Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.)

Fan, Yu; Lai, Dili; Yang, Hao; Xue, Guoxing; He, Ailing; Chen, Long; Feng, Liang; Ruan, Jingjun; Xiang, Dabing; Yan, Jun; Cheng, Jianping

doi:10.1186/s12864-021-08095-y

Cited by 24 publications

(28 citation statements)

References 102 publications

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“…The clustering of LsbHLHs based on their protein sequence is indicative of functional homogeneity among these genes. This number of bHLH genes is similar to those found in other plant species, such as foxtail millet, where 187 bHLH genes were identified and classified into 21 subfamilies ( Fan et al, 2021) . Tomato also had a high number of bHLH genes, with 159 identified and classified into 21 subfamilies through phylogenetic analysis ( Sun et al, 2015) .…”

Section: Discussionsupporting

confidence: 78%

Genome-wide identification, characterization, and validation of the bHLH transcription factors in grass pea

et al. 2023

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Background: The basic helix-loop-helix (bHLH) transcription factor is a vital component in plant biology, with a significant impact on various aspects of plant growth, cell development, and physiological processes. Grass pea is a vital agricultural crop that plays a crucial role in food security. However, the lack of genomic information presents a major challenge to its improvement and development. This highlights the urgency for deeper investigation into the function of bHLH genes in grass pea to improve our understanding of this important crop.Results: The identification of bHLH genes in grass pea was performed on a genome-wide scale using genomic and transcriptomic screening. A total of 122 genes were identified as having conserved bHLH domains and were functionally and fully annotated. The LsbHLH proteins could be classified into 18 subfamilies. There were variations in intron-exon distribution, with some genes lacking introns. The cis-element and gene enrichment analyses showed that the LsbHLHs were involved in various plant functions, including response to phytohormones, flower and fruit development, and anthocyanin synthesis. A total of 28 LsbHLHs were found to have cis-elements associated with light response and endosperm expression biosynthesis. Ten conserved motifs were identified across the LsbHLH proteins. The protein-protein interaction analysis showed that all LsbHLH proteins interacted with each other, and nine of them displayed high levels of interaction. RNA-seq analysis of four Sequence Read Archive (SRA) experiments showed high expression levels of LsbHLHs across a range of environmental conditions. Seven highly expressed genes were selected for qPCR validation, and their expression patterns in response to salt stress showed that LsbHLHD4, LsbHLHD5, LsbHLHR6, LsbHLHD8, LsbHLHR14, LsbHLHR68, and LsbHLHR86 were all expressed in response to salt stress.Conclusion: The study provides an overview of the bHLH family in the grass pea genome and sheds light on the molecular mechanisms underlying the growth and evolution of this crop. The report covers the diversity in gene structure, expression patterns, and potential roles in regulating plant growth and response to environmental stress factors in grass pea. The identified candidate LsbHLHs could be utilized as a tool to enhance the resilience and adaptation of grass pea to environmental stress.

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Section: Discussionsupporting

confidence: 78%

Genome-wide identification, characterization, and validation of the bHLH transcription factors in grass pea

et al. 2023

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“…All encoded proteins showed signi cant differences; for example, the amino acid length ranged from 94 (BvbHLH62) to 911 (BvbHLH77) amino acids, and the theoretical pI ranged from 4.32 (BvbHLH37) to 11.57 (BvbHLH20) kDa, indicating that the bHLH transcription factor family has diverged inconsistently over the long-term evolution of B. vulgaris, leading to its high complexity [40]. Among them, 80.21% of the BvbHLH proteins had pIs of less than 7, indicating that the B. vulgaris bHLH gene family is rich in acidic amino acids, which is in agreement with ndings related to the bHLH gene family in monocotyledons [35,44,45]. Subcellular localization predictions showed that the vast majority of BvbHLH proteins (90.6%) were localized in the nucleus, suggesting that this family of transcription factors plays a dominant regulatory role, mainly in the nucleus.…”

Section: Identi Cation and Structural Analysis Of The Bvbhlh Genessupporting

confidence: 81%

“…Subcellular localization predictions showed that 87 BvbHLH genes were located in the nucleus, 8 BvbHLH genes were located in the chloroplasts, and BvbHLH16 was located only in the cytoskeleton. The proportion of BvbHLH genes to total genes in the B. vulgaris genome was approximately 0.47%, which was close to Solanum lycopersicum (0.46%) [33], lower than A. thaliana (0.59%) [13], Brachypodium distachyon (0.55%) [16], Fagopyrum tataricum (0.49%) [34], Setaria italica (0.48%) [35], higher than that of O. sativa (0.44%) [16], PopulusL (0.40%) [36], and Hordeum vulgare (0.35%) [37].…”

Section: Characterization Of the Bvbhlh Genementioning

confidence: 99%

Identification, bioinformatics analysis, and expression profiling of the bHLH supergene family members in Beta vulgaris

Yang,

Peng,

Xue

et al. 2023

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Background Basic helix-loop-helix (bHLH) is one of the largest families of transcription factors in plants, animals, and microorganisms and plays an important complex physiological role in plant growth and development, metabolic regulation, and adversity stress. With the development of bioinformatics, bHLH transcription factor families have been continuously identified and analyzed, but the bHLH family of Beta vulgaris has not yet been analyzed and reported. Results Using whole-genome sequencing data from B. vulgaris, we identified 96 BvbHLHs genes with relatively large differences in physicochemical properties that were unevenly distributed across nine chromosomes. A phylogenetic developmental tree was constructed using the BvbHLH and AtbHLH proteins, which were ultimately categorized into 21 subgroups and one unclassified group. The gene structure, conserved motifs, gene duplication events, and evolutionary relationships of the 96 BvbHLH genes were analyzed using various bioinformatics approaches. The results showed that motifs 1 and 2 were widely distributed in BvbHLHs, had highly conserved gene structures within the same subfamily, presence of four tandem duplication events, and six pairs of segmental duplication events, and were more closely homologous to dicotyledonous plants. We also analyzed the tissue-specific expression of 12 BvbHLH genes during B. vulgaris maturity and their responses to eight abiotic stresses using quantitative real-time polymerase chain reaction. Conclusions A total of 96 BvbHLH genes were identified. Bioinformatics analysis of the gene structure, evolutionary relationship, and expression pattern of the B. vulgaris bHLH gene family lays a foundation for the evolution of the bHLH gene family and the screening of candidate genes in B. vulgaris.

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“…These proteins play important roles in plants, including controlling flower development [ 2 , 3 ], carbon and nitrogen metabolism [ 4 ], the circadian clock [ 5 ], cell differentiation [ 6 ], hormone response [ 7 ], and disease resistance [ 8 ]. At present, many TFs have been identified and analyzed in foxtail millet, such as NAC [ 9 ], bHLH [ 10 ], AP2/ERF [ 11 ], GRAS [ 12 ], WRKY [ 13 ], and bZIP [ 14 ]. However, few studies have focused on the GATA TF family in foxtail millet.…”

Section: Introductionmentioning

confidence: 99%

Genome‑wide identification, phylogenetic and expression pattern analysis of GATA family genes in foxtail millet (Setaria italica)

et al. 2022

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Background Transcription factors (TFs) play important roles in plants. Among the major TFs, GATA plays a crucial role in plant development, growth, and stress responses. However, there have been few studies on the GATA gene family in foxtail millet (Setaria italica). The release of the foxtail millet reference genome presents an opportunity for the genome-wide characterization of these GATA genes. Results In this study, we identified 28 GATA genes in foxtail millet distributed on seven chromosomes. According to the classification method of GATA members in Arabidopsis, SiGATA was divided into four subfamilies, namely subfamilies I, II, III, and IV. Structural analysis of the SiGATA genes showed that subfamily III had more introns than other subfamilies, and a large number of cis-acting elements were abundant in the promoter region of the SiGATA genes. Three tandem duplications and five segmental duplications were found among SiGATA genes. Tissue-specific results showed that the SiGATA genes were mainly expressed in foxtail millet leaves, followed by peels and seeds. Many genes were significantly induced under the eight abiotic stresses, such as SiGATA10, SiGATA16, SiGATA18, and SiGATA25, which deserve further attention. Conclusions Collectively, these findings will be helpful for further in-depth studies of the biological function of SiGATA, and will provide a reference for the future molecular breeding of foxtail millet.

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Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.)

Cited by 24 publications

References 102 publications

Genome-wide identification, characterization, and validation of the bHLH transcription factors in grass pea

Genome-wide identification, characterization, and validation of the bHLH transcription factors in grass pea

Identification, bioinformatics analysis, and expression profiling of the bHLH supergene family members in Beta vulgaris

Genome‑wide identification, phylogenetic and expression pattern analysis of GATA family genes in foxtail millet (Setaria italica)

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