scholarly journals NHX Gene Family in Camellia sinensis: In-silico Genome-Wide Identification, Expression Profiles, and Regulatory Network Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Abhirup Paul ◽  
Archita Chatterjee ◽  
Shreya Subrahmanya ◽  
Guoxin Shen ◽  
Neelam Mishra
Keyword(s):  
Camellia Sinensis ◽  
Regulatory Network ◽  
Expression Profiles ◽  
Abiotic Factors ◽  
Purifying Selection ◽  
Tea Plant ◽  
Functional Study ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search

Salt stress affects the plant growth and productivity worldwide and NHX is one of those genes that are well known to improve salt tolerance in transgenic plants. It is well characterized in several plants, such as Arabidopsis thaliana and cotton; however, not much is known about NHXs in tea plant. In the present study, NHX genes of tea were obtained through a genome-wide search using A. thaliana as reference genome. Out of the 9 NHX genes in tea, 7 genes were localized in vacuole while the remaining 2 genes were localized in the endoplasmic reticulum (ER; CsNHX8) and plasma membrane (PM; CsNHX9), respectively. Furthermore, phylogenetic relationships along with structural analysis which includes gene structure, location, and protein-conserved motifs and domains were systematically examined and further, predictions were validated by the expression analysis. The dN/dS values show that the majority of tea NHX genes is subjected to strong purifying selection under the course of evolution. Also, functional interaction was carried out in Camellia sinensis based on the orthologous genes in A. thaliana. The expression profiles linked to various stress treatments revealed wide involvement of NHX genes from tea in response to various abiotic factors. This study provides the targets for further comprehensive identification, functional study, and also contributed for a better understanding of the NHX regulatory network in C. sinensis.

scholarly journals In-silico genome wide identification, expressional profiling and regulation of NHX (Sodium/ Hydrogen Antiporter) gene family in Camellia sinensis

2021 ◽  
Author(s):  
Abhirup Paul ◽  
Archita Chatterjee ◽  
shreya Subrahmanya ◽  
Guoxin Shen ◽  
Neelam Mishra
Keyword(s):  
Expression Profiles ◽  
Abiotic Factors ◽  
Purifying Selection ◽  
Tea Plant ◽  
Functional Study ◽  
Functional Interaction ◽  
Orthologous Genes ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search

Abstract Background Salt stress affects the plant growth and productivity worldwide and NHX is one of those genes that are well known to improve salt tolerance in transgenic plants. It is well characterized in several plants such as Arabidopsis and cotton however not much is known about NHXs in tea plant. Result In the present study, NHX genes of tea were obtained through a genome wide search using Arabidopsis thaliana as reference genome. Out of the 9 NHX genes in tea, 7 genes were localized in vacuole while the remaining 2 genes were localized in the endoplasmic reticulum (ER) (TEA014468.1) and plasma membrane (PM) (TEA006997.1) respectively. Furthermore, phylogenetic relationships along with structural analysis which includes gene structure, location as well as protein conserved motifs and domains, were systematically examined and further, predictions were validated by the expression analysis. The dN/dS values show that the majority of tea NHX genes are subjected to strong purifying selection under the course of evolution. Also, functional interaction was carried out in C. sinensis based on the orthologous genes in Arabidopsis. The expression profiles linked to various stress treatments revealed wide involvement of NHX genes from tea in response to various abiotic factors. Conclusion This study provides the targets for further comprehensive identification, functional study, and also contributed for a better understanding of the NHX regulatory network in C. sinensis.

scholarly journals MAPK cascade gene family in Camellia sinensis: In-silico identification, expression profiles and regulatory network analysis

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Archita Chatterjee ◽  
Abhirup Paul ◽  
G. Meher Unnati ◽  
Ruchika Rajput ◽  
Trisha Biswas ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Camellia Sinensis ◽  
Regulatory Network ◽  
Expression Profiles ◽  
Abiotic Factors ◽  
Mapk Cascade ◽  
Mitogen Activated Protein Kinase ◽  
Functional Study ◽  
A Genome ◽  
Mitogen Activated Protein

Abstract Background Mitogen Activated Protein Kinase (MAPK) cascade is a fundamental pathway in organisms for signal transduction. Though it is well characterized in various plants, there is no systematic study of this cascade in tea. Result In this study, 5 genes of Mitogen Activated Protein Kinase Kinase (MKK) and 16 genes of Mitogen Activated Protein Kinase (MPK) in Camellia sinensis were found through a genome-wide search taking Arabidopsis thaliana as the reference genome. Also, phylogenetic relationships along with structural analysis which includes gene structure, location as well as protein conserved motifs and domains, were systematically examined and further, predictions were validated by the results. The plant species taken for comparative study clearly displayed segmental duplication, which was a significant candidate for MAPK cascade expansion. Also, functional interaction was carried out in C. sinensis based on the orthologous genes in Arabidopsis. The expression profiles linked to various stress treatments revealed wide involvement of MAPK and MAPKK genes from Tea in response to various abiotic factors. In addition, the expression of these genes was analysed in various tissues. Conclusion This study provides the targets for further comprehensive identification, functional study, and also contributed for a better understanding of the MAPK cascade regulatory network in C. sinensis.

scholarly journals Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley

2019 ◽  
Author(s):  
Licao Cui ◽  
Guang Yang ◽  
Jali Yan ◽  
Yan Pan ◽  
Xiaojun Nie
Keyword(s):  
Regulatory Network ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Mapk Cascade ◽  
Mitogen Activated Protein Kinase ◽  
Functional Study ◽  
Systematic Analysis ◽  
Protein Motifs ◽  
Genome Wide ◽  
A Genome

Abstract Background Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms. Although it has been well characterized in many plants, no systematic analysis has been conducted in barley. Results Here, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs in barley through a genome-wide search against the updated reference genome. Then, phylogenetic relationship, gene structure and conserved protein motifs organization of them were systematically analyzed and results supported the predictions. Gene duplication analysis revealed that segmental and tandem duplication events contributed to the expansion of barley MAPK cascade genes and the duplicated gene pairs were found to undergone strong purifying selection. Expression profiles of them were further investigated in different organs and under diverse abiotic stresses using the available 173 RNA-seq datasets, and then the tissue-specific and stress-responsive candidates were found. Finally, co-expression regulatory network of MAPK cascade genes was constructed by WGCNA tool, resulting in a complicated network composed of a total of 72 branches containing 46 HvMAPK cascade genes and 46 miRNAs. Conclusion This study provides the targets for further functional study and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.

scholarly journals Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Licao Cui ◽  
Guang Yang ◽  
Jiali Yan ◽  
Yan Pan ◽  
Xiaojun Nie
Keyword(s):  
Regulatory Network ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Mapk Cascade ◽  
Mitogen Activated Protein Kinase ◽  
Functional Study ◽  
Systematic Analysis ◽  
Protein Motifs ◽  
Genome Wide ◽  
A Genome

Abstract Background Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms. Although it has been well characterized in many plants, no systematic analysis has been conducted in barley. Results Here, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs in barley through a genome-wide search against the updated reference genome. Then, phylogenetic relationship, gene structure and conserved protein motifs organization of them were systematically analyzed and results supported the predictions. Gene duplication analysis revealed that segmental and tandem duplication events contributed to the expansion of barley MAPK cascade genes and the duplicated gene pairs were found to undergone strong purifying selection. Expression profiles of them were further investigated in different organs and under diverse abiotic stresses using the available 173 RNA-seq datasets, and then the tissue-specific and stress-responsive candidates were found. Finally, co-expression regulatory network of MAPK cascade genes was constructed by WGCNA tool, resulting in a complicated network composed of a total of 72 branches containing 46 HvMAPK cascade genes and 46 miRNAs. Conclusion This study provides the targets for further functional study and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.

scholarly journals Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley

2019 ◽  
Author(s):  
Licao Cui ◽  
Guang Yang ◽  
Jali Yan ◽  
Yan Pan ◽  
Xiaojun Nie
Keyword(s):  
Regulatory Network ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Mapk Cascade ◽  
Mitogen Activated Protein Kinase ◽  
Functional Study ◽  
Systematic Analysis ◽  
Protein Motifs ◽  
Genome Wide ◽  
A Genome

Abstract Background Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms. Although it has been well characterized in many plants, no systematic analysis has been conducted in barley. Results Here, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs in barley through a genome-wide search against the updated reference genome. Then, phylogenetic relationship, gene structure and conserved protein motifs organization of them were systematically analyzed and results supported the predictions. Gene duplication analysis revealed that segmental and tandem duplication events contributed to the expansion of barley MAPK cascade genes and the duplicated gene pairs were found to undergone strong purifying selection. Expression profiles of them were further investigated in different organs and under diverse abiotic stresses using the available 173 RNA-seq datasets, and then the tissue-specific and stress-responsive candidates were found. Finally, co-expression regulatory network of MAPK cascade genes was constructed by WGCNA tool, resulting in a complicated network composed of a total of 72 branches containing 46 HvMAPK cascade genes and 46 miRNAs. Conclusion This study provides the targets for further functional study and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.

scholarly journals Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley

2019 ◽  
Author(s):  
Licao Cui ◽  
Guang Yang ◽  
Jali Yan ◽  
Yan Pan ◽  
Xiaojun Nie
Keyword(s):  
Regulatory Network ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Mapk Cascade ◽  
Mitogen Activated Protein Kinase ◽  
Systematic Analysis ◽  
Functional Studies ◽  
Genome Wide ◽  
A Genome ◽  
Duplication Events

Abstract Background Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organism. Although it has been well characterized in many plants, no systematic analysis has been conducted in the model cereal crop barley. Results Here, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs through a genome-wide search method using the latest published barley genomic data. Phylogenetic analysis assigned all the MAPK cascade genes into three groups in accordance to MAPK, MAPKK and MAPKKK family. Gene duplication revealed that segmental and tandem duplication events contributed to the expansion of barley MAPK cascade genes and the duplicated gene pairs were found to undergone strong purifying selection. Expression profiles of the HvMAPK, HvMAPKK and HvMAPKKKs were then investigated in different organs and under diverse stresses using the available 132 RNA-seq datasets, and then the tissue-specific and stress-responsive ones were found. Finally, co-expression regulatory network of MAPK cascade genes was constructed by WGCNA tool, resulting in a complicated network composed of a total of 72 branches containing 46 HvMAPK cascade genes and 46 miRNAs. Conclusion This study provides the candidates for further functional studies and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.

scholarly journals Genome-Wide Identification of CsATGs in Tea Plant and the Involvement of CsATG8e in Nitrogen Utilization

2020 ◽  
Vol 21 (19) ◽  
pp. 7043
Author(s):  
Wei Huang ◽  
Dan-Ni Ma ◽  
Hong-Ling Liu ◽  
Jie Luo ◽  
Pu Wang ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Woody Species ◽  
Nutrient Utilization ◽  
Tea Plant ◽  
Plant Genome ◽  
Wild Type ◽  
Genome Wide ◽  
A Genome ◽  
Phosphorus And Potassium ◽  
Stage 1

Nitrogen (N) is a macroelement with an indispensable role in the growth and development of plants, and tea plant (Camellia sinensis) is an evergreen perennial woody species with young shoots for harvest. During senescence or upon N stress, autophagy has been shown to be induced in leaves, involving a variety of autophagy-related genes (ATGs), which have not been characterized in tea plant yet. In this study, a genome-wide survey in tea plant genome identified a total of 80 Camellia Sinensis autophagy-related genes, CsATGs. The expression of CsATG8s in the tea plant showed an obvious increase from S1 (stage 1) to S4 (stage 4), especially for CsATG8e. The expression levels of AtATGs (Arabidopsis thaliana) and genes involved in N transport and assimilation were greatly improved in CsATG8e-overexpressed Arabidopsis. Compared with wild type, the overexpression plants showed earlier bolting, an increase in amino N content, as well as a decrease in biomass and the levels of N, phosphorus and potassium. However, the N level was found significantly higher in APER (aerial part excluding rosette) in the overexpression plants relative to wild type. All these results demonstrated a convincing function of CsATG8e in N remobilization and plant development, indicating CsATG8e as a potential gene for modifying plant nutrient utilization.

scholarly journals Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis

2020 ◽  
Author(s):  
Zheng Liu ◽  
Xiao-Xia Ge ◽  
Xiao-Meng Wu ◽  
Qiang Xu ◽  
Ross G. Atkinson ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Sweet Orange ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionary Features ◽  
Duplication Events

Abstract Background: In citrus, genetic improvement via biotechnology is hindered by the obstacle of in vitro regeneration via somatic embryogenesis (SE). Although a few B3 transcription factors are reported to regulate embryogenesis, little is known about the B3 superfamily in citrus, and which members might be involved in SE.Results: Genome-wide sequence analysis identified 72 (CsB3) and 69 (CgB3) putative B3 superfamily members in the genomes of sweet orange (Citrus sinensis, polyembryonic) and pummelo (C. grandis, monoembryonic), respectively. Genome duplication analysis indicated that segmental and tandem duplication events contributed to the expansion of the B3 superfamily in citrus, and that the B3 superfamily evolved under the effect of purifying selection. Phylogenetic relationships were well supported by conserved gene structure and motifs outside the B3 domain, which allowed possible functions to be inferred by comparison with homologous genes from Arabidopsis. Expression analysis identified 23 B3 superfamily members that were expressed during SE in citrus and 17 that may play functional roles at late SE stages. Eight B3 genes were identified that were specific to the genome of polyembryonic sweet orange compared to monoembryonic pummelo. Of these eight B3 genes, CsARF19 was found to be specifically expressed at higher levels in embryogenic callus (EC), implying its possible involvement in EC initiation. Conclusions: This study provides a genome-wide analysis of the citrus B3 superfamily, including its genome organization, evolutionary features and expression profiles, and identifies specific family members that may be associated with SE.

scholarly journals A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling Their Expression Profiles under Abiotic Stress in Rapeseed

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1072 ◽  
Author(s):  
Cailin Qiao ◽  
Jing Yang ◽  
Yuanyuan Wan ◽  
Sirou Xiang ◽  
Mingwei Guan ◽  
...  
Keyword(s):  
Differential Expression ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Purifying Selection ◽  
High Similarity ◽  
Genome Wide ◽  
A Genome ◽  
Duplication Events ◽  
Group 2 ◽  
Genome Wide Survey

The multidrug and toxic compound extrusion (MATE) protein family is important in the export of toxins and other substrates, but detailed information on this family in the Brassicaceae has not yet been reported compared to Arabidopsis thaliana. In this study, we identified 57, 124, 81, 85, 130, and 79 MATE genes in A. thaliana, Brassica napus, Brassica oleracea, Brassica rapa, Brassica juncea, and Brassica nigra, respectively, which were unevenly distributed on chromosomes owing to both tandem and segmental duplication events. Phylogenetic analysis showed that these genes could be classified into four subgroups, shared high similarity and conservation within each group, and have evolved mainly through purifying selection. Furthermore, numerous B. napusMATE genes showed differential expression between tissues and developmental stages and between plants treated with heavy metals or hormones and untreated control plants. This differential expression was especially pronounced for the Group 2 and 3 BnaMATE genes, indicating that they may play important roles in stress tolerance and hormone induction. Our results provide a valuable foundation for the functional dissection of the different BnaMATE homologs in B. napus and its parental lines, as well as for the breeding of more stress-tolerant B. napus genotypes.

scholarly journals Genome-Wide Analysis of Myeloblastosis-Related Genes in Brassica napus L. and Positive Modulation of Osmotic Tolerance by BnMRD107

2021 ◽  
Vol 12 ◽  
Author(s):  
Jian Li ◽  
Keyun Lin ◽  
Shuai Zhang ◽  
Jian Wu ◽  
Yujie Fang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Brassica Napus ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Functional Study ◽  
Evolutionary Analysis ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Myeloblastosis (MYB)-related transcription factors comprise a large subfamily of the MYB family. They play significant roles in plant development and in stress responses. However, MYB-related proteins have not been comprehensively investigated in rapeseed (Brassica napus L.). In the present study, a genome-wide analysis of MYB-related transcription factors was performed in rapeseed. We identified 251 Brassica napus MYB (BnMYB)-related members, which were divided phylogenetically into five clades. Evolutionary analysis suggested that whole genome duplication and segmental duplication events have played a significant role in the expansion of BnMYB-related gene family. Selective pressure of BnMYB-related genes was estimated using the Ka/Ks ratio, which indicated that BnMYB-related genes underwent strong purifying selection during evolution. In silico analysis showed that various development-associated, phytohormone-responsive, and stress-related cis-acting regulatory elements were enriched in the promoter regions of BnMYB-related genes. Furthermore, MYB-related genes with tissue or organ-specific, stress-responsive expression patterns were identified in B. napus based on temporospatial and abiotic stress expression profiles. Among the stress-responsive MYB-related genes, BnMRD107 was strongly induced by drought stress, and was therefore selected for functional study. Rapeseed seedlings overexpressing BnMRD107 showed improved resistance to osmotic stress. Our findings not only lay a foundation for further functional characterization of BnMYB-related genes, but also provide valuable clues to determine candidate genes for future genetic improvement of B. napus.

Sign in / Sign up

Export Citation Format

Share Document