Bioinformatics Study of Aux/IAA Family Genes and Their Expression in Response to Different Hormones Treatments during Japanese Apricot Fruit Development and Ripening

Iqbal, Shahid; Hayat, Faisal; Mushtaq, Naveed Ul; Khalil-Ur-Rehman, Muhammad; Khan, Ummara; Yasoob, Talat Bilal; Khan, Muhammad Nawaz; Ni, Zhaojun; Shi, Ting; Gao, Zhihong

doi:10.3390/plants11151898

Cited by 6 publications

(6 citation statements)

References 67 publications

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“…In the present study, a total of 29 Aux/IAA genes were identified in watermelon. Among these, 24 genes exhibited amino acid sequences consisting of less than 500 residues, which aligns with the findings reported in previous studies conducted on Arabidopsis [43], tomato [5], cucumber [6], and Japanese apricot [9] crops. Conversely, only five genes (ClIAA4, 5, 8, 17, and 29) displayed unusually elongated sequences, ranging from 714 to 1491 amino acids.…”

Section: Discussionsupporting

confidence: 88%

“…Furthermore, the up-regulation of FaAux/IAAs transcripts may be partially attributed to auxin-induced fruit growth and the delayed ripening process in strawberry [21]. Additionally, similar key Aux/IAA genes associated with fruit ripening have been identified in Japanese apricot and papaya [7,9]. In a recent study, the utilization of BSA-Seq sequencing in conjunction with transcriptome data analysis unveiled the potential role of an IAA protein (cla004102) and an ethylene response factor (cla004120) as putative regulators of watermelon flesh firmness [22].…”

Section: Introductionmentioning

confidence: 92%

“…The Aux/IAA gene family, an early auxin-responsive group, holds a central role in auxin-mediated responses [4]. The Aux/IAA gene family has been detected in numerous fruit genomes, such as 25 in tomato (Solanum lycopersicum) [5], 29 in cucumber (Cucumis sativus) [6], 18 in papaya (Carica papaya L.) [7], 42 in apple (Malus domestica) [8], and 19 in Japanese apricot (Prunus mume) [9]. Nevertheless, the available information regarding this gene family in watermelon is limited.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification of AUX/IAA Genes in Watermelon Reveals a Crucial Role for ClIAA16 during Fruit Ripening

Hu,

Yang,

Meng

et al. 2023

Horticulturae

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The auxin/indole-3-acetic acid (Aux/IAA) gene family plays a critical role in auxin-mediated responses and fruit development. However, studies on its role in watermelon are limited. In this study, 29 ClIAA gene members were identified in the watermelon genome and classified into eleven groups. Of note, ClIAA16, which was found to be up-regulated during fruit ripening, was targeted using CRISPR/Cas9 gene editing. Knockout mutants of ClIAA16 exhibited a 3–4 day delay in ripening compared to the wild type, highlighting the regulatory importance of ClIAA16. Our findings shed light on the importance of ClIAA genes in watermelon fruit ripening and pave the way for further functional studies.

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Section: Discussionsupporting

confidence: 88%

Section: Introductionmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification of AUX/IAA Genes in Watermelon Reveals a Crucial Role for ClIAA16 during Fruit Ripening

Hu,

Yang,

Meng

et al. 2023

Horticulturae

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“…As a primary auxin-responsive gene family, Aux/IAA genes respond quickly to auxin treatment to regulate downstream genes [ 39 ]. Previous studies have focused on tissue expression patterns and plant development of Aux/IAA genes [ 40 ]. In this study, to understand how the MoIAAs respond to NAA treatment in callus induction and shoot regeneration of M. oleifera , the leaf explants were inoculated with different NAA concentrations.…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of the Aux/IAA Gene Family of the Drumstick Tree (Moringa oleifera Lam.) Reveals Regulatory Effects on Shoot Regeneration

Yang

et al. 2022

IJMS

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Auxin plays a critical role in organogenesis in plants. The classical auxin signaling pathway holds that auxin initiates downstream signal transduction by degrading Aux/IAA transcription repressors that interact with ARF transcription factors. In this study, 23 MoIAA genes were identified in the drumstick tree genome. All MoIAA genes were located within five subfamilies based on phylogenetic evolution analysis; the gene characteristics and promoter cis-elements were also analyzed. The protein interaction network between the MoIAAs with MoARFs was complex. The MoIAA gene family responded positively to NAA treatment, exhibiting different patterns and degrees, notably for MoIAA1, MoIAA7 and MoIAA13. The three genes expressed and functioned in the nucleus; only the intact encoding protein of MoIAA13 exhibited transcriptional activation activity. The shoot regeneration capacity in the 35S::MoIAA13-OE transgenic line was considerably lower than in the wild type. These results establish a foundation for further research on MoIAA gene function and provide useful information for improved tissue culture efficiency and molecular breeding of M. oleifera.

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“…GmDNJ1 was extensively expressed under ideal growth circumstances and significantly activated in abiotic stress treatments. GmDNJ1 (a type-I HSP40) is important for soybean plant development and heat tolerance, likely due to its role in monitoring misfolded proteins for refolding to maintain the range of cellular activities [ 41 ]. The BIL gene encodes a protein belonging to the mitochondrial Hsp40 family.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Analysis of the Hsp40/J-Protein Family Reveals Its Role in Soybean (Glycine max) Growth and Development

Razzaq

Rani

Xing

et al. 2023

Genes

Self Cite

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The J-protein family comprises molecular chaperones involved in plant growth, development, and stress responses. Little is known about this gene family in soybean. Hence, we characterized J-protein genes in soybean, with the most highly expressed and responsive during flower and seed development. We also revealed their phylogeny, structure, motif analysis, chromosome location, and expression. Based on their evolutionary links, we divided the 111 potential soybean J-proteins into 12 main clades (I–XII). Gene-structure estimation revealed that each clade had an exon-intron structure resembling or comparable to others. Most soybean J-protein genes lacked introns in Clades I, III, and XII. Moreover, transcriptome data obtained from a publicly accessible soybean database and RT-qPCR were used to examine the differential expression of DnaJ genes in various soybean tissues and organs. The expression level of DnaJ genes indicated that, among 14 tissues, at least one tissue expressed the 91 soybean genes. The findings suggest that J-protein genes could be involved in the soybean growth period and offer a baseline for further functional research into J-proteins' role in soybean. One important application is the identification of J-proteins that are highly expressed and responsive during flower and seed development in soybean. These genes likely play crucial roles in these processes, and their identification can contribute to breeding programs to improve soybean yield and quality.

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Bioinformatics Study of Aux/IAA Family Genes and Their Expression in Response to Different Hormones Treatments during Japanese Apricot Fruit Development and Ripening

Cited by 6 publications

References 67 publications

Genome-Wide Identification of AUX/IAA Genes in Watermelon Reveals a Crucial Role for ClIAA16 during Fruit Ripening

Genome-Wide Identification of AUX/IAA Genes in Watermelon Reveals a Crucial Role for ClIAA16 during Fruit Ripening

Genome-Wide Identification and Expression Analysis of the Aux/IAA Gene Family of the Drumstick Tree (Moringa oleifera Lam.) Reveals Regulatory Effects on Shoot Regeneration

Genome-Wide Identification and Analysis of the Hsp40/J-Protein Family Reveals Its Role in Soybean (Glycine max) Growth and Development

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