Genome Wide Identification and Characterization of Apple bHLH Transcription Factors and Expression Analysis in Response to Drought and Salt Stress

Mao, Ke; Dong, Qinglong; Li, Chao; Liu, Changhai; Ma, Fengwang

doi:10.3389/fpls.2017.00480

Cited by 174 publications

(173 citation statements)

References 66 publications

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“…Network interaction analysis has been demonstrated to be an effective method to analyse the gene function [40]. We used the online software STRING 10 to predict the protein interaction network with the 142 CsbHLH protein sequences as queries, which formed a complex interaction network constructed with orthologs in Arabidopsis.…”

Section: The Protein Interaction Network Predictions For Csbhlh Orthomentioning

confidence: 99%

“…The basic helix-loop-helix (bHLH) transcription factor family is the second largest family in eukaryotes [10,44] and extensive studies of bHLH families have been identified in various plants [2]. For example, 166 bHLH genes have been identified in Arabidopsis [2,10], 115 bHLH genes in Nelumbo nucifera [45], 188 bHLH genes in apple [40], 167 bHLH genes in rice [12] and 159 bHLH genes in tomato [13]. The bHLH transcription factors have been involved in multiple biological processes in plants, especially in regulating defense against biotic and abiotic stresses [46].…”

Section: Characterization Of the Cucumber Bhlh Familymentioning

confidence: 99%

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Genome wide identification and characterization of cucumber bHLH family genes and the functional characterization of CsbHLH041 in NaCl and ABA tolerance in Arabidopsis and cucumber

Wang

Han

et al. 2020

Preprint

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Background: The basic/helix-loop-helix (bHLH) transcription factor family exists in all three eukaryotic kingdoms as important regulatory components in biological growth and development. To date, there has been relatively little effort to systematically carry out comprehensive genomic and functional analyses of bHLH genes in cucumber ( Cucumis sativus L.). Results: Here, a total of 142 bHLH genes were identified in the recently released cucumber genome and further classified into 32 subgroups based on the phylogenetic analysis, conserved motifs and gene structures. Multiple sequence alignment analyses showed that the sequences of CsbHLH proteins were highly conserved. The chromosomal distribution, synteny analysis, and gene duplications of these 142 CsbHLHs were further analysed. A cis-element analysis revealed many elements related to stress responsiveness and plant hormones in the promoter regions of CsbHLH genes. Phylogenetic comparison of the bHLH members between cucumber and Arabidopsis , revealed that cucumber bHLH proteins were clustered into the different functional clades of Arabidopsis bHLH members. The transcript abundance analysis of selected CsbHLHs under abiotic stresses (NaCl, ABA and low-temperature treatments) identified five CsbHLH genes that could simultaneously respond to the three abiotic stresses. Tissue-specific expression profiles of these five genes were also analysed. In addition, 35S : CsbHLH041 enhanced the tolerance to salt and ABA in transgenic Arabidopsis and in cucumber seedlings, suggesting CsbHLH041 is an important regulator in response to abiotic stresses. Finally, the functional interoperability network among the CsbHLH proteins was analysed. Conclusion: This study provided a good foundation for further research into the functions and regulatory mechanisms of CsbHLH proteins and identified candidate genes for stress resistance in cucumber.

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Section: The Protein Interaction Network Predictions For Csbhlh Orthomentioning

confidence: 99%

Section: Characterization Of the Cucumber Bhlh Familymentioning

confidence: 99%

Genome wide identification and characterization of cucumber bHLH family genes and the functional characterization of CsbHLH041 in NaCl and ABA tolerance in Arabidopsis and cucumber

Wang

Han

et al. 2020

Preprint

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show abstract

“…The protein interaction network predictions for CsbHLH orthologs in Arabidopsis that were crucial for the abiotic stress response Network interaction analysis has been demonstrated to be an effective method to analyse the gene function [40]. We used the software STRING 10 to predict the protein interaction network among the 142 CsbHLH proteins (Fig.…”

Section: Expression Analysis Of Csbhlh Genes Under Different Stress Cmentioning

confidence: 99%

“…The basic helix-loop-helix (bHLH) transcription factor family is the second largest family in eukaryotes [10,44] and extensive studies of bHLH families have been identi ed in various plants [2]. For example, 166 bHLH genes have been identi ed in Arabidopsis [2,10], 115 bHLH genes in Nelumbo nucifera [45], 188 bHLH genes in apple [40], 167 bHLH genes in rice [12] and 159 bHLH genes in tomato [13]. The bHLH TFs have been involved in multiple biological processes in plants, especially in regulating defense against biotic and abiotic stresses [46].…”

Section: Characterization Of the Cucumber Bhlh Familymentioning

confidence: 99%

Genome-wide identification and characterization of cucumber bHLH family genes and the functional characterization of CsbHLH041 in NaCl and ABA tolerance in Arabidopsis and cucumber

Wang

Han

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: The basic/helix-loop-helix (bHLH) transcription factor family exists in all three eukaryotic kingdoms as important participants in biological growth and development. To date, the comprehensive genomic and functional analyses of bHLH genes has not been reported in cucumber (Cucumis sativus L.). Results: Here, a total of 142 bHLH genes were identified and classified into 32 subfamilies according to the conserved motifs, phylogenetic analysis and gene structures in cucumber. The sequences of CsbHLH proteins were highly conserved based on the results of multiple sequence alignment analyses. The chromosomal distribution, synteny analysis, and gene duplications of these 142 CsbHLHs were further analysed. Many elements related to stress responsiveness and plant hormones were present in the promoter regions of CsbHLH genes based on a cis-element analysis. By comparing the phylogeny of cucumber and Arabidopsis bHLH proteins, we found that cucumber bHLH proteins were clustered into different functional clades of Arabidopsis bHLH proteins. The expression analysis of selected CsbHLHs under abiotic stresses (NaCl, ABA and low-temperature treatments) identified five CsbHLH genes that could simultaneously respond to the three abiotic stresses. Tissue-specific expression profiles of these five genes were also analysed. In addition, 35S:CsbHLH041 enhanced the tolerance to salt and ABA in transgenic Arabidopsis and in cucumber seedlings, suggesting CsbHLH041 is an important regulator in response to abiotic stresses. Lastly, the functional interoperability network among the CsbHLH proteins was analysed. Conclusion: This study provided a good foundation for further research into the functions and regulatory mechanisms of CsbHLH proteins and identified candidate genes for stress resistance in cucumber.

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“…These genes are putative transcription factor bHLH63 (Cc05_g16570) and transcription factor bHLH135 (Cc07_g03240). According to Mao et al (2017), under salt stress condition some special bHLH TFs are activated and bind to the promoter of the key genes involved in various signaling pathways and regulate the stress tolerance of plants by regulating the transcription level of these target genes. In this experiment, two down regulated STP transcription factor genes were significantly expressed under salt stress condition.…”

Section: E-23mentioning

confidence: 99%

Transcriptome profiling of the coffee (C. arabica L.) seedlings under salt stress condition

Haile

Kang

2018

J Plant Biotechnol

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This research was conducted to study the gene expression of coffee (Coffea arabica L.) seedlings under salt stress condition. A solution of five percent (2.3 dS m-1) deep sea water was used for the salt treatment, and it was thereby compared to normal irrigation water (0.2 dS m-1) used for the control treatment. The mRNA was extracted from the leaves of the coffee seedlings for a comprehensive analysis. In this study, a total of 19,581 genes were identified and aligned to the reference sequences available in the coffee genome database. The gene ontology analysis was performed to estimate the number of genes associated with the identified biological processes, cellular components and molecular functions. Among the 19,581 genes, 7369 (37.64%) were associated with biological processes, 5909 (30.18%) with cellular components, and 5325 (27.19%) with molecular functions. The remaining 978 (4.99%) genes were therefore grouped as unclassified. A differential gene expression analysis was performed using the DESeq2 package to identify the genes that were differentially expressed between the treatments based on fold changes and p-values. Namely, a total of 611 differentially expressed genes were identified (treatment/control) in that case. Among these, 336 genes were up-regulated while 275 of the genes were downregulated. Of the differentially expressed genes, 60 genes showed statistically significant (p < 0.05) expression, 44 of which were up-regulated and 16 which were down-regulated. We also identified 11 differentially expressed transcription factor genes, 6 of which were up-regulated and rest 5 genes were down-regulated. The data generated from this study will help in the continued interest and understanding of the responses of coffee seedlings genes associated with salinity stress, in particular. This study will also provide important resources for further functional genomics studies.

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Genome Wide Identification and Characterization of Apple bHLH Transcription Factors and Expression Analysis in Response to Drought and Salt Stress

Cited by 174 publications

References 66 publications

Genome wide identification and characterization of cucumber bHLH family genes and the functional characterization of CsbHLH041 in NaCl and ABA tolerance in Arabidopsis and cucumber

Genome wide identification and characterization of cucumber bHLH family genes and the functional characterization of CsbHLH041 in NaCl and ABA tolerance in Arabidopsis and cucumber

Genome-wide identification and characterization of cucumber bHLH family genes and the functional characterization of CsbHLH041 in NaCl and ABA tolerance in Arabidopsis and cucumber

Transcriptome profiling of the coffee (C. arabica L.) seedlings under salt stress condition

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