Genome-Wide Characterization and Expression Analysis of the SBP-Box Gene Family in Sweet Orange (Citrus sinensis)

Song, Na; Cheng, Yulin; Peng, Weiye; Peng, Erping; Zhao, Zengling; Liu, Tiantian; Yi, Tuyong; Dai, Liangying; Wang, Bing; Yu, Hong

doi:10.3390/ijms22168918

Cited by 17 publications

(10 citation statements)

References 47 publications

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“…Abiotic stresses, such as extreme temperature, abscisic acid, salicylic acid, JA and its derivates, exert considerable effects on plant development and the accumulation of specialized metabolisms [31,32]. In this study, the MeJA-responsive CREs were the most abundant among all CREs responsive to phytohormones, indicating that JA and its derivates profoundly correlated with the functions of DzCYP72As.…”

Section: Discussionmentioning

confidence: 52%

Genome-Wide Identification of CYP72A Gene Family and Expression Patterns Related to Jasmonic Acid Treatment and Steroidal Saponin Accumulation in Dioscorea zingiberensis

Hou

Yuan

et al. 2021

IJMS

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Dioscorea zingiberensis is a medicinal herb containing a large amount of steroidal saponins, which are the major bioactive compounds and the primary storage form of diosgenin. The CYP72A gene family, belonging to cytochromes P450, exerts indispensable effects on the biosynthesis of numerous bioactive compounds. In this work, a total of 25 CYP72A genes were identified in D. zingiberensis and categorized into two groups according to the homology of protein sequences. The characteristics of their phylogenetic relationship, intron–exon organization, conserved motifs and cis-regulatory elements were performed by bioinformatics methods. The transcriptome data demonstrated that expression patterns of DzCYP72As varied by tissues. Moreover, qRT-PCR results displayed diverse expression profiles of DzCYP72As under different concentrations of jasmonic acid (JA). Likewise, eight metabolites in the biosynthesis pathway of steroidal saponins (four phytosterols, diosgenin, parvifloside, protodeltonin and dioscin) exhibited different contents under different concentrations of JA, and the content of total steroidal saponin was largest at the dose of 100 μmol/L of JA. The redundant analysis showed that 12 DzCYP72As had a strong correlation with specialized metabolites. Those genes were negatively correlated with stigmasterol and cholesterol but positively correlated with six other specialized metabolites. Among all DzCYP72As evaluated, DzCYP72A6, DzCYP72A16 and DzCYP72A17 contributed the most to the variation of specialized metabolites in the biosynthesis pathway of steroidal saponins. This study provides valuable information for further research on the biological functions related to steroidal saponin biosynthesis.

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Section: Discussionmentioning

confidence: 52%

Genome-Wide Identification of CYP72A Gene Family and Expression Patterns Related to Jasmonic Acid Treatment and Steroidal Saponin Accumulation in Dioscorea zingiberensis

Hou

Yuan

et al. 2021

IJMS

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“…3 ). Likewise, CsSBP12 and CsSBP10b in sweet orange and AtSPL14 in Arabidopsis with the same ANK- domain were separately in sensitivity to pathogen Diaporthe citri and fungal toxin Fumonisin B1 (FB1) ( Stone et al, 2005 ; Song et al, 2021 ). It perhaps indicates that CnSBP8 plays a pivotal role in biotic stresses such as pathogen fungal infection.…”

Section: Discussionmentioning

confidence: 99%

“…Besides, separate branch members in GI and GIII owned more complex motifs and gene structures implying that CnSBP8 and CnSBP14 may perform additional functions and independent evolution similar to CsSBP11 in sweet orange ( Fig. 3 ) ( Song et al, 2021 ). Intriguingly, on the basis of amino acid sequence alignments, it seemed that CnSBP8 owned a comparable AHA-like domain outside the N-terminal and a IRPGC motif outside the C-terminal of the SBP-domain, which was characteristic of many transcriptional activation domains consistent with CRR1 in C. reinhardtii ( Fig.…”

Section: Discussionmentioning

confidence: 99%

“…So it is of great significance to explore the functions of SBP-box gene family in chrysanthemum. Since then, SBP-box genes have been isolated and characterized in many plants ranging from the single-celled alga ( Chlamydomonas reinhardtii ) ( Kropat et al, 2005 ) to model plant, Arabidopsis thaliana ( Cardon et al, 1999 ) and from world-wide cultivated crops like rice ( Oryza sativa ) ( Xie, Wu & Xiong, 2006 ), Chinese cabbage ( Brassica rapa ) ( Cheng et al, 2016 ) and wheat ( Triticum aestivum ) ( Li et al, 2020 ) to fruits like sweet orange ( Citrus sinensis ) ( Song et al, 2021 ), apple ( Malus × domestica Borkh.) ( Li et al, 2013 ) and sugarcane ( Saccharum spontaneum ) ( Feng et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and expression analysis of SBP-box gene family reveal their involvement in hormone response and abiotic stresses in Chrysanthemum nankingense

Yang

Chen

Xia

et al. 2022

PeerJ

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SQUAMOSA promoter-binding-protein (SBP)-box family proteins are a class of plant-specific transcription factors, and widely regulate the development of floral and leaf morphology in plant growth and involve in environment and hormone signal response. In this study, we isolated and identified 21 non-redundant SBP-box genes in Chrysanthemum nankingense with bioinformatics analysis. Sequence alignments of 21 CnSBP proteins discovered a highly conserved SBP domain including two zinc finger-like structures and a nuclear localization signal region. According to the amino acid sequence alignments, 67 SBP-box genes from Arabidopsis thaliana, rice, Artemisia annua and C. nankingense were clustered into eight groups, and the motif and gene structure analysis also sustained this classification. The gene evolution analysis indicated the CnSBP genes experienced a duplication event about 10 million years ago (Mya), and the CnSBP and AtSPL genes occurred a divergence at 24 Mya. Transcriptome data provided valuable information for tissue-specific expression profiles of the CnSBPs, which highly expressed in floral tissues and differentially expressed in leaf, root and stem organs. Quantitative Real-time Polymerase Chain Reaction data showed expression patterns of the CnSBPs under exogenous hormone and abiotic stress treatments, separately abscisic acid, salicylic acid, gibberellin A3, methyl jasmonate and ethylene spraying as well as salt and drought stresses, indicating that the candidate CnSBP genes showed differentiated spatiotemporal expression patterns in response to hormone and abiotic stresses. Our study provides a systematic genome-wide analysis of the SBP-box gene family in C. nankingense. In general, it provides a fundamental theoretical basis that SBP-box genes may regulate the resistance of stress physiology in chrysanthemum via exogenous hormone pathways.

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“…The different stress treatments performed in this study were carried out as previously described, with each experiment being conducted with three replicates ( Song N. et al, 2021 ). For the purposes of stress analysis, we used 1-month-old sweet orange plants that had been grown in greenhouse at 25°C under an 8-h dark/16-h light photoperiod.…”

Section: Methodsmentioning

confidence: 99%

TALE Transcription Factors in Sweet Orange (Citrus sinensis): Genome-Wide Identification, Characterization, and Expression in Response to Biotic and Abiotic Stresses

Peng

Yang

et al. 2022

Front. Plant Sci.

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Three-amino-acid-loop-extension (TALE) transcription factors comprise one of the largest gene families in plants, in which they contribute to regulation of a wide variety of biological processes, including plant growth and development, as well as governing stress responses. Although sweet orange (Citrus sinensis) is among the most commercially important fruit crops cultivated worldwide, there have been relatively few functional studies on TALE genes in this species. In this study, we investigated 18 CsTALE gene family members with respect to their phylogeny, physicochemical properties, conserved motif/domain sequences, gene structures, chromosomal location, cis-acting regulatory elements, and protein–protein interactions (PPIs). These CsTALE genes were classified into two subfamilies based on sequence homology and phylogenetic analyses, and the classification was equally strongly supported by the highly conserved gene structures and motif/domain compositions. CsTALEs were found to be unevenly distributed on the chromosomes, and duplication analysis revealed that segmental duplication and purifying selection have been major driving force in the evolution of these genes. Expression profile analysis indicated that CsTALE genes exhibit a discernible spatial expression pattern in different tissues and differing expression patterns in response to different biotic/abiotic stresses. Of the 18 CsTALE genes examined, 10 were found to be responsive to high temperature, four to low temperature, eight to salt, and four to wounding. Moreover, the expression of CsTALE3/8/12/16 was induced in response to infection with the fungal pathogen Diaporthe citri and bacterial pathogen Candidatus Liberibacter asiaticus, whereas the expression of CsTALE15/17 was strongly suppressed. The transcriptional activity of CsTALE proteins was also verified in yeast, with yeast two-hybrid assays indicating that CsTALE3/CsTALE8, CsTALE3/CsTALE11, CsTALE10/CsTALE12, CsTALE14/CsTALE8, CsTALE14/CsTALE11 can form respective heterodimers. The findings of this study could lay the foundations for elucidating the biological functions of the TALE family genes in sweet orange and contribute to the breeding of stress-tolerant plants.

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Genome-Wide Characterization and Expression Analysis of the SBP-Box Gene Family in Sweet Orange (Citrus sinensis)

Cited by 17 publications

References 47 publications

Genome-Wide Identification of CYP72A Gene Family and Expression Patterns Related to Jasmonic Acid Treatment and Steroidal Saponin Accumulation in Dioscorea zingiberensis

Genome-Wide Identification of CYP72A Gene Family and Expression Patterns Related to Jasmonic Acid Treatment and Steroidal Saponin Accumulation in Dioscorea zingiberensis

Genome-wide identification and expression analysis of SBP-box gene family reveal their involvement in hormone response and abiotic stresses in Chrysanthemum nankingense

TALE Transcription Factors in Sweet Orange (Citrus sinensis): Genome-Wide Identification, Characterization, and Expression in Response to Biotic and Abiotic Stresses

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