bhlh genes
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2021 ◽  
Author(s):  
Pengwei Duan ◽  
Xiaojian Ma ◽  
Lizhe Qin ◽  
Jizhuang Du ◽  
Guoliang Xu ◽  
...  

Abstract Background:Coloring is an important external quality of ‘Fuji’ apple (Malus domestica Borkh.) and there are two color patterns of apple peels, i.e., stripe and blush. The objectives of this study were to reveal the anthocyanin biosynthesis metabolic pathway in striped and blushed peels of Malus domestica using metabolomics and transcriptomics, to identify different anthocyanin metabolites, and to analyze the differentially expressed genes involved in anthocyanin biosynthesis.Result:The metabolite concentration and gene expression were profiled in the striped and blushed fruit peels of apple harvested at three ripening periods to elucidate the color formation mechanism. At the green fruit period, there were 83 DAMs,including 30 flavonoids, 674 DEGs (521 up-regulated and 153 down-regulated),including 3 MYB related genes (up-regulated, LOC103415449, LOC103421948, LOC103432338) and 2 bHLH genes(up-regulated, LOC103436250, LOC103437863) between striped and blushed apple.At the color turning period, there were 48 DAMs,including 20 flavonoids, 880 DEGs (274 up-regulated and 606 down-regulated), including 3 differentially expressed E2.3.1.133, HCT genes(down-regulated), 2 differentially expressed F3H genes (down-regulated), 1 differentially expressed BZ1 gene (down-regulated) and 2 differentially expressed ANS genes (up-regulated) and 2 up-regulated MYB related genes (LOC103411576, LOC103412495), 5 down-regulated MYB related genes(LOC103400953, LOC103408672, LOC103415404, LOC103420697, LOC103421948), 1 differentially expressed bHLH gene(down-regulated, LOC103400870). At the complete coloring period,there were 95 DAMs,including 34 flavonoids, 2258 DEGs (1159 up- and 1099 down-regulated), including 3 differentially expressed E2.3.1.133, HCT genes(down-regulated), 1 differentially expressed E2.3.1.133, HCT genes(up-regulated), 2 differentially expressed CYP98A genes (up-regulated), 4 differentially expressed CHS genes (up-regulated), 2 differentially expressed E5.5.1.6 genes(up-regulated), 2 differentially expressed CYP75B1 genes (up-regulated), 2 differentially expressed F3R genes (up-regulated), 2 differentially expressed ANS genes (up-regulated), 1 differentially expressed DFR genes (up-regulated), 2 differentially expressed BZ1 genes (up-regulated) and 1 differentially expressed MYB related gene (up-regulated, LOC103401575) .There were both 10 kinds of cyanidin in apple peel at color turning period and complete coloring period, Keracyanin and Cyanin were up-regulated at color turning period and Cyanidin-3-O-(6''-O-malonyl)glucoside was up-regulated at complete coloring period.Conclusions: Our researches provide important information on the anthocyanin metabolites and the candidate genes involved in the anthocyanin biosynthesis pathways of Fuji apple in M.domestcia.


2021 ◽  
Vol 22 (24) ◽  
pp. 13274
Author(s):  
Yongyan Zhang ◽  
Fan Liu ◽  
Bin Wang ◽  
Huan Wu ◽  
Junwei Wu ◽  
...  

Basic helix-loop-helix proteins (bHLHs) play very important roles in the anthocyanin biosynthesis of many plant species. However, the reports on blueberry anthocyanin biosynthesis-related bHLHs were very limited. In this study, six anthocyanin biosynthesis-related bHLHs were identified from blueberry genome data through homologous protein sequence alignment. Among these blueberry bHLHs, VcAN1, VcbHLH42-1, VcbHLH42-2 and VcbHLH42-3 were clustered into one group, while VcbHLH1-1 and VcbHLH1-2 were clustered into the other group. All these bHLHs were of the bHLH-MYC_N domain, had DNA binding sites and reported conserved amino acids in the bHLH domain, indicating that they were all G-box binding proteins. Protein subcellular location prediction result revealed that all these bHLHs were nucleus-located. Gene structure analysis showed that VcAN1 gDNA contained eight introns, while all the others contained seven introns. Many light-, phytohormone-, stress- and plant growth and development-related cis-acting elements and transcription factor binding sites (TFBSs) were identified in their promoters, but the types and numbers of cis-elements and TFBSs varied greatly between the two bHLH groups. Quantitative real-time PCR results showed that VcAN1 expressed highly in old leaf, stem and blue fruit, and its expression increased as the blueberry fruit ripened. Its expression in purple podetium and old leaf was respectively significantly higher than in green podetium and young leaf, indicating that VcAN1 plays roles in anthocyanin biosynthesis regulation not only in fruit but also in podetium and leaf. VcbHLH1-1 expressed the highest in young leaf and stem, and the lowest in green fruit. The expression of VcbHLH1-1 also increased as the fruit ripened, and its expression in blue fruit was significantly higher than in green fruit. VcbHLH1-2 showed high expression in stem but low expression in fruit, especially in red fruit. Our study indicated that the anthocyanin biosynthesis regulatory functions of these bHLHs showed certain spatiotemporal specificity. Additionally, VcAN1 might be a key gene controlling the anthocyanin biosynthesis in blueberry, whose function is worth exploring further for its potential applications in plant high anthocyanin breeding.


Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2721
Author(s):  
Chao Tan ◽  
Huilei Qiao ◽  
Ming Ma ◽  
Xue Wang ◽  
Yunyun Tian ◽  
...  

The basic helix-loop-helix (bHLH) transcription factor family is one of the largest transcription factor families in plants and plays crucial roles in plant development. Melon is an important horticultural plant as well as an attractive model plant for studying fruit ripening. However, the bHLH gene family of melon has not yet been identified, and its functions in fruit growth and ripening are seldom researched. In this study, 118 bHLH genes were identified in the melon genome. These CmbHLH genes were unevenly distributed on chromosomes 1 to 12, and five CmbHLHs were tandem repeat on chromosomes 4 and 8. There were 13 intron distribution patterns among the CmbHLH genes. Phylogenetic analysis illustrated that these CmbHLHs could be classified into 16 subfamilies. Expression patterns of the CmbHLH genes were studied using transcriptome data. Tissue specific expression of the CmbHLH32 gene was analysed by quantitative RT-PCR. The results showed that the CmbHLH32 gene was highly expressed in female flower and early developmental stage fruit. Transgenic melon lines overexpressing CmbHLH32 were generated, and overexpression of CmbHLH32 resulted in early fruit ripening compared to wild type. The CmbHLH transcription factor family was identified and analysed for the first time in melon, and overexpression of CmbHLH32 affected the ripening time of melon fruit. These findings laid a foundation for further study on the role of bHLH family members in the growth and development of melon.


Author(s):  
Rong Jin ◽  
Ho-Soo Kim ◽  
Tao Yu ◽  
Aijun Zhang ◽  
Yufeng Yang ◽  
...  

2021 ◽  
Vol 12 ◽  
Author(s):  
Miaoyu Song ◽  
Haomiao Wang ◽  
Zhe Wang ◽  
Hantang Huang ◽  
Shangwu Chen ◽  
...  

The basic helix–loop–helix (bHLH) transcription factor family is the second largest transcription factor family in plants, and participates in various plant growth and development processes. A total of 118 bHLH genes were identified from fig (Ficus carica L.) by whole-genome database search. Phylogenetic analysis with Arabidopsis homologs divided them into 25 subfamilies. Most of the bHLHs in each subfamily shared a similar gene structure and conserved motifs. Seventy-two bHLHs were found expressed at fragments per kilobase per million mapped (FPKM) > 10 in the fig fruit; among them, 15 bHLHs from eight subfamilies had FPKM > 100 in at least one sample. bHLH subfamilies had different expression patterns in the female flower tissue and peel during fig fruit development. Comparing green and purple peel mutants, 13 bHLH genes had a significantly different (≥ 2-fold) expression. Light deprivation resulted in 68 significantly upregulated and 22 downregulated bHLH genes in the peel of the fruit. Sixteen bHLH genes in subfamily III were selected by three sets of transcriptomic data as candidate genes related to anthocyanin synthesis. Interaction network prediction and yeast two-hybrid screening verified the interaction between FcbHLH42 and anthocyanin synthesis-related genes. The transient expression of FcbHLH42 in tobacco led to an apparent anthocyanin accumulation. Our results confirm the first fig bHLH gene involved in fruit color development, laying the foundation for an in-depth functional study on other FcbHLH genes in fig fruit quality formation, and contributing to our understanding of the evolution of bHLH genes in other horticulturally important Ficus species.


2021 ◽  
Vol 12 ◽  
Author(s):  
Aiqin Ding ◽  
Anqi Ding ◽  
Ping Li ◽  
Jia Wang ◽  
Tangren Cheng ◽  
...  

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.


2021 ◽  
Vol 22 (18) ◽  
pp. 9787
Author(s):  
Ruonan Xu ◽  
Ronghui Pan ◽  
Yuchan Zhang ◽  
Yanlei Feng ◽  
Ujjal Kumar Nath ◽  
...  

Purple-colored leaves in plants attain much interest for their important biological functions and could be a potential source of phenotypic marker in selecting individuals in breeding. The transcriptional profiling helps to precisely identify mechanisms of leaf pigmentation in crop plants. In this study, two genetically unlike rice genotypes, the mutant purple leaf (pl) and wild (WT) were selected for RNA-sequencing and identifying the differentially expressed genes (DEGs) that are regulating purple leaf color. In total, 609 DEGs were identified, of which 513 and 96 genes were up- and down-regulated, respectively. The identified DEGs are categorized into metabolic process, carboxylic acid biosynthesis, phenylpropanoids, and phenylpropanoid biosynthesis process enrichment by GO analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) confirmed their association with phenylpropanoid synthesis, flavonoid synthesis, and phenylalanine metabolism. To explore molecular mechanism of purple leaf color, a set of anthocyanin biosynthetic and regulatory gene expression patterns were checked by qPCR. We found that OsPAL (Os02g0626100, Os02g0626400, Os04g0518400, Os05g0427400 and Os02g0627100), OsF3H (Os03g0122300), OsC4HL (Os05g0320700), and Os4CL5 (Os08g0448000) are associated with anthocyanin biosynthesis, and they were up-regulated in pl leaves. Two members of regulatory MYB genes (OsMYB55; Os05g0553400 and Os08g0428200), two bHLH genes (Os01g0196300 and Os04g0300600), and two WD40 genes (Os11g0132700 and Os11g0610700) also showed up-regulation in pl mutant. These genes might have significant and vital roles in pl leaf coloration and could provide reference materials for further experimentation to confirm the molecular mechanisms of anthocyanin biosynthesis in rice.


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