Genome-wide identification, characterisation, and evolution of <i>ABF/AREB</i> subfamily in nine Rosaceae species and expression analysis in mei (<i>Prunus mume</i>)

Xue, Yong; Zheng, Tangchun; Zhuo, Xiaokang; Ahmad, Sagheer; Li, Lulu; Li, Ping; Yu, Jiayao; Wang, Jia; Cheng, Tangren; Zhang, Qixiang

doi:10.7717/peerj.10785

Cited by 11 publications

(11 citation statements)

References 57 publications

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“…The grapevine bZIP family gene VvbZIP19 is a homolog of Arabidopsis AtABI5 and is expressed mainly in seeds [ 25 ]. The group A member PmABF7 (with the highest homology to Arabidopsis AtABI5 ) was highly expressed in buds and fruits in Prunus mume [ 39 ]. In addition, AtABI5 was involved in the regulation of flowering through direct action on FLC transcription [ 15 , 40 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification, Classification, Expression and Duplication Analysis of bZIP Family Genes in Juglans regia L.

Zhang

Quan

Niu

et al. 2022

IJMS

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Basic leucine zipper (bZIP), a conserved transcription factor widely found in eukaryotes, has important regulatory roles in plant growth. To understand the information related to the bZIP gene family in walnut, 88 JrbZIP genes were identified at the genome-wide level and classified into 13 subfamilies (A, B, C, D, E, F, G, H, I, J, K, M, and S) using a bioinformatic approach. The number of exons in JrbZIPs ranged from 1 to 12, the number of amino acids in JrbZIP proteins ranged from 145 to 783, and the isoelectric point ranged from 4.85 to 10.05. The majority of JrbZIP genes were localized in the nucleus. The promoter prediction results indicated that the walnut bZIP gene contains a large number of light-responsive and jasmonate-responsive action elements. The 88 JrbZIP genes were involved in DNA binding and nucleus and RNA biosynthetic processes of three ontological categories, molecular functions, cellular components and biological processes. The codon preference analysis showed that the bZIP gene family has a stronger bias for AGA, AGG, UUG, GCU, GUU, and UCU than other codons. Moreover, the transcriptomic data showed that JrbZIP genes might play an important role in floral bud differentiation. The results of a protein interaction network map and kegg enrichment analysis indicated that bZIP genes were mainly involved in phytohormone signaling, anthocyanin synthesis and flowering regulation. qRT-PCR demonstrated the role of the bZIP gene family in floral bud differentiation. Co-expression network maps were constructed for 29 walnut bZIP genes and 6 flowering genes, and JrCO (a homolog of AtCO) was significantly correlated (p < 0.05) with 13 JrbZIP genes in the level of floral bud differentiation expression, including JrbZIP31 (homolog of AtFD), and JrLFY was significantly and positively correlated with JrbZIP10,11,51,59,67 (p < 0.05), and the above results suggest that bZIP family genes may act together with flowering genes to regulate flower bud differentiation in walnut. This study was the first genome-wide report of the walnut bZIP gene family, which could improve our understanding of walnut bZIP proteins and provide a solid foundation for future cloning and functional analyses of this gene family.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification, Classification, Expression and Duplication Analysis of bZIP Family Genes in Juglans regia L.

Zhang

Quan

Niu

et al. 2022

IJMS

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“…This indicates that the tomato ABF/AREB gene family underwent purifying selection after the replication event. A Ka/Ks value of less than one implies purifying selection, Ka/Ks = 1 represents neutral selection and Ka/Ks >1 indicates positive selection ( Yong et al, 2021 ).…”

Section: Resultsmentioning

confidence: 99%

“…It can be seen that the more the number of chromosomes, the more the corresponding number of ABF/AREB genes. The possible reasons for its occurrence are the whole genome duplication event (WGD) and tandem gene duplication ( Yong et al, 2021 ). In Actinidia chinensis , AchnABF2 is localized in the nucleus ( Wei et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

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Identification of ABF/AREB gene family in tomato (Solanum lycopersicum L.) and functional analysis of ABF/AREB in response to ABA and abiotic stresses

Pan¹,

Wang²,

Liu³

et al. 2023

PeerJ

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Abscisic acid (ABA) is a plant hormone that plays an important regulatory role in plant growth and stress response. The AREB (ABA-responsive element binding protein)/ABF (ABRE-binding factor) are important ABA-signaling components that participate in abiotic stress response. However, genome-scale analysis of ABF/AREB has not been systemically investigated in tomato. This study was conducted to identify tomato ABF/AREB family members and analyze their response to ABA and abiotic stresses. The results show that a total of 10 ABF/AREB members were identified in tomato, which are randomly distributed on five chromosomes. Domain analysis showed that these members exhibit high protein similarity, especially in the basic leucine zipper (bZIP) domain region. Subcellular localization analysis indicated that all 10 ABF/AREB members are localized in the nucleus. Phylogenetic tree analysis showed that tomato ABF/AREB genes are divided into two groups, and they are similar with the orthologs of other plants. The analysis of cis-acting elements showed that most tomato ABF/AREB genes contain a variety of hormones and stress-related elements. Expression profiles of different tissues indicated that SlABF2 and SlABF10 play an important role in fruit ripening. Finally, qRT-PCR analysis revealed that 10 tomato ABF/AREB genes respond to ABA, with SlABF3 being the most sensitive. SlABF3, SlABF5 and SlABF10 positively respond to salt and cold stresses. SlABF1, SlABF3 and SlABF10 are significantly induced under UV radiation treatment. SlABF3 and SlABF5 are significantly induced in osmotic stress. Overall, this study may provide insight into the role of tomato ABF/AREB homologues in plant response to abiotic stresses, which laid a foundation for future functional study of ABF/AREB in tomato.

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“…The ABA signaling pathway has been found to play a crucial role in regulating growth, development, and the response to stress in many plants pp. [20][21][22][23][24]. In the grapevine, APGs play a key role in resisting low and high-temperature stresses [25].…”

Section: Introductionmentioning

confidence: 99%

Identification of ABA Signaling Pathway Genes and Their Differential Regulation in Response to Suboptimal Light Stress in Grape (Vitis vinifera L.)

Zhang

Chen

et al. 2023

Horticulturae

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Suboptimal light stress in grapevines is increasing worldwide with the spread of grapevine cultivation, which can affect grapevine physiology and productivity, such as in Southern China. Abscisic acid (ABA) is an important hormone in plant adaptive responses to abiotic stress, including low light stress. However, ABA signaling pathway genes (APGs) are not well characterized in the grapevine, and little is known of their potentially mitigating role in grapevine growth under weak light stress. Our study aimed to explore the potential role of the ABA signaling pathway in the response of grapevines to suboptimal light conditions. In this study, APGs were identified in the grapevine genome, and the distribution of conserved motifs was shown to reflect their phylogenetic relationships. Gene duplication analysis indicated that segmental duplication was an important driver for gene expansion in the grapevine ABA signaling pathway. Suboptimal conditions of light were shown to seriously affect the growth of grapevine leaves and berries, with the differential regulation of APGs in the grapevine. Our study summarizes the basic characteristics of APGs in grapevine, which can now be examined further for their roles in grapevine’s response to suboptimal light conditions.

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Genome-wide identification, characterisation, and evolution of ABF/AREB subfamily in nine Rosaceae species and expression analysis in mei (Prunus mume)

Cited by 11 publications

References 57 publications

Genome-Wide Identification, Classification, Expression and Duplication Analysis of bZIP Family Genes in Juglans regia L.

Genome-Wide Identification, Classification, Expression and Duplication Analysis of bZIP Family Genes in Juglans regia L.

Identification of ABF/AREB gene family in tomato (Solanum lycopersicum L.) and functional analysis of ABF/AREB in response to ABA and abiotic stresses

Identification of ABA Signaling Pathway Genes and Their Differential Regulation in Response to Suboptimal Light Stress in Grape (Vitis vinifera L.)

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