Genome-Wide Identification, Expression Analysis, and Subcellular Localization of Carthamus tinctorius bHLH Transcription Factors

The basic helix–loop–helix (bHLH) family is the second largest superfamily of transcription factors that belongs to all three eukaryotic kingdoms. The key function of this superfamily is the regulation of growth and developmental mechanisms in plants. However, the bHLH gene family in Carthamus tinctorius has not yet been studied. Here, we identified 41 bHLH genes in Carthamus tinctorius that were classified into 23 subgroups. Further, we conducted a phylogenetic analysis and identified 10 conserved protein motifs found in the safflower bHLH family. We comprehensively analyzed a group of bHLH genes that could be associated with flavonoid biosynthesis in safflower by gene expression analysis, gene ontology annotation, protein interaction network prediction, subcellular localization of the candidate CtbHLH40 gene, and real-time quantitative expression analysis. This study provides genome-wide identification of the genes related to biochemical and physiological processes in safflower.

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Genome-wide identification and expression analysis of bZIP gene family in Carthamus tinctorius L.

Scientific Reports ◽

10.1038/s41598-020-72390-z ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Haoyang Li ◽

Lixia Li ◽

Guodong ShangGuan ◽

Chang Jia ◽

Sinan Deng ◽

...

Keyword(s):

Transcription Factors ◽

Functional Characterization ◽

Draft Genome ◽

Functional Differentiation ◽

Regulatory Elements ◽

Carthamus Tinctorius ◽

Specific Pattern ◽

Basic Leucine Zipper ◽

Protein Motifs ◽

Genome Wide

Abstract The basic leucine zipper (bZIP) is a widely known transcription factors family in eukaryotes. In plants, the role of bZIP proteins are crucial in various biological functions such as plant growth and development, seed maturation, response to light signal and environmental stress. To date, bZIP protein family has been comprehensively identified in Arabidopsis, castor, rice, ramie, soybean and other plant species, however, the complete genome-wide investigation of Carthamus tinctorius-bZIP family still remains unexplained. Here, we identified 52 putative bZIP genes from Carthamus tinctorius using a draft genome assembly and further analyzed their evolutionary classification, physicochemical properties, Conserved domain analysis, functional differentiation and the investigation of expression level in different tissues. Based on the common bZIP domain, CtbZIP family were clustered into 12 subfamilies renamed as (A–J, S, X), of which the X is a unique subfamily to Carthamus tinctorius. A total of 20 conserved protein motifs were found in CtbZIP proteins. The expression profiling of CtbZIP genes deciphered their tissue-specific pattern. Furthermore, the changes in CtbZIP transcript abundance suggested that their transcription regulation could be highly influenced by light intensity and hormones. Collectively, this study highlights all functional and regulatory elements of bZIP transcription factors family in Carthamus tinctorius which may serve as potential candidates for functional characterization in future.

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Genome-wide Identification, Evolution and Expression Analysis of Basic Helix-loop-helix (bHLH) Gene Family in Barley (Hordeum vulgare L.)

Current Genomics ◽

10.2174/1389202921999201102165537 ◽

2020 ◽

Vol 21 (8) ◽

pp. 624-644

Author(s):

Qinglin Ke ◽

Wenjing Tao ◽

Tingting Li ◽

Wenqiu Pan ◽

Xiaoyun Chen ◽

...

Keyword(s):

Stress Tolerance ◽

Expression Analysis ◽

Expression Profiles ◽

Regulatory Function ◽

Bhlh Transcription Factor ◽

Basic Helix Loop Helix ◽

Helix Loop Helix ◽

Genome Wide ◽

A Genome ◽

Bhlh Genes

Background: The basic helix-loop-helix (bHLH) transcription factor is one of the most important gene families in plants, playing a key role in diverse metabolic, physiological, and developmental processes. Although it has been well characterized in many plants, the significance of the bHLH family in barley is not well understood at present. Methods: Through a genome-wide search against the updated barley reference genome, the genomic organization, evolution and expression of the bHLH family in barley were systematically analyzed. Results: We identified 141 bHLHs in the barley genome (HvbHLHs) and further classified them into 24 subfamilies based on phylogenetic analysis. It was found that HvbHLHs in the same subfamily shared a similar conserved motif composition and exon-intron structures. Chromosome distribution and gene duplication analysis revealed that segmental duplication mainly contributed to the expansion of HvbHLHs and the duplicated genes were subjected to strong purifying selection. Furthermore, expression analysis revealed that HvbHLHs were widely expressed in different tissues and also involved in response to diverse abiotic stresses. The co-expression network was further analyzed to underpin the regulatory function of HvbHLHs. Finally, 25 genes were selected for qRT-PCR validation, the expression profiles of HvbHLHs showed diverse patterns, demonstrating their potential roles in relation to stress tolerance regulation. Conclusion: This study reported the genome organization, evolutionary characteristics and expression profile of the bHLH family in barley, which not only provide the targets for further functional analysis, but also facilitate better understanding of the regulatory network bHLH genes involved in stress tolerance in barley.

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Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in Brachypodium distachyon

BMC Genomics ◽

10.1186/s12864-016-2968-8 ◽

2016 ◽

Vol 17 (1) ◽

Cited By ~ 29

Author(s):

Licao Cui ◽

Kewei Feng ◽

Mengxing Wang ◽

Meng Wang ◽

Pingchuan Deng ◽

...

Keyword(s):

Transcription Factors ◽

Expression Analysis ◽

Brachypodium Distachyon ◽

Genome Wide ◽

Erf Transcription Factors

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A Classification of Basic Helix-Loop-Helix Transcription Factors of Soybean

International Journal of Genomics ◽

10.1155/2015/603182 ◽

2015 ◽

Vol 2015 ◽

pp. 1-10 ◽

Cited By ~ 16

Author(s):

Karen A. Hudson ◽

Matthew E. Hudson

Keyword(s):

Transcription Factors ◽

Genome Sequence ◽

Search Algorithm ◽

Soybean Genome ◽

Binding Potential ◽

Future Research ◽

Basic Helix Loop Helix ◽

Helix Loop Helix ◽

Bhlh Genes ◽

Wide Range

The complete genome sequence of soybean allows an unprecedented opportunity for the discovery of the genes controlling important traits. In particular, the potential functions of regulatory genes are a priority for analysis. The basic helix-loop-helix (bHLH) family of transcription factors is known to be involved in controlling a wide range of systems critical for crop adaptation and quality, including photosynthesis, light signalling, pigment biosynthesis, and seed pod development. Using a hidden Markov model search algorithm, 319 genes with basic helix-loop-helix transcription factor domains were identified within the soybean genome sequence. These were classified with respect to their predicted DNA binding potential, intron/exon structure, and the phylogeny of the bHLH domain. Evidence is presented that the vast majority (281) of these 319 soybean bHLH genes are expressed at the mRNA level. Of these soybean bHLH genes, 67% were found to exist in two or more homeologous copies. This dataset provides a framework for future studies on bHLH gene function in soybean. The challenge for future research remains to define functions for the bHLH factors encoded in the soybean genome, which may allow greater flexibility for genetic selection of growth and environmental adaptation in this widely grown crop.

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A genome-wide survey on basic helix-loop-helix transcription factors in rat and mouse

Mammalian Genome ◽

10.1007/s00335-009-9176-7 ◽

2009 ◽

Vol 20 (4) ◽

pp. 236-246 ◽

Cited By ~ 29

Author(s):

X. Zheng ◽

Y. Wang ◽

Q. Yao ◽

Z. Yang ◽

K. Chen

Keyword(s):

Transcription Factors ◽

Basic Helix Loop Helix ◽

Helix Loop Helix ◽

Genome Wide ◽

A Genome ◽

Genome Wide Survey

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Genome-wide Identification and Expression Analysis of Autophagy-related Genes (ATGs) in Medicago Truncatula

10.21203/rs.3.rs-109125/v1 ◽

2020 ◽

Author(s):

Mingkang Yang ◽

Liping Wang ◽

Xu Guo ◽

Chuanglie Lin ◽

Wei Huang ◽

...

Keyword(s):

Medicago Truncatula ◽

Expression Analysis ◽

Interaction Network ◽

Degradation Process ◽

Abiotic Stress Response ◽

Biotic And Abiotic Stress ◽

Comprehensive Overview ◽

Genome Wide ◽

Evolutionarily Conserved ◽

Gene Structures

Abstract Background: Autophagy is a highly conserved degradation process of cytoplasmic constituents in eukaryotes. Autophagy is known to be involved in the regulation of plant growth and development, as well as biotic and abiotic stress response. Although autophagy-related genes (ATGs) have been identified and characterized in many plant species, little is known about the autophagy process in Medicago truncatula. Results: In this study, 39 ATGs were identiﬁed in M. truncatula (MtATGs), and the gene structures and conserved domains of MtATGs were systematically characterized. In addition, many cis-elements which are related to hormone and stress responsiveness were identified in the promoters of MtATGs. Furthermore, phylogenetic analysis and interaction network analysis suggested that the function of MtATGs is evolutionarily conserved in Arabidopsis and M. truncatula. Gene expression analysis showed that most MtATGs were largely induced during seed development, but repressed by nodulation. Moreover, MtATGs were up-regulated in response to salt and drought stresses.Conclusion: These results provide a comprehensive overview of the MtATGs, which provided important clues for further functional analysis of autophagy in M. truncatula.

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Genome-Wide Identification and Characterization of Heat-Shock Transcription Factors in Rubber Tree

Forests ◽

10.3390/f10121157 ◽

2019 ◽

Vol 10 (12) ◽

pp. 1157 ◽

Cited By ~ 1

Author(s):

Yan Li ◽

Wencai Yu ◽

Yueyi Chen ◽

Shuguang Yang ◽

Shaohua Wu ◽

...

Keyword(s):

Transcription Factors ◽

Heat Shock ◽

Cold Stress ◽

Expression Patterns ◽

Rubber Tree ◽

Protein Motifs ◽

Heat Shock Transcription Factors ◽

Genome Wide ◽

Cold Tolerant ◽

Oligomerization Domain

Heat-shock transcription factors (Hsfs) play a pivotal role in the response of plants to various stresses. The present study aimed to characterize the Hsf genes in the rubber tree, a primary global source of natural rubber. In this study, 30 Hsf genes were identified in the rubber tree using genome-wide analysis. They possessed a structurally conserved DNA-binding domain and an oligomerization domain. On the basis of the length of the insert region between HR-A and HR-B in the oligomerization domain, the 30 members were clustered into three classes, Classes A (18), B (10), and C (2). Members within the same class shared highly conserved gene structures and protein motifs. The background expression levels of 11 genes in cold-tolerant rubber-tree clone 93-14 were significantly higher than those in cold-sensitive rubber-tree clone Reken501, while four genes exhibited inverse expression patterns. Upon cold stress, 20 genes were significantly upregulated in 93-114. Of the upregulated genes, HbHsfA2b, HbHsfA3a, and HbHsfA7a were also significantly upregulated in three other cold-tolerant rubber-tree clones at one or more time intervals upon cold stress. Their nuclear localization was verified, and the protein–protein interaction network was predicted. This study provides a basis for dissecting Hsf function in the enhanced cold tolerance of the rubber tree.

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