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 Analysis of MDHAR Gene Family in Four Cotton Species Provides Insights into Fiber Development via Regulating AsA Redox Homeostasis

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 227
Author(s):  
Fangfang Zhou ◽  
Bowen Zheng ◽  
Fei Wang ◽  
Aiping Cao ◽  
Shuangquan Xie ◽  
...  
Keyword(s):  
Ascorbic Acid ◽  
Gene Family ◽  
Expression Analysis ◽  
Redox Regulation ◽  
Redox Homeostasis ◽  
Evolutionary Relationship ◽  
Fiber Elongation ◽  
Genome Wide ◽  
Cotton Species ◽  
A Genome

Monodehydroasorbate reductase (MDHAR) (EC1.6.5.4), a key enzyme in ascorbate-glutathione recycling, plays important roles in cell growth, plant development and physiological response to environmental stress via control of ascorbic acid (AsA)-mediated reduction/oxidation (redox) regulation. Until now, information regarding MDHAR function and regulatory mechanism in Gossypium have been limited. Herein, a genome-wide identification and comprehensive bioinformatic analysis of 36 MDHAR family genes in four Gossypium species, Gossypium arboreum, G. raimondii, G. hirsutum, and G. barbadense, were performed, indicating their close evolutionary relationship. Expression analysis of GhMDHARs in different cotton tissues and under abiotic stress and phytohormone treatment revealed diverse expression features. Fiber-specific expression analysis showed that GhMDHAR1A/D, 3A/D and 4A/D were preferentially expressed in fiber fast elongating stages to reach peak values in 15-DPA fibers, with corresponding coincident observances of MDHAR enzyme activity, AsA content and ascorbic acid/dehydroascorbic acid (AsA/DHA) ratio. Meanwhile, there was a close positive correlation between the increase of AsA content and AsA/DHA ratio catalyzed by MDHAR and fiber elongation development in different fiber-length cotton cultivars, suggesting the potential important function of MDHAR for fiber growth. Following H2O2 stimulation, GhMDHAR demonstrated immediate responses at the levels of mRNA, enzyme, the product of AsA and corresponding AsA/DHA value, and antioxidative activity. These results for the first time provide a comprehensive systemic analysis of the MDHAR gene family in plants and the four cotton species and demonstrate the contribution of MDHAR to fiber elongation development by controlling AsA-recycling-mediated cellular redox homeostasis.

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 Analysis of Dynamin Gene Family in cassava (Manihot esculenta Crantz) and Transcriptional Regulation of Family Members ARC5 in Hormonal Treatments

2019 ◽  
Vol 20 (20) ◽  
pp. 5094
Author(s):  
Cao ◽  
Liu ◽  
Guo ◽  
Chen ◽  
Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Defense Mechanism ◽  
Developmental Stages ◽  
Manihot Esculenta Crantz ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Hormonal Treatments

The Dynamin gene family play a significance role in many physiological processes, especially ARC5 (Accumulation and replication of chloroplasts 5) in the process of plastid division. We performed a genome-wide analysis of the cassava Dynamin family based on the published cassava genome sequence and identified ARC5. 23 cassava Dynamins (MeDynamins) were identified and renamed. 23 MeDynamins were further divided into five major groups based on their structural and phylogenetic characteristics. The segmental duplication events have a significant impact on the expansion of MeDynamins. ARC5 expression analysis showed that there were differences between leaves and roots of cassava at different developmental stages. The tissue-specific expression analysis of the MeDynamins showed that most of MeDynamins were expressed in stem apical meristem and embryogenesis, whereas ARC5 was mainly expressed in leaves. The processing of IAA (Indole-3-acetic Acid) and MeJA (Methyl Jasmonate) verified the prediction results of cis-elements, and ACR5 was closely related to plant growth and positively correlated. It also indicated that high concentrations of MeJA treatment caused the cassava defense mechanism to function in advance. In conclusion, these findings provide basic insights for functional validation of the ARC5 genes in exogenous hormonal treatments.

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 the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.)

2020 ◽  
Author(s):  
Fan Yang ◽  
Fushuang Dong ◽  
Fanghui Hu ◽  
Yongwei Liu ◽  
Jianfang Chai ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Expression Analysis ◽  
Developmental Regulation ◽  
Expression Profiles ◽  
Transcription Activator ◽  
Tissue Specific ◽  
Calmodulin Binding ◽  
Genome Wide ◽  
A Genome

Abstract Background: Plant calmodulin-binding transcription activator (CAMTA) proteins play important roles in hormone signal transduction, developmental regulation, and environmental stress tolerance. However, in wheat, the CAMTA gene family has not been systematically characterized. Results: In this work, 15 wheat CAMTA genes were identified using a genome-wide search method. Their chromosome location, physicochemical properties, subcellular localization, gene structure, protein domain, and promoter cis-elements were systematically analyzed. Phylogenetic analysis classified the TaCAMTA genes into three groups (groups A, B, and C), numbered 7, 6, and 2, respectively. The results showed that most TaCAMTA genes contained stress-related cis-elements. Finally, to obtain tissue-specific and stress-responsive candidates, the expression profiles of the TaCAMTAs in various tissues and under biotic and abiotic stresses were investigated. Tissue-specific expression analysis showed that all of the 15 TaCAMTA genes were expressed in multiple tissues with different expression levels, as well as under abiotic stress, the expressions of each TaCAMTA gene could respond to at least one abiotic stress. It also found that 584 genes in wheat genome were predicted to be potential target genes by CAMTA, demonstrating that CAMTA can be widely involved in plant development and growth, as well as coping with stresses. Conclusions: This work systematically identified the CAMTA gene family in wheat at the whole-genome-wide level, providing important candidates for further functional analysis in developmental regulation and the stress response in wheat.

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 Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.)

2020 ◽  
Author(s):  
Fan Yang ◽  
Fushuang Dong ◽  
Fanghui Hu ◽  
Yongwei Liu ◽  
Jianfang Chai ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Expression Analysis ◽  
Developmental Regulation ◽  
Expression Profiles ◽  
Transcription Activator ◽  
Tissue Specific ◽  
Calmodulin Binding ◽  
Genome Wide ◽  
A Genome

Abstract Background: Plant calmodulin-binding transcription activator (CAMTA) proteins play important roles in hormone signal transduction, developmental regulation, and environmental stress tolerance. However, in wheat, the CAMTA gene family has not been systematically characterized. Results: In this work, 15 wheat CAMTA genes were identified using a genome-wide search method. Their chromosome location, physicochemical properties, subcellular localization, gene structure, protein domain, and promoter cis-elements were systematically analyzed. Phylogenetic analysis classified the TaCAMTA genes into three groups (groups A, B, and C), numbered 7, 6, and 2, respectively. The results showed that most TaCAMTA genes contained stress-related cis-elements. Finally, to obtain tissue-specific and stress-responsive candidates, the expression profiles of the TaCAMTAs in various tissues and under biotic and abiotic stresses were investigated. Tissue-specific expression analysis showed that all of the 15 TaCAMTA genes were expressed in multiple tissues with different expression levels, as well as under abiotic stress, the expressions of each TaCAMTA gene could respond to at least one abiotic stress. It also found that 584 genes in wheat genome were predicted to be potential target genes by CAMTA, demonstrating that CAMTA can be widely involved in plant development and growth, as well as coping with stresses. Conclusions: This work systematically identified the CAMTA gene family in wheat at the whole-genome-wide level, providing important candidates for further functional analysis in developmental regulation and the stress response in wheat.

scholarly journals Genome-Wide Identification of the Vacuolar H+-ATPase Gene Family in Five Rosaceae Species and Expression Analysis in Pear (Pyrus bretschneideri)

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1661
Author(s):  
Hongsheng Zhou ◽  
Wen Huang ◽  
Shufen Luo ◽  
Huali Hu ◽  
Yingtong Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Prunus Persica ◽  
Proton Pumps ◽  
Event Analysis ◽  
Specific Expression ◽  
Rosaceae Species ◽  
Genome Wide ◽  
A Genome ◽  
Atpase Gene

Vacuolar H+-ATPases (V-ATPase) are multi-subunit complexes that function as ATP hydrolysis-driven proton pumps. They play pivotal roles in physiological processes, such as development, metabolism, stress, and growth. However, there have been very few studies on the characterisation of V-ATPase (VHA) genes in Rosaceae species. Therefore, in the present study, we performed a genome-wide analysis and identified VHA gene family members in five Rosaceae species (Pyrus bretschneideri, Malus domestica, Prunus persica, Fragaria vesca, and Prunus mume). A total of 159 VHA genes were identified, and were classified into 13 subfamilies according to the phylogenetic analysis. The structure of VHA proteins revealed high similarity among different VHA genes within the same subgroup. Gene duplication event analysis revealed that whole-genome duplications represented the major pathway for expansion of the Pyrus bretschneideri VHA genes (PbrVHA genes). The tissue-specific expression analysis of the pear showed that 36 PbrVHA genes were expressed in major tissues. Seven PbrVHA genes were significantly downregulated when the pollen tube growth stopped. Moreover, many PbrVHA genes were differentially expressed during fruit development and storage, suggesting that VHA genes play specific roles in development and senescence. The present study provides fundamental information for further elucidating the potential roles of VHA genes during development and senescence.

scholarly journals Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.)

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Fan Yang ◽  
Fu-shuang Dong ◽  
Fang-hui Hu ◽  
Yong-wei Liu ◽  
Jian-fang Chai ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Expression Analysis ◽  
Developmental Regulation ◽  
Expression Profiles ◽  
Transcription Activator ◽  
Tissue Specific ◽  
Calmodulin Binding ◽  
Genome Wide ◽  
A Genome

Abstract Background Plant calmodulin-binding transcription activator (CAMTA) proteins play important roles in hormone signal transduction, developmental regulation, and environmental stress tolerance. However, in wheat, the CAMTA gene family has not been systematically characterized. Results In this work, 15 wheat CAMTA genes were identified using a genome-wide search method. Their chromosome location, physicochemical properties, subcellular localization, gene structure, protein domain, and promoter cis-elements were systematically analyzed. Phylogenetic analysis classified the TaCAMTA genes into three groups (groups A, B, and C), numbered 7, 6, and 2, respectively. The results showed that most TaCAMTA genes contained stress-related cis-elements. Finally, to obtain tissue-specific and stress-responsive candidates, the expression profiles of the TaCAMTAs in various tissues and under biotic and abiotic stresses were investigated. Tissue-specific expression analysis showed that all of the 15 TaCAMTA genes were expressed in multiple tissues with different expression levels, as well as under abiotic stress, the expressions of each TaCAMTA gene could respond to at least one abiotic stress. It also found that 584 genes in wheat genome were predicted to be potential target genes by CAMTA, demonstrating that CAMTA can be widely involved in plant development and growth, as well as coping with stresses. Conclusions This work systematically identified the CAMTA gene family in wheat at the whole-genome-wide level, providing important candidates for further functional analysis in developmental regulation and the stress response in wheat.

scholarly journals Genome-Wide Identification of MATE Gene Family in Potato (Solanum tuberosum L.) and Expression Analysis in Heavy Metal Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Yun Huang ◽  
Guandi He ◽  
Weijun Tian ◽  
Dandan Li ◽  
Lulu Meng ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Gene Family ◽  
Expression Analysis ◽  
Molecular Mechanisms ◽  
Solanum Tuberosum L ◽  
Heavy Metal Stress ◽  
Metal Stress ◽  
Expression Levels ◽  
Genome Wide ◽  
A Genome

A genome-wide identification and expression analysis of multidrug and toxic compound extrusion (MATE) gene family in potato was carried out to explore the response of MATE proteins to heavy meta stress. In this study, we identified 64 MATE genes from potato genome, which are located on 12 chromosomes, and are divided into I–IV subfamilies based on phylogenetic analysis. According to their order of appearance on the chromosomes, they were named from StMATE1–64. Subcellular location prediction showed that 98% of them are located on the plasma membrane as transporters. Synteny analysis showed that five pairs of collinearity gene pairs belonged to members of subfamily I and subfamily II had two pairs indicating that the duplication is of great significance to the evolution of genes in subfamilies I and II. Gene exon–intron structures and motif composition are more similar in the same subfamily. Every StMATE gene contained at least one cis-acting element associated with regulation of hormone transport. The relative expression levels of eight StMATE genes were significantly upregulated under Cu2+ stress compared with the non-stress condition (0 h). After Cd2+ stress for 24 h, the expression levels of StMATE33 in leaf tissue were significantly increased, indicating its crucial role in the process of Cd2+ stress. Additionally, StMATE18/60/40/33/5 were significantly induced by Cu2+ stress, while StMATE59 (II) was significantly induced by Ni2+ stress. Our study initially explores the biological functions of StMATE genes in the regulation of heavy metal stress, further providing a theoretical basis for studying the subsequent molecular mechanisms in detail.

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