scholarly journals Genome-Wide Characterization of B-BOX Gene Family and Their Responses to Light Quality and Cold Stress in Tomato

2020 ◽  
Author(s):  
Xin Bu ◽  
Xiujie Wang ◽  
Jiarong Yan ◽  
Ying Zhang ◽  
Shunyuan Zhou ◽  
...  
Keyword(s):  
Gene Family ◽  
Low Temperatures ◽  
Light Quality ◽  
Genome Mapping ◽  
Regulatory Elements ◽  
Protein Motif ◽  
Genome Wide ◽  
A Genome ◽  
Duplication Events ◽  
High Conservation

Abstract Background: Perceiving incoming environmental information is critical for optimizing plant growth and development. Multiple B-box proteins (BBXs) play essential roles in light-dependent developmental processes in plants. However, whether BBXs function as a signal integrator between light and temperature in tomato plants remains elusive.Results: In this study, 31 SlBBX genes were identified from the newly released tomato (Solanum lycopersicum) genome sequences, and were clustered into five subgroups with phylogenetic analysis. Gene structure and protein motif analyses showed relatively high conservation of closely clustered SlBBX genes within each subgroup; however, genome mapping analysis indicated the uneven distribution of the SlBBX genes on tomato chromosomes. Synteny analysis indicated that segmental duplication events happened in the expansion of the SlBBX genes in tomato. Promoter cis-regulatory elements prediction indicated that SlBBX genes were highly responsive to light, hormones, and stress conditions. Furthermore, the transcript analysis revealed that various SlBBX genes differed significantly in expression after exposure to different light quality and low temperatures, while 61.3% of SlBBX genes were responsive to both light and low temperatures. Conclusions: Our study presented a genome-wide survey of SlBBX gene family in tomato, and emphasized their functions in perceiving light quality and low temperature, which may improve the current understanding of SlBBX gene functions in integrating light and temperature signals for plant adaptation to adverse environments.

scholarly journals Identification of the WUSCHEL-Related Homeobox (WOX) Gene Family, and Interaction and Functional Analysis of TaWOX9 and TaWUS in Wheat

2020 ◽  
Vol 21 (5) ◽  
pp. 1581 ◽  
Author(s):  
Zheng Li ◽  
Dan Liu ◽  
Yu Xia ◽  
Ziliang Li ◽  
Doudou Jing ◽  
...  
Keyword(s):  
Gene Family ◽  
Oryza Sativa L ◽  
Dynamic Balance ◽  
Functional Characterization ◽  
Gene Families ◽  
Triticum Aestivum L ◽  
Genome Wide ◽  
A Genome ◽  
Paralogous Copy ◽  
Duplication Events

The WUSCHEL-related homeobox (WOX) is a family of plant-specific transcription factors, with important functions, such as regulating the dynamic balance of division and differentiation of plant stem cells and plant organ development. We identified 14 distinct TaWOX genes in the wheat (Triticum aestivum L.) genome, based on a genome-wide scan approach. All of the genes under evaluation had positional homoeologs on subgenomes A, B and D except TaWUS and TaWOX14. Both TaWOX14a and TaWOX14d had a paralogous copy on the same genome due to tandem duplication events. A phylogenetic analysis revealed that TaWOX genes could be divided into three groups. We performed functional characterization of TaWOX genes based on the evolutionary relationships among the WOX gene families of wheat, rice (Oryza sativa L.), and Arabidopsis. An overexpression analysis of TaWUS in Arabidopsis revealed that it affected the development of outer floral whorl organs. The overexpression analysis of TaWOX9 in Arabidopsis revealed that it promoted the root development. In addition, we identified some interaction between the TaWUS and TaWOX9 proteins by screening wheat cDNA expression libraries, which informed directions for further research to determine the functions of TaWUS and TaWOX9. This study represents the first comprehensive data on members of the WOX gene family in wheat.

scholarly journals Genome-wide Identification and Expression Analysis of the Cucumber PP2C Genes Family

2021 ◽  
Author(s):  
Guobin Zhang ◽  
Zeyu Zhang ◽  
Shilei Luo ◽  
Xia Li ◽  
Jian Lyu ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Structure ◽  
Expression Patterns ◽  
Cold Treatment ◽  
Negative Regulator ◽  
Motif Analysis ◽  
Response Elements ◽  
Genome Wide ◽  
A Genome ◽  
Duplication Events

Abstract Background: Type 2C protein phosphatase (PP2Cs) is a negative regulator of ABA signaling pathway, which play important roles in stress signal transduction in plants. However, cucumber (Cucumis sativus L.), as an important economic vegetable, has little research on its PP2C genes family. Results: This study conducted a genome-wide investigation of CsPP2C gene family. Through bioinformatics analysis, 56 CsPP2C genes were identified in cucumber. Based on phylogenetic analysis, the PP2C genes of cucumber and Arabidopsis were divided into 13 groups. Gene structure and conserved motif analysis showed that CsPP2C genes in the same group had similar gene structure and conserved domains. Collinearity analysis showed that segmental duplication events played a key role in the expansion of cucumber PP2C genes family. In addition, the expression of CsPP2Cs under different abiotic treatments was analyzed by qRT-PCR. The results showed that CsPP2C family genes showed different expression patterns under ABA, drought, salt and cold treatment, and a significantly responsive gene CsPP2Cs was obtained (CsPP2C3). By predicting the cis-elements in the promoter, we found that all CsPP2C members contained ABA response elements (ABRE) and drought response elements (MYC). Additionally, the expression patterns of CsPP2C genes were specific in different tissues. Conclusions: The results of this study provide a reference for the genome-wide identification of PP2C gene family in other species, and provide a basis for future studies on the function of PP2C gene in cucumber.

scholarly journals The TIFY Gene Family in Wheat and its Progenitors: Genome-wide Identification, Evolution and Expression Analysis

2019 ◽  
Vol 20 (5) ◽  
pp. 371-388
Author(s):  
Songfeng Xie ◽  
Licao Cui ◽  
Xiaole Lei ◽  
Guang Yang ◽  
Jun Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Regulatory Element ◽  
Aegilops Tauschii ◽  
Vital Role ◽  
Pcr Analysis ◽  
Protein Motif ◽  
Genome Wide ◽  
A Genome ◽  
As Stress

Background: The TIFY gene family is a group of plant-specific proteins involved in the jasmonate (JA) metabolic process, which plays a vital role in plant growth and development as well as stress response. Although it has been extensively studied in many species, the significance of this family is not well studied in wheat. Objective: To comprehensively understand the genome organization and evolution of TIFY family in wheat, a genome-wide identification was performed in wheat and its two progenitors using updated genome information provided here. Results: In total, 63, 13 and 17 TIFY proteins were identified in wheat, Triticum urartu and Aegilops tauschii respectively. Phylogenetic analysis clustered them into 18 groups with 14 groups possessing A, B and D copies in wheat, demonstrating the completion of the genome as well as the two rounds of allopolyploidization events. Gene structure, conserved protein motif and cis-regulatory element divergence of A, B, D homoeologous copies were also investigated to gain insight into the evolutionary conservation and divergence of homoeologous genes. Furthermore, the expression profiles of the genes were detected using the available RNA-seq and the expression of 4 drought-responsive candidates was further validated through qRT-PCR analysis. Finally, the co-expression network was constructed and a total of 22 nodes with 121 edges of gene pairs were found. Conclusion: This study systematically reported the characteristics of the wheat TIFY family, which ultimately provided important targets for further functional analysis and also facilitated the elucidation of the evolution mechanism of TIFY genes in wheat and more.

scholarly journals Genome Wide Identification, Classification and Functional Characterization of IQD Gene Family in Diploid and Tetraploid Cotton (Gossypium)

2021 ◽  
Author(s):  
Abdul Rehman ◽  
Zhen Peng ◽  
Hongge Li ◽  
Guangyong Qin ◽  
Yinhua Jia ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Calcium Binding ◽  
Regulatory Elements ◽  
Venn Diagram ◽  
Tetraploid Cotton ◽  
Genome Wide ◽  
Cotton Species ◽  
A Genome ◽  
Promotor Analysis

Abstract AimsCalmodulin (CaM) is considered as the most significant Ca+ signaling messenger that mediate various biochemical and physiological reactions. Whereas the calcium level can by provoked by extracellular or intracellular stimuli. CaM is activated by calcium binding proteins (CaMBPs) to regulate physiology of the cell. IQ domain (IQD) proteins are plant specific CML/CaM calcium binding which are characterized by domains of 67 amino acids. MethodsHerein, we accomplished a genome wide comparison and analysis of IQD gene family with in two diploid and tetraploid cotton species. Conserved motifs, gene structure, chromosomal map, evolutionary tree, Ka/Ks distribution, promotor analysis, venn diagram for orthologues genes, and collinearity analysis within genome and between genomes of IQD gene family in four cotton species were performed first time. Expression analysis was performed in four species of cotton from SRA database of NCBI.Results293 nonredundant IQD genes were identified from G. arboreum (A2), G. raimondii (D5), G. barbadense (AD2) and G. hirsutum (AD1) and clustered in the reference genomes from cotton functional genomics database. 50, 50, 94, and 99 IQD genes were detected from G. arboreum, G. raimondii, G. barbadense and G. hirsutum respectively. IQD gene family in four species of cotton elucidated the role of allopolyploid and hybridization during evolutionary cascade of allotetraploid cotton. Comparatively, existence of more orthologous genes in cotton species than Arabidopsis, advocated that polyploidization produced new cotton specific orthologous gene clusters. Duplication of gene events depicts that IQD gene family of cotton evolution was under strong purifying selection. G. hirsutum exhibited high level synteny. Expression analysis revealed that GarIQD18, GarIQD25 and GarIQD50 exhibited up regulated expression trend in ovule and fiber in G. arboreum. GarIQD25 also exhibited high expression in stem, root and flower. In G. raimondii, GraIQD03 demonstrated upregulation expression across stem, ovule, fiber and seed. GbaIQD11 and GbaIQD62 exhibited upregulation fiber development in G. barbadense. GhiIQD69 recognized as main candidate genes for plant parts, floral tissues, fiber and ovule development. Promotor analysis identified cis-regulatory elements which are involved in plant defense and stress response mechanisms. ConclusionsOverwhelmingly, present study paves the way to better understand the evolution of cotton IQD genes and lays a foundation for future investigation of IQD genes in improving abiotic stress tolerance in cotton.

scholarly journals Genome-Wide Characterization of B-Box Gene Family and Its Roles in Responses to Light Quality and Cold Stress in Tomato

2021 ◽  
Vol 12 ◽  
Author(s):  
Xin Bu ◽  
Xiujie Wang ◽  
Jiarong Yan ◽  
Ying Zhang ◽  
Shunyuan Zhou ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Genome Mapping ◽  
Electron Flow ◽  
Regulatory Elements ◽  
Photochemical Quenching ◽  
Protein Motif ◽  
Tomato Plants ◽  
High Conservation ◽  
Non Photochemical Quenching

Perceiving incoming environmental information is critical for optimizing plant growth and development. Multiple B-box proteins (BBXs) play essential roles in light-dependent developmental processes in plants. However, whether BBXs function as a signal integrator between light and temperature in tomato plants remains elusive. In this study, 31 SlBBX genes were identified from the newly released tomato (Solanum lycopersicum) genome sequences and were clustered into five subgroups. Gene structure and protein motif analyses showed relatively high conservation of closely clustered SlBBX genes within each subgroup; however, genome mapping analysis indicated the uneven distribution of the SlBBX genes on tomato chromosomes. Promoter cis-regulatory elements prediction and gene expression indicated that SlBBX genes were highly responsive to light, hormones, and stress conditions. Reverse genetic approaches revealed that disruption of SlBBX7, SlBBX9, and SlBBX20 largely suppressed the cold tolerance of tomato plants. Furthermore, the impairment of SlBBX7, SlBBX9, and SlBBX20 suppressed the photosynthetic response immediately after cold stress. Due to the impairment of non-photochemical quenching (NPQ), the excess photon energy and electron flow excited by low temperature were not consumed in SlBBX7-, SlBBX9-, and SlBBX20- silenced plants, leading to the over reduction of electron carriers and damage of the photosystem. Our study emphasized the positive roles of light signaling transcription factors SlBBXs in cold tolerance in tomato plants, which may improve the current understanding of how plants integrate light and temperature signals to adapt to adverse environments.

scholarly journals Systematic analysis of NAC transcription factors in Gossypium barbadense uncovers their roles in response to Verticillium wilt

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7995 ◽  
Author(s):  
Zhanji Liu ◽  
Mingchuan Fu ◽  
Hao Li ◽  
Yizhen Chen ◽  
Liguo Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Verticillium Wilt ◽  
Stress Responses ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Hormone Regulation ◽  
Genome Wide ◽  
A Genome

As one of the largest plant-specific gene families, the NAC transcription factor gene family plays important roles in various plant physiological processes that are related to plant development, hormone signaling, and biotic and abiotic stresses. However, systematic investigation of the NAC gene family in sea-island cotton (Gossypium babardense L.) has not been reported, to date. The recent release of the complete genome sequence of sea-island cotton allowed us to perform systematic analyses of G. babardense NAC GbNAC) genes. In this study, we performed a genome-wide survey and identified 270 GbNAC genes in the sea-island cotton genome. Genome mapping analysis showed that GbNAC genes were unevenly distributed on 26 chromosomes. Through phylogenetic analyses of GbNACs along with their Arabidopsis counterparts, these proteins were divided into 10 groups (I–X), and each contained a different number of GbNACs with a similar gene structure and conserved motifs. One hundred and fifty-four duplicated gene pairs were identified, and almost all of them exhibited strong purifying selection during evolution. In addition, various cis-acting regulatory elements in GbNAC genes were found to be related to major hormones, defense and stress responses. Notably, transcriptome data analyses unveiled the expression profiles of 62 GbNAC genes under Verticillium wilt (VW) stress. Furthermore, the expression profiles of 15 GbNAC genes tested by quantitative real-time PCR (qPCR) demonstrated that they were sensitive to methyl jasmonate (MeJA) and salicylic acid (SA) treatments and that they could be involved in pathogen-related hormone regulation. Taken together, the genome-wide identification and expression profiling pave new avenues for systematic functional analysis of GbNAC candidates, which may be useful for improving cotton defense against VW.

scholarly journals Genome-wide identification and expression analysis of sucrose nonfermenting-1-related protein kinase (SnRK) genes in Triticum aestivum in response to abiotic stress

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shefali Mishra ◽  
Pradeep Sharma ◽  
Rajender Singh ◽  
Ratan Tiwari ◽  
Gyanendra Pratap Singh
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Phylogenetic Analyses ◽  
Abiotic Stress Tolerance ◽  
Functional Characterization ◽  
Protein Motif ◽  
Element Analysis ◽  
Genome Wide ◽  
A Genome

AbstractThe SnRK gene family is a key regulator that plays an important role in plant stress response by phosphorylating the target protein to regulate subsequent signaling pathways. This study was aimed to perform a genome-wide analysis of the SnRK gene family in wheat and the expression profiling of SnRKs in response to abiotic stresses. An in silico analysis identified 174 SnRK genes, which were then categorized into three subgroups (SnRK1/2/3) on the basis of phylogenetic analyses and domain types. The gene intron–exon structure and protein-motif composition of SnRKs were similar within each subgroup but different amongst the groups. Gene duplication and synteny between the wheat and Arabidopsis genomes was also investigated in order to get insight into the evolutionary aspects of the TaSnRK family genes. The result of cis-acting element analysis showed that there were abundant stress- and hormone-related cis-elements in the promoter regions of 129 SnRK genes. Furthermore, quantitative real-time PCR data revealed that heat, salt and drought treatments enhanced TaSnRK2.11 expression, suggesting that it might be a candidate gene for abiotic stress tolerance. We also identified eight microRNAs targeting 16 TaSnRK genes which are playing important role across abiotic stresses and regulation in different pathways. These findings will aid in the functional characterization of TaSnRK genes for further research.

scholarly journals Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cuili Pan ◽  
Zhaoxiong Lei ◽  
Shuzhe Wang ◽  
Xingping Wang ◽  
Dawei Wei ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Adipocyte Differentiation ◽  
Bos Taurus ◽  
Adipogenic Differentiation ◽  
Critical Role ◽  
Bos Indicus ◽  
Specific Expression ◽  
Genome Wide ◽  
A Genome

Abstract Background Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation. Results We performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets. Conclusion In this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.

scholarly journals Genome-wide identification and expression analysis of the Brassica oleracea L. chitin-binding genes and response to pathogens infections

Planta ◽  
2021 ◽  
Vol 253 (4) ◽  
Author(s):  
Mingzhao Zhu ◽  
Shujin Lu ◽  
Mu Zhuang ◽  
Yangyong Zhang ◽  
Honghao Lv ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Gene Family ◽  
Brassica Oleracea ◽  
Downy Mildew ◽  
Fusarium Wilt ◽  
Black Spot ◽  
Housekeeping Genes ◽  
Chitinase Gene ◽  
Genome Wide ◽  
A Genome

Abstract Main conclusion Chitinase family genes were involved in the response of Brassica oleracea to Fusarium wilt, powdery mildew, black spot and downy mildew. Abstract Abstract Chitinase, a category of pathogenesis-related proteins, is believed to play an important role in defending against external stress in plants. However, a comprehensive analysis of the chitin-binding gene family has not been reported to date in cabbage (Brassica oleracea L.), especially regarding the roles that chitinases play in response to various diseases. In this study, a total of 20 chitinase genes were identified using a genome-wide search method. Phylogenetic analysis was employed to classify these genes into two groups. The genes were distributed unevenly across six chromosomes in cabbage, and all of them contained few introns (≤ 2). The results of collinear analysis showed that the cabbage genome contained 1–5 copies of each chitinase gene (excluding Bol035470) identified in Arabidopsis. The heatmap of the chitinase gene family showed that these genes were expressed in various tissues and organs. Two genes (Bol023322 and Bol041024) were relatively highly expressed in all of the investigated tissues under normal conditions, exhibiting the expression characteristics of housekeeping genes. In addition, under four different stresses, namely, Fusarium wilt, powdery mildew, black spot and downy mildew, we detected 9, 5, 8 and 8 genes with different expression levels in different treatments, respectively. Our results may help to elucidate the roles played by chitinases in the responses of host plants to various diseases.

scholarly journals A genome-wide map of regulatory elements in zebrafish

Lab Animal ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 17-17
Author(s):  
Alexandra Le Bras
Keyword(s):  
Regulatory Elements ◽  
Genome Wide ◽  
A Genome
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