scholarly journals Genome-Wide Identification and Transcriptional Expression Profiles of the F-box Gene Family in Common Walnut (Juglans regia L.)

Forests ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 275 ◽  
Author(s):  
Feng Yan ◽  
Huijuan Zhou ◽  
Ming Yue ◽  
Ge Yang ◽  
Huaizhu Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Plant Development ◽  
Juglans Regia ◽  
Critical Role ◽  
Transcriptional Expression ◽  
Genome Wide ◽  
A Genome ◽  
Male Flowers ◽  
Common Walnut ◽  
Female Flowers

The common walnut (or Persian walnut), Juglans regia L., is an economically important temperate tree species valued for both its edible nut and high-quality wood. F-box gene family members are involved in plant development, which includes regulating plant development, reproduction, cellular protein degradation, response to biotic and abiotic stresses, and flowering. However, in common walnut (J. regia), there are no reports about the F-box gene family. Here, we report a genome-wide identification of J. regia F-box genes and analyze their phylogeny, duplication, microRNA, pathway, and transcriptional expression profile. In this study, 74 F-box genes were identified and clustered into three groups based on phylogenetic analysis and eight subfamilies based on special domains in common walnut. These common walnut F-box genes are distributed on 31 different pseudo-chromosomes. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and microRNA profiles showed that the F-box gene family might play a critical role in the flowering of common walnut. The expressions were significantly higher in female flowers and male flowers compared with leaf and hull tissues at a transcriptome level. The results revealed that the expressions of the F-box gene in female flowers were positively correlated with male flowers, but there was no correlation between any other tissue combinations in common walnut. Our results provided insight into the general characteristics of the F-box genes in common walnut.

scholarly journals Genome-Wide Identification and Transcriptional Expression of the PAL Gene Family in Common Walnut (Juglans Regia L.)

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 46 ◽  
Author(s):  
Feng Yan ◽  
Huaizhu Li ◽  
Peng Zhao
Keyword(s):  
Gene Family ◽  
Juglans Regia ◽  
Expression Patterns ◽  
Critical Role ◽  
Phenylpropanoid Pathway ◽  
Transcriptional Expression ◽  
Genome Wide ◽  
A Genome ◽  
The Common ◽  
Common Walnut

Juglans regia L. is an economically important crop cultivated worldwide for its high quality and quantity of wood and nuts. Phenylalanine ammonia-lyase (PAL) is the first enzyme in the phenylpropanoid pathway that plays a critical role in plant growth, development, and adaptation, but there have been few reports of the PAL gene family in common walnut. Here, we report a genome-wide study of J. regia PAL genes and analyze their phylogeny, duplication, microRNA, and transcriptional expression. A total of 12 PAL genes were identified in the common walnut and clustered into two subfamilies based on phylogenetic analysis. These common walnut PALs are distributed on eight different pseudo-chromosomes. Seven of the 12 PALs (JrPAL2-3, JrPAL4-2, JrPAL2-1, JrPAL4-1, JrPAL8, JrPAL9, and JrPAL6) were specific found in J. regia, and JrPAL3, JrPAL5, JrPAL1-2, JrPAL7, and JrPAL2-2 were found to be closely associated with the woody plant Populus trichocarpa. Additionally, the expression patterns of JrPAL3, JrPAL7, JrPAL9, and JrPAL2-1 showed that they had high expression in female and male flowers. The miRNA ath-miR830-5p regulates two genes, JrPAL5 and JrPAL1, such that they have low expression in the male and female flowers of the common walnut. Our research provides useful information for further research into the function of PAL genes in common walnut and Juglans.

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, Structure Characterization and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula

2021 ◽  
Vol 22 (14) ◽  
pp. 7269
Author(s):  
Jean-Stéphane Venisse ◽  
Eele Õunapuu-Pikas ◽  
Maxime Dupont ◽  
Aurélie Gousset-Dupont ◽  
Mouadh Saadaoui ◽  
...  
Keyword(s):  
Cold Stress ◽  
Gene Family ◽  
Betula Pendula ◽  
Large Family ◽  
Biochemical Properties ◽  
Silver Birch ◽  
Structure Characterization ◽  
Transcriptional Expression ◽  
Genome Wide ◽  
A Genome

Aquaporin water channels (AQPs) constitute a large family of transmembrane proteins present throughout all kingdoms of life. They play key roles in the flux of water and many solutes across the membranes. The AQP diversity, protein features, and biological functions of silver birch are still unknown. A genome analysis of Betula pendula identified 33 putative genes encoding full-length AQP sequences (BpeAQPs). They are grouped into five subfamilies, representing ten plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight NOD26-like intrinsic proteins (NIPs), four X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). The BpeAQP gene structure is conserved within each subfamily, with exon numbers ranging from one to five. The predictions of the aromatic/arginine selectivity filter (ar/R), Froger’s positions, specificity-determining positions, and 2D and 3D biochemical properties indicate noticeable transport specificities to various non-aqueous substrates between members and/or subfamilies. Nevertheless, overall, the BpePIPs display mostly hydrophilic ar/R selective filter and lining-pore residues, whereas the BpeTIP, BpeNIP, BpeSIP, and BpeXIP subfamilies mostly contain hydrophobic permeation signatures. Transcriptional expression analyses indicate that 23 BpeAQP genes are transcribed, including five organ-related expressions. Surprisingly, no significant transcriptional expression is monitored in leaves in response to cold stress (6 °C), although interesting trends can be distinguished and will be discussed, notably in relation to the plasticity of this pioneer species, B. pendula. The current study presents the first detailed genome-wide analysis of the AQP gene family in a Betulaceae species, and our results lay a foundation for a better understanding of the specific functions of the BpeAQP genes in the responses of the silver birch trees to cold stress.

scholarly journals Expression Profiling of the Dof Gene Family Under Abiotic Stresses in Spinach

2021 ◽  
Author(s):  
Hongying Yu ◽  
Yaying Ma ◽  
Yijing Lu ◽  
Jingjing Yue ◽  
Ray Ming
Keyword(s):  
Transcription Factors ◽  
Gene Family ◽  
Stress Responses ◽  
Expression Profiling ◽  
Abiotic Stresses ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Male Flowers

Abstract DNA-binding with one finger (Dof) transcription factors are plant-specific transcription factors involved in numerous pathways of plant development, especially in respond to abiotic stresses. Although genome-wide analysis of this gene family has been performed in many species, Dof genes in spinach have not been thoroughly analyzed. We performed a genome-wide analysis and characterization of Dof gene family in spinach. Twenty two Dof genes were identified and classified into four groups with nine subgroups, which was further corroborated by gene structure and motif analyses. Ka/Ks analysis revealed that SoDofs were subjected to purify selection. Using Cis-acting elements analysis, SoDofs were involved in plant growth and development, plant hormones and stress responses. Expression profiling demonstrated that SoDofs expressed in leaf and inflorescence, and responded to cold, heat, and drought stresses. SoDof22 expressed the highest level in male flowers and under cold stress. These results provided a genome-wide analysis of SoDof genes, their gender- and tissue-specific expression, and response to abiotic stresses. The knowledge and resources gained from these analyses will benefit spinach improvement.

scholarly journals Genome-Wide Identification and Transcriptional Expression Profiles of Transcription Factor WRKY in Common Walnut (Juglans regia L.)

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1444
Author(s):  
Fan Hao ◽  
Ge Yang ◽  
Huijuan Zhou ◽  
Jiajun Yao ◽  
Deruilin Liu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Gene Family ◽  
Expression Profiles ◽  
Juglans Regia ◽  
Enrichment Analysis ◽  
Wrky Gene ◽  
Genome Wide ◽  
Plant Pathogen Interaction ◽  
High Degree ◽  
Common Walnut

The transcription factor WRKY is widely distributed in the plant kingdom, playing a significant role in plant growth, development and response to stresses. Walnut is an economically important temperate tree species valued for both its edible nuts and high-quality wood, and its response to various stresses is an important factor that determines the quality of its fruit. However, in walnut trees themselves, information about the WRKY gene family remains scarce. In this paper, we perform a comprehensive study of the WRKY gene family in walnut. In total, we identified 103 WRKY genes in the common walnut that are clustered into 4 groups and distributed on 14 chromosomes. The conserved domains all contained a WRKY domain, and motif 2 was observed in most WRKYs, suggesting a high degree of conservation and similar functions within each subfamily. However, gene structure was significantly differentiated between different subfamilies. Synteny analysis indicates that there were 56 gene pairs in J. regia and A. thaliana, 76 in J. regia and J. mandshurica, 75 in J. regia and J. microcarpa, 76 in J. regia and P. trichocarpa, and 33 in J. regia and Q. robur, indicating that the WRKY gene family may come from a common ancestor. GO and KEGG enrichment analysis showed that the WRKY gene family was involved in resistance traits and the plant-pathogen interaction pathway. In anthracnose-resistant F26 fruits (AR) and anthracnose-susceptible F423 fruits (AS), transcriptome and qPCR analysis results showed that JrWRKY83, JrWRKY73 and JrWRKY74 were expressed significantly more highly in resistant cultivars, indicating that these three genes may be important contributors to stress resistance in walnut trees. Furthermore, we investigate how these three genes potentially target miRNAs and interact with proteins. JrWRKY73 was target by the miR156 family, including 12 miRNAs; this miRNA family targets WRKY genes to enhance plant defense. JrWRKY73 also interacted with the resistance gene AtMPK6, showing that it may play a crucial role in walnut defense.

scholarly journals Genome-wide identification, genomic organization, and expression profiling of the CONSTANS-like (COL) gene family in petunia under multiple stresses

2021 ◽  
Author(s):  
Khadiza Khatun ◽  
Sourav Debnath ◽  
Arif Hasan Khan Robin ◽  
Antt Htet Wai ◽  
Ujjal Kumar Nath ◽  
...  
Keyword(s):  
Stress Response ◽  
Plant Growth ◽  
Gene Family ◽  
Plant Development ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Flowering Plants ◽  
Genome Wide ◽  
A Genome ◽  
Photoperiod Sensitive

Abstract BackgroundCONSTANS-like (CO-like, COL) is a putative zinc-finger transcription factor family that plays a key role in the control of flowering time in photoperiod-sensitive plants. Besides, the COL family protein is also involved in plant development, responses to stresses. However, information on plant development and stress response related function has not been previously performed in any solanaceous crop. In this study, a genome-wide analysis of COL gene family was conducted in Petunia hybrida cv. Mirage Rose to elucidate their roles in organ development and stress response.ResultsA total of 15 COL genes were identified in petunia. Based on their amino acid sequence identity and domain composition they were phylogenetically classified into three groups those are conserved among the flowering plants. Similar gene structure and motif distribution were observed in the same group. Subcellular localization assays demonstrated that all PaCOL proteins were localized in nucleus. Furthermore, differential expression patterns of PaCOL genes were observed in various tissues. The expression patterns of PaCOL genes were observed under various abiotic and phytohormone treatment to explore their relatedness in different stresses. Moreover, several stress and light-responsive cis-elements were detected for different PaCOL genes.ConclusionThe COL genes of petunia genome, those were clustered into three distinct groups, are conserved among flowering plants, were expressed in different tissues and induced under multiple abiotic stress treatments indicating their involvement in plant growth and development and stress response mechanism. This work laid the significant foundation for functional characterization of PaCOL gene family to uncover their biological roles in plant growth, development and in stress response.

scholarly journals Genome-Wide Identification of WOX Gene Family and Expression Analysis during Rejuvenational Rhizogenesis in Walnut (Juglans regia L.)

Forests ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 16 ◽  
Author(s):  
Yingying Chang ◽  
Xiaobo Song ◽  
Qixiang Zhang ◽  
Hao Liu ◽  
Yongchao Bai ◽  
...  
Keyword(s):  
Gene Family ◽  
Cell Fate ◽  
Zygotic Embryo ◽  
Expression Profiles ◽  
Juglans Regia ◽  
Conserved Motifs ◽  
Significance Level ◽  
Immature Fruit ◽  
Genome Wide ◽  
A Genome

Rejuvenation is an efficient approach used in the cuttings of trees and horticultural crops, to improve their rooting ability, especially in difficult-to-root trees. WOX gene family members are involved in cell-fate transformation through balancing the maintenance and proliferation of the stem cells. However, there are no reports about the WOX gene family in Walnut (Juglans regia L.) and its relationship between rejuvenation and adventitious roots formation (ARF). Here, a genome-wide identification of JrWOX genes and their physical and chemical properties, phylogeny, and expression profiles in different organs and during rejuvenation-induced ARF is reported. The phenotype and histology characteristics of mature and rejuvenated cuttings (Mc and Rc) are also observed. In this study, 12 genes were identified and clustered into three groups based on phylogenetics, special domains, and conserved motifs. The gene structures and conserved motifs were relatively conserved, while the 12 sequences of the JrWOXs domain were diversified. Gene expression in root, stem, leaf, female flower, immature fruit, and zygotic embryo revealed that the expression levels of JrWOX4a, JrWOX4b, JrWOX5, JrWOX11, and JrWOX13 in the root were significantly higher than those of other JrWOXs, while only the expression of JrWOX11 was exclusive to the root organ. Additionally, rejuvenation treatment significantly induced almost all JrWOX genes, except JrWOX4a, JrWOX4b, and JrWOX13 (Rc 0 vs. Mc 0). During the ARF process, the transcripts of JrWOX11 and JrWOX5 were consecutively increased on a significance level; in contrast, the transcription levels of the other JrWOXs decreased or changed insignificantly. The phenotype and histology observation indicate that rejuvenation treatment made the base of the stem expand and reduced the thickness and density of sclerenchyma between the cortex and phloem. This might provide the conditions for the formation of new meristem niches. The results provided insight into the JrWOX genes’ general characteristics and their roles in rejuvenation-induced ARF.

scholarly journals Genome-Wide Identification and Transcriptional Expression of the METTL21C Gene Family in Chicken

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 628 ◽  
Author(s):  
Ge Yang ◽  
Hongzhao Lu ◽  
Ling Wang ◽  
Jiarong Zhao ◽  
Wenxian Zeng ◽  
...  
Keyword(s):  
Gene Family ◽  
Muscle Development ◽  
Quantitative Polymerase Chain Reaction ◽  
Reference Value ◽  
Transcriptional Expression ◽  
Nutritional Values ◽  
Genome Wide ◽  
A Genome ◽  
Chicken Muscles

The chicken is a common type of poultry that is economically important both for its medicinal and nutritional values. Previous studies have found that free-range chickens have more skeletal muscle mass. The methyltransferase-like 21C gene (METTL21C) plays an important role in muscle development; however, there have been few reports on the role of METTL21C in chickens. In this study, we performed a genome-wide identification of chicken METTL21C genes and analyzed their phylogeny, transcriptional expression profile, and real-time quantitative polymerase chain reaction (qPCR). We identified 10 GgMETTL21C genes from chickens, 11 from mice, and 32 from humans, and these genes were divided into six groups, which showed a large amount of variation among these three species. A total of 15 motifs were detected in METTL21C genes, and the intron phase of the gene structure showed that the METTL21C gene family was conservative in evolution. Further, both the transcript data and qPCR showed that a single gene’s (GgMETTL21C3) expression level increased with the muscle development of chickens, indicating that the METTL21C genes are involved in the development of chicken muscles. Our results provide some reference value for the subsequent study of the function of METTL21C.

scholarly journals New Insights Into Structure and Function of TIFY Genes in Zea mays and Solanum lycopersicum: A Genome-Wide Comprehensive Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Parviz Heidari ◽  
Sahar Faraji ◽  
Mostafa Ahmadizadeh ◽  
Sunny Ahmar ◽  
Freddy Mora-Poblete
Keyword(s):  
Zea Mays ◽  
Gene Family ◽  
Solanum Lycopersicum ◽  
Plant Species ◽  
Active Sites ◽  
Critical Role ◽  
Comprehensive Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Plant Genes

The TIFY gene family, a key plant-specific transcription factor (TF) family, is involved in diverse biological processes including plant defense and growth regulation. Despite TIFY proteins being reported in some plant species, a genome-wide comparative and comprehensive analysis of TIFY genes in plant species can reveal more details. In the current study, the members of the TIFY gene family were significantly increased by the identification of 18 and six new members using maize and tomato reference genomes, respectively. Thus, a genome-wide comparative analysis of the TIFY gene family between 48 tomato (Solanum lycopersicum, a dicot plant) genes and 26 maize (Zea mays, a monocot plant) genes was performed in terms of sequence structure, phylogenetics, expression, regulatory systems, and protein interaction. The identified TIFYs were clustered into four subfamilies, namely, TIFY-S, JAZ, ZML, and PPD. The PPD subfamily was only detected in tomato. Within the context of the biological process, TIFY family genes in both studied plant species are predicted to be involved in various important processes, such as reproduction, metabolic processes, responses to stresses, and cell signaling. The Ka/Ks ratios of the duplicated paralogous gene pairs indicate that all of the duplicated pairs in the TIFY gene family of tomato have been influenced by an intense purifying selection, whereas in the maize genome, there are three duplicated blocks containing Ka/Ks > 1, which are implicated in evolution with positive selection. The amino acid residues present in the active site pocket of TIFY proteins partially differ in each subfamily, although the Mg or Ca ions exist heterogeneously in the centers of the active sites of all the predicted TIFY protein models. Based on the expression profiles of TIFY genes in both plant species, JAZ subfamily proteins are more associated with the response to abiotic and biotic stresses than other subfamilies. In conclusion, globally scrutinizing and comparing the maize and tomato TIFY genes showed that TIFY genes play a critical role in cell reproduction, plant growth, and responses to stress conditions, and the conserved regulatory mechanisms may control their expression.

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