Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response

Aslam, Mohammad; Jakada, Bello Hassan; Fakher, Beenish; Greaves, Joseph G.; Niu, Xiaoping; Su, Zhenxia; Cheng, Yan; Cao, Shijiang; Wang, Xiaomei; Qin, Yuan

doi:10.1186/s12864-020-07152-2

Cited by 26 publications

(13 citation statements)

References 53 publications

(88 reference statements)

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“…Since the transcriptome data are not comprehensive in this study, and the genome of A. argyi has not been published, some bHLH family were still might not be identified yet. Based on genome data, 147 bHLH genes in Arabidopsis thaliana ( Toledo-Ortiz et al, 2003 ), 121 bHLH genes in pineapple ( Aslam M. et al, 2020 ) and 174 bHLH genes in sorghum ( Fan et al, 2021 ) were identified. Therefore, the identification of bHLH family members needs to be improved by genomic data.…”

Section: Discussionmentioning

confidence: 99%

Integrated Analysis of Basic Helix Loop Helix Transcription Factor Family and Targeted Terpenoids Reveals Candidate AarbHLH Genes Involved in Terpenoid Biosynthesis in Artemisia argyi

Wang²,

Lan³

et al. 2022

Front. Plant Sci.

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Artemisia argyi is a valuable traditional medicinal plant in Asia. The essential oil from its leaves is rich in terpenoids and has been used to enhance health and well-being. In China, the market scale of industries related to A. argyi has attained tens of billions of Chinese Yuan. The basic helix-loop-helix (bHLH) family is one of the largest transcription factors families in plants that plays crucial roles in diverse biological processes and is an essential regulatory component of terpenoid biosynthesis. However, the bHLH TFs and their regulatory roles in A. argyi remain unknown. Here, 53 AarbHLH genes were identified from the transcriptome of A. argyi and were classified into 15 subfamilies based on the classification of bHLH proteins in Arabidopsis thaliana. The MEME analysis showed that the conserved motif 1 and motif 2 constituted the most conserved bHLH domain and distributed in most AarbHLH proteins. Additionally, integrated analysis of the expression profiles of AarbHLH genes and the contents of targeted terpenoids in different tissues group and JA-treated group were performed. Eleven up-regulated AarbHLHs and one down-regulated AarbHLH were screened as candidate genes that may participate in the regulation of terpenoid biosynthesis (TPS-AarbHLHs). Correlation analysis between gene expression and terpenoid contents indicated that the gene expression of these 12 TPS-AarbHLHs was significantly correlated with the content changes of 1,8-cineole or β-caryophyllene. Protein–protein interaction networks further illustrated that these TPS-AarbHLHs might be involved in terpenoid biosynthesis in A. argyi. This finding provides a basis to further investigate the regulation mechanism of AarbHLH genes in terpenoid biosynthesis, and will be helpful to improve the quality of A. argyi.

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Section: Discussionmentioning

confidence: 99%

Integrated Analysis of Basic Helix Loop Helix Transcription Factor Family and Targeted Terpenoids Reveals Candidate AarbHLH Genes Involved in Terpenoid Biosynthesis in Artemisia argyi

Wang²,

Lan³

et al. 2022

Front. Plant Sci.

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“…The bHLH family has been widely identified in many plants, including Brassica rapa ssp. pekinensis [ 11 ], Solanum lycopersicum [ 12 ], common bean [ 13 ], Malus pumila [ 14 ], Arachis hypogaea [ 15 ], Brachypodium distachyon [ 16 ], Zea mays [ 17 ], Triticum aestivum [ 18 ], Phyllostachys edulis [ 19 ], Carthamus tinctorius [ 20 ], Chinese jujube [ 21 ], Piper nigrum [ 22 ], Jilin ginseng [ 23 ], Ananas comosus [ 24 ], Fagopyrum tataricum [ 25 ], and sorghum [ 26 ]. The bHLH genes have been conserved in the evolutionary history of the plant kingdom.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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Background Members of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. However, the bHLH family in foxtail millet (Setaria italica), an important food and feed crop, has not been thoroughly studied. Results In this study, 187 bHLH genes of foxtail millet (SibHLHs) were identified and renamed according to the chromosomal distribution of the SibHLH genes. Based on the number of conserved domains and gene structure, the SibHLH genes were divided into 21 subfamilies and two orphan genes via phylogenetic tree analysis. According to the phylogenetic tree, the subfamilies 15 and 18 may have experienced stronger expansion in the process of evolution. Then, the motif compositions, gene structures, chromosomal spread, and gene duplication events were discussed in detail. A total of sixteen tandem repeat events and thirty-eight pairs of segment duplications were identified in bHLH family of foxtail millet. To further investigate the evolutionary relationship in the SibHLH family, we constructed the comparative syntenic maps of foxtail millet associated with representative monocotyledons and dicotyledons species. Finally, the gene expression response characteristics of 15 typical SibHLH genes in different tissues and fruit development stages, and eight different abiotic stresses were analysed. The results showed that there were significant differences in the transcription levels of some SibHLH members in different tissues and fruit development stages, and different abiotic stresses, implying that SibHLH members might have different physiological functions. Conclusions In this study, we identified 187 SibHLH genes in foxtail millet and further analysed the evolution and expression patterns of the encoded proteins. The findings provide a comprehensive understanding of the bHLH family in foxtail millet, which will inform further studies on the functional characteristics of SibHLH genes.

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“…Moreover, bHLH and MADS-box gene family members play a key role in plant reproductive development. For example, a previous study showed the early flowering phenotype in the Arabidopsis cib2 mutant and the complementation of the early flowering phenotype by 35S::AcCIB2 -GFP [ 58 ]. The ectopic overexpression of one Phyllostachys edulis MADS-box gene, PeMADS5 , triggered earlier flowering in Arabidopsis and the development of an aberrant flower phenotype [ 59 ].…”

Section: Discussionmentioning

confidence: 99%

Integrative Analyses of Transcriptomes and Metabolomes Reveal Associated Genes and Metabolites with Flowering Regulation in Common Vetch (Vicia sativa L.)

Zhou

Cui

Dong

et al. 2022

IJMS

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As an important source of protein for livestock and human consumption, Vicia sativa is cultivated worldwide, but its seed production is hampered at high altitudes because of the short frost-free period. Flowering represents the transition from a vegetative to a reproductive period, and early flowering benefits plant seed production at high altitudes. However, the molecular mechanisms of flowering regulation in V. sativa remain elusive. In the present study, two V. sativa accessions with different flowering characteristics were used: Lan3 (early-flowering) was cultivated by our laboratory, and 503 (late-flowering) was selected from 222 V. sativa accessions after three years of field experiments. The shoot samples (shoot tip length = 10 cm) of these two accessions were collected 63, 70, and 77 days after sowing, and the molecular regulatory mechanism of the flowering process was identified by integrative analyses of the transcriptomes and metabolomes. Kyoto Encyclopedia of Genes and Genomes enrichment showed that the synthesis and signal transduction of plant hormone pathways were the most enriched pathways in 4,274 differentially expressed genes (DEGs) and in 259 differential metabolites between Lan3 and 503. Moreover, the contents of three metabolites related to salicylic acid biosynthesis and the transcription levels of two DEGs related to salicylic acid signal transduction in Lan3 were higher than those in 503. Further verification in various accessions indicated that salicylic acid metabolism may be involved in the flowering regulation process of V. sativa. These findings provide valuable information for understanding the flowering mechanism and for promoting breeding research in V. sativa.

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Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response

Cited by 26 publications

References 53 publications

Integrated Analysis of Basic Helix Loop Helix Transcription Factor Family and Targeted Terpenoids Reveals Candidate AarbHLH Genes Involved in Terpenoid Biosynthesis in Artemisia argyi

Integrated Analysis of Basic Helix Loop Helix Transcription Factor Family and Targeted Terpenoids Reveals Candidate AarbHLH Genes Involved in Terpenoid Biosynthesis in Artemisia argyi

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

Integrative Analyses of Transcriptomes and Metabolomes Reveal Associated Genes and Metabolites with Flowering Regulation in Common Vetch (Vicia sativa L.)

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