements ◽  
Composition Analysis ◽  
Myb Gene ◽  
Hedychium Coronarium

The MYB gene family is one of the largest groups of transcription factors (TFs) playing diverse roles in several biological processes. Hedychium coronarium (white ginger lily) is a renowned ornamental plant both in tropical and subtropical regions due to its flower shape and strong floral scent mainly composed of terpenes and benzenoids. However, there is no information available regarding the role of the MYB gene family in H. coronarium. In the current study, the MYB gene family was identified and extensively analyzed. The identified 253 HcMYB genes were unevenly mapped on 17 chromosomes at a different density. Promoter sequence analysis showed numerous phytohormones related to cis-regulatory elements. The majority of HcMYB genes contain two to three introns and motif composition analysis showed their functional conservation. Phylogenetic analysis revealed that HcMYBs could be classified into 15 distinct clades, and the segmental duplication events played an essential role in the expansion of the HcMYB gene family. Tissue-specific expression patterns of HcMYB genes displayed spatial and temporal expression. Furthermore, seven HcMYB (HcMYB7/8/75/79/145/238/248) were selected for further investigation. Through RT-qPCR, the response of candidates HcMYB genes toward jasmonic acid methyl ester (MeJA), abscisic acid (ABA), ethylene, and auxin was examined. Yeast one-hybrid (Y1H) assays revealed that candidate genes directly bind to the promoter of bottom structural volatile synthesis genes (HcTPS1, HcTPS3, HcTPS10, and HcBSMT2). Moreover, yeast two-hybrid (Y2H) assay showed that HcMYB7/8/75/145/248 interact with HcJAZ1 protein. In HcMYB7/8/79/145/248-silenced flowers, the floral volatile contents were decreased and downregulated the expression of key structural genes, suggesting that these genes might play crucial roles in floral scent formation in H. coronarium by regulating the expression of floral scent biosynthesis genes. Collectively, these findings indicate that HcMYB genes might be involved in the regulatory mechanism of terpenoids and benzenoid biosynthesis in H. coronarium.

scholarly journals Genome-wide identification and characterization of lectin receptor-like kinase gene family in cucumber and expression profiling analysis under different treatments

2020 ◽  
Author(s):  
Duo Lv ◽  
Gang Wang ◽  
Yue Chen ◽  
Liang-Rong Xiong ◽  
Jing-Xian Sun ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Kinase Gene ◽  
Cucumis Sativus L ◽  
Lectin Receptor ◽  
Genome Wide ◽  
Cucumber Genome ◽  
And Function

Abstract Background Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber ( Cucumis sativus L.).Results In this study, 46 putative LecRLK genes were identified in cucumber genome, including 23 G-type, 22 L-type and 1 C-type LecRLK genes. They unequally distributed on all 7 chromosomes with a clustering trendency. Most of the genes in the cucumber LecRLK (Cs LecRLK) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormone and stress on these genes’ promoters. Transcriptome data demonstrated that distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real time PCR (qRT-PCR) analysis.Conclusion This study provides a better understanding of the evolution and function of LecRLK gene family in cucumber, and opens the possibility to explore the roles that LecRLK s might play in the life cycle of cucumber.

scholarly journals Genomic profiling and expression analysis of the diacylglycerol kinase gene family in heterologous hexaploid wheat

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12480
Author(s):  
Xiaowei Jia ◽  
Xuyang Si ◽  
Yangyang Jia ◽  
Hongyan Zhang ◽  
Shijun Tian ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Gene Structure ◽  
Catalytic Domain ◽  
Diacylglycerol Kinase ◽  
Regulatory Elements ◽  
Amino Acid Sequences ◽  
Developmental Expression ◽  
Kinase Gene ◽  
Chinese Spring Wheat

The inositol phospholipid signaling system mediates plant growth, development, and responses to adverse conditions. Diacylglycerol kinase (DGK) is one of the key enzymes in the phosphoinositide-cycle (PI-cycle), which catalyzes the phosphorylation of diacylglycerol (DAG) to form phosphatidic acid (PA). To date, comprehensive genomic and functional analyses of DGKs have not been reported in wheat. In this study, 24 DGK gene family members from the wheat genome (TaDGKs) were identified and analyzed. Each putative protein was found to consist of a DGK catalytic domain and an accessory domain. The analyses of phylogenetic and gene structure analyses revealed that each TaDGK gene could be grouped into clusters I, II, or III. In each phylogenetic subgroup, the TaDGKs demonstrated high conservation of functional domains, for example, of gene structure and amino acid sequences. Four coding sequences were then cloned from Chinese Spring wheat. Expression analysis of these four genes revealed that each had a unique spatial and developmental expression pattern, indicating their functional diversification across wheat growth and development processes. Additionally, TaDGKs were also prominently up-regulated under salt and drought stresses, suggesting their possible roles in dealing with adverse environmental conditions. Further cis-regulatory elements analysis elucidated transcriptional regulation and potential biological functions. These results provide valuable information for understanding the putative functions of DGKs in wheat and support deeper functional analysis of this pivotal gene family. The 24 TaDGKs identified and analyzed in this study provide a strong foundation for further exploration of the biological function and regulatory mechanisms of TaDGKs in response to environmental stimuli.

scholarly journals Genome-Wide Analysis of SRNF Genes in Gossypium hirsutum Reveals the Role of GhSRNF18 in Primary Root Growth

2021 ◽  
Vol 12 ◽  
Author(s):  
Li Yu ◽  
Shuojun Zhang ◽  
Hailun Liu ◽  
Yufei Wang ◽  
Yiting Wei ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Family ◽  
Plant Species ◽  
Primary Root ◽  
Regulatory Elements ◽  
Virus Induced Gene Silencing ◽  
Cis Acting ◽  
Over Expression ◽  
Root Morphogenesis

Root systems are instrumental for water and nutrient uptake and the anchorage of plants in the soil. Root regulating GL2-interacting repressors (GIRs) contain a Short RING-like Zinc-Finger (SRNF) domain, but there has been no comprehensive characterization about this gene family in any plant species. Here, we renamed the GIR-like proteins as SRNF proteins due to their conserved domain and identified 140 SRNF genes from 16 plant species including 24 GhSRNF genes in Gossypium hirsutum. Phylogenetic analysis of the SRNFs revealed both similarities and divergences between five subfamilies. Notably, synteny analysis revealed that polyploidization and whole-genome duplication contribute to the expansion of the GhSRNF gene family. Various cis-acting regulatory elements were shown to be pertinent to light, phytohormone, defense responsive, and meristem regulation. Furthermore, GhSRNF2/15 were predominantly expressed in root, whereas the expression of GhSRNF18 is positively correlated with the primary root (PR) length in G. hirsutum, quantified by quantitative real-time PCR (qRT-PCR). Over-expression of GhSRNF18 in Arabidopsis and virus-induced gene silencing (VIGS) of GhSRNF18 in G. hirsutum has revealed the role of GhSRNF18 in PR growth. The over-expression of GhSRNF18 in Arabidopsis resulted in an increase of meristematic activities and auxin accumulations in PRs, which were consistent with the transcriptomic data. Our results suggested that GhSRNF18 positively regulates PR growth. This study increased our understanding of the SRNF gene family in plants and provided a novel rationale for the further investigation of cotton root morphogenesis regulated by the GhSRNFs.

scholarly journals Genome-Wide Identification, Characterization and Expression Analysis of Non-Arginine Aspartate Receptor like kinase gene family under Colletotrichum truncatum stress conditions in Hot pepper

2020 ◽  
Author(s):  
R Srideepthi ◽  
MSR Krishna ◽  
P Suneetha ◽  
R Sai Krishna ◽  
S Karthikeyan
Keyword(s):  
Disease Resistance ◽  
Gene Family ◽  
Expression Profiles ◽  
Regulatory Elements ◽  
Hot Pepper ◽  
Colletotrichum Truncatum ◽  
Kinase Gene ◽  
Improvement Programs ◽  
Arginine Aspartate ◽  
Six Genes

AbstractReceptor Like kinases (RLKs) are conserved upstream signaling molecules that regulate several biological processes, including plant development and stress adaptation. Non arginine aspartate (non-RD) an important class of RLKs plays a vital role in disease resistance and apoptosis in plants. In present investigation, a comprehensive Insilco analysis for non-RD Kinase gene family including identification, sequence similarity, phylogeny, chromosomal localization, gene structures, gene duplication analysis, promoter analysis and transcript expression profiles were elucidated. In this study twenty six genes were observed on nine out of twelve chromosomes. All these genes were clustered into seven subfamilies under large monophyletic group termed as Interleukin-1 Receptor-Associated Kinase (IRAK) family. Structural diversity in genomic structure among non-RD kinase gene family were identified and presence of pathogen induced cis regulatory elements like STRE, MYC, MYB,W box were found. Expression profiles of genes involved in providing resistance to anthracnose pathogen Colletotrichum truncatum in hot pepper were analyzed at different infective stages in both resistant and susceptible genotypes. Among twenty six genes, CaRLK1 gene belonging to LRRXII subfamily was up regulated under severe stress after infection in resistant genotype PBC-80. This integrative approach has helped us to identify candidate genes involved in disease resistance which would be helpful in future crop improvement programs.

scholarly journals Genome-wide identification, phylogenetic, and expression analysis under abiotic stress conditions of LIM gene family in Medicago sativa L.

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252213
Author(s):  
Lili Nian ◽  
Xuelu Liu ◽  
Yingbo Yang ◽  
Xiaolin Zhu ◽  
Xianfeng Yi ◽  
...  
Keyword(s):  
Gene Family ◽  
Medicago Sativa ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Promoter Sequence ◽  
Regulatory Elements ◽  
Segmental Duplications ◽  
Conserved Motifs ◽  
Functional Studies ◽  
Genome Wide

The LIM (Lin-11, Isl-1 and Mec-3 domains) family is a key transcription factor widely distributed in animals and plants. The LIM proteins in plants are involved in the regulation of a variety of biological processes, including cytoskeletal organization, the development of secondary cell walls, and cell differentiation. It has been identified and analyzed in many species. However, the systematic identification and analysis of the LIM genes family have not yet been reported in alfalfa (Medicago sativa L.). Based on the genome-wide data of alfalfa, a total of 21 LIM genes were identified and named MsLIM01-MsLIM21. Comprehensive analysis of the chromosome location, physicochemical properties of the protein, evolutionary relationship, conserved motifs, and responses to abiotic stresses of the LIM gene family in alfalfa using bioinformatics methods. The results showed that these MsLIM genes were distributed unequally on 21 of the 32 chromosomes in alfalfa. Gene duplication analysis showed that segmental duplications were the major contributors to the expansion of the alfalfa LIM family. Based on phylogenetic analyses, the LIM gene family of alfalfa can be divided into four subfamilies: αLIM subfamily, βLIM subfamily, γLIM subfamily, and δLIM subfamily, and approximately all the LIM genes within the same subfamily shared similar gene structure. The 21 MsLIM genes of alfalfa contain 10 Motifs, of which Motif1 and Motif3 are the conserved motifs shared by these genes. Furthermore, the analysis of cis-regulatory elements indicated that regulatory elements related to transcription, cell cycle, development, hormone, and stress response are abundant in the promoter sequence of MsLIM genes. Real-time quantitative PCR demonstrated that MsLIM gene expression is induced by low temperature and salt. The present study serves as a basic foundation for future functional studies on the alfalfa LIM family.

scholarly journals Genome-wide identification and characterization of lectin receptor-like kinase gene family in cucumber and expression profiling analysis under different treatments

2020 ◽  
Author(s):  
Duo Lv ◽  
Gang Wang ◽  
Liang-Rong Xiong ◽  
Jing-Xian Sun ◽  
Yue Chen ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Kinase Gene ◽  
Lectin Receptor ◽  
Genome Wide ◽  
Cucumber Genome ◽  
And Function

Abstract Background: Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber (Cucumis sativus L.). Results: In this study, 46 putative LecRLK genes were identified in cucumber genome, including 23 G-type, 22 L-type and 1 C-type LecRLK genes. They unequally distributed on all 7 chromosomes with a clustering trendency. Most of the genes in the cucumber LecRLK (CsLecRLK) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormone and stress on these genes’ promoters. Transcriptome data demonstrated that distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real time PCR (qRT-PCR) analysis.Conclusion: This study provides a better understanding of the evolution and function of LecRLK gene family in cucumber, and opens the possibility to explore the roles that LecRLKs might play in the life cycle of cucumber.

scholarly journals Genome-Wide Identification and Characterization of Lectin Receptor-Like Kinase Gene Family in Cucumber and Expression Profiling Analysis under Different Treatments

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1032 ◽  
Author(s):  
Duo Lv ◽  
Gang Wang ◽  
Liang-Rong Xiong ◽  
Jing-Xian Sun ◽  
Yue Chen ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Kinase Gene ◽  
Cucumis Sativus L ◽  
Lectin Receptor ◽  
Genome Wide ◽  
And Function

Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber (Cucumis sativus L.). In this study, 46 putative LecRLK genes were identified in the cucumber genome, including 23 G-type and 22 L-type, and one C-type LecRLK gene. They were unequally distributed on all seven chromosomes, with a clustering tendency. Most of the genes in the cucumber LecRLK (CsLecRLK) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormones and stress on these genes’ promoters. Transcriptome data demonstrated distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real-time PCR (qRT-PCR) analysis. This study provides a better understanding of the character and function of the LecRLK gene family in cucumber and opens up the possibility to exploring the roles that LecRLKs might play in the life cycle of cucumber.

Prediction and validation of cis-regulatory elements in 5′ upstream regulatory regions of lectin receptor-like kinase gene family in rice

PROTOPLASMA ◽  
2016 ◽  
Vol 254 (2) ◽  
pp. 669-684 ◽  
Author(s):  
Nishat Passricha ◽  
Shabnam Saifi ◽  
Mohammad W. Ansari ◽  
Narendra Tuteja
Keyword(s):  
Gene Family ◽  
Regulatory Elements ◽  
Kinase Gene ◽  
Regulatory Regions ◽  
Lectin Receptor ◽  
Receptor Like Kinase ◽  
Upstream Regulatory Regions
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