Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.)

Zhao, Wei; Liu, Yonghui; Li, Lin; Meng, Hao; Yang, Ying; Dong, Zhaobin; Wang, Lei; Wang, Guoliang

doi:10.3389/fgene.2021.632509

Cited by 28 publications

(28 citation statements)

References 48 publications

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“…In addition, the transcription factor family has contributed to resisting adverse environmental factors in plants, such as drought resistance, salt tolerance, cold tolerance, plant iron deficiency stress, and so on (Toledo-Ortiz et al, 2003). A great many bHLH genes have been distinguished in the plant kingdom, including A. thaliana (162) (Pires and Dolan, 2010), Hibiscus hamabo (162) (Ni et al, 2021), Helianthus annuus (183) (Li et al, 2021), Capsicum annuum (107) , Sorghum bicolor (174) (Fan et al, 2021), Osmanthus fragrans (206) (Li et al, 2020), Camellia sinensis (134) , Juglans regia (102) (Zhao et al, 2021), Pyrus bretschneideri (197) (Dong et al, 2021). The number of bHLH transcription factors changed widely among various plants.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Low-Temperature Expression Analysis of bHLH Genes in Prunus mume

Ding

et al. 2021

Front. Genet.

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Prunus mume is an illustrious ornamental woody plant with colorful flowers, delicate fragrances, and graceful tree forms. Low temperature limits its geographical distribution. The basic helix-loop-helix (bHLH) proteins exist in most eukaryotes as a transcription factor superfamily, which play a crucial role in metabolism, physiology, development, and response to various stresses of higher organisms. However, the characteristics of the bHLH gene family and low-temperature response remain unknown in P. mume. In the present study, we distinguished 95 PmbHLH genes in the P. mume whole-genome and analyzed their features. PmbHLHs were divided into 23 subfamilies and one orphan by phylogenetic analysis. Similar gene structures and conserved motifs appeared in the same subfamily. These genes were situated in eight chromosomes and scaffolds. Gene duplication events performed a close relationship to P. mume, P. persica, and P. avium. Tandem duplications probably promoted the expansion of PmbHLHs. According to predicted binding activities, the PmbHLHs were defined as the Non-DNA-binding proteins and DNA-binding proteins. Furthermore, PmbHLHs exhibited tissue-specific and low-temperature induced expression patterns. By analyzing transcriptome data, 10 PmbHLHs which are responsive to low-temperature stress were selected. The qRT-PCR results showed that the ten PmbHLH genes could respond to low-temperature stress at different degrees. There were differences in multiple variations among different varieties. This study provides a basis to research the evolution and low-temperature tolerance of PmbHLHs, and might enhance breeding programs of P. mume by improving low-temperature tolerance.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Low-Temperature Expression Analysis of bHLH Genes in Prunus mume

Ding

et al. 2021

Front. Genet.

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“…In Arabidopsis thaliana, for example, 162 bHLH genes were discovered and divided into 21 subfamilies [14]; 115 bHLH genes, divided into 21 subfamilies, were identified in spine grapes [15]. In red walnut, 102 bHLH genes were discovered, which were split into 15 subfamilies [16]. In pepper, 122 bHLH genes were discovered and split into 21 subfamilies [17].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Analysis of Basic Helix-Loop-Helix Family Genes and Expression Analysis in Response to Drought and Salt Stresses in Hibiscus hamabo Sieb. et Zucc

Wang

et al. 2021

IJMS

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The basic helix-loop-helix (bHLH) family of transcription factors is one of the most significant and biggest in plants. It is involved in the regulation of both growth and development, as well as stress response. Numerous members of the bHLH family have been found and characterized in woody plants in recent years. However, no systematic study of the bHLH gene family has been published for Hibiscus hamabo Sieb. et Zucc. In this research, we identified 162 bHLH proteins (HhbHLHs) from the genomic and transcriptomic datasets of H. hamabo, which were phylogenetically divided into 19 subfamilies. According to a gene structural study, the number of exon-introns in HhbHLHs varied between zero and seventeen. MEME research revealed that the majority of HhbHLH proteins contained three conserved motifs, 1, 4, and 5. The examination of promoter cis-elements revealed that the majority of HhbHLH genes had several cis-elements involved in plant growth and development and abiotic stress responses. In addition, the overexpression of HhbHLH2 increased salt and drought stress tolerance in Arabidopsis.

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“…However, phenotype traits of walnut varieties are close, with green leaves and yellow-brown or gray-yellow seed coat. Luckily, a red walnut accession 'RW-1' was found by our research group, with the red color leaf, pericarp, seed coat and xylem owing to high anthocyanin content [22], and several bHLH TFs and CHS structural genes were identi ed in anthocyanin biosynthesis [23,24]. However, the molecular mechanism of anthocyanin biosynthesis has not yet been clearly elucidated in red walnut.…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, 92.23-95.27% of the total clean reads were unique matches with the walnut reference genome[23,24,33], 4,131 novel genes were identi ed, including 3,154 annotated genes.…”

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confidence: 99%

Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in red walnut

Wang¹,

Li²,

Zhao³

et al. 2021

Preprint

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Background Walnut is one of the most important dry fruit crops worldwide, typically green leaves and yellow-brown or gray-yellow seed coats. A specific walnut type, red walnut ‘RW-1’ with red leaves and seed coats was selected as plant material because of higher anthocyanins contents. Anthocyanins are important colorants with strong antioxidant activity, especially, benefic for human health. However, few studies focused on the molecular mechanism of anthocyanin biosynthesis in walnut. Results From the results of Widely Targeted Metabolome and anthocyanidin detection analysis, 395 substances, including 4 procyanidins and 26 anthocyanins, were identified from the red-leaf walnuts of RW-1 natural hybrid progenies (SR) and the green-leaf walnuts of RW-1 natural hybrid progenies (SG). Among these, all the anthocyanins in SR were significantly up-accumulated comparing with SG. Also, delphinidin 3-O-galactoside, cyanidin 3-O-galactoside, delphinidin 3-O-glucoside and cyanidin 3-O-glucoside were identified to the primary components of anthocyanidins because of the higher contents. It was noted that 9 anthocyanins including malvidin 3-O-galactoside, malvidin 3-O-arabinoside, cyanidin 3-O-(6-O-malonyl-beta-D-glucoside), delphinidin 3-O-glucoside, delphinidin 3,5-O-diglucoside (Delphin), peonidin 3-O-(6-O-malonyl-beta-D-glucoside), petunidin 3-O-(6-O-malonyl-beta-D-glucoside), petunidin 3-O-arabinoside and pelargonidin 3-O-(6-O-malonyl-beta-D-glucoside) were detected only in SR walnut. Furthermore, transcriptome analysis demonstrated that the expression of structural genes (C4H, F3H, F3’5’H and UFGTs), and four MYBs in anthocyanin biosynthetic pathway were significantly higher in SR walnut. Conclusions We identified the color formation of SR leaves is due to the accumulation of anthocyanins. And our results obtained the valuable information on the anthocyanin metabolites and candidate genes in anthocyanin biosynthesis, which provided new insights into the anthocyanin biosynthesis in walnuts.

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Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.)

Cited by 28 publications

References 48 publications

Genome-Wide Identification and Low-Temperature Expression Analysis of bHLH Genes in Prunus mume

Genome-Wide Identification and Low-Temperature Expression Analysis of bHLH Genes in Prunus mume

Genome-wide Analysis of Basic Helix-Loop-Helix Family Genes and Expression Analysis in Response to Drought and Salt Stresses in Hibiscus hamabo Sieb. et Zucc

Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in red walnut

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