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Genome-wide investigation and characterization of heat shock transcription factors in papaya (Carica papaya): Mining of the HSF transcription factor in papaya Le, Thi Man; Azar, Sahar; Thi Thanh Tran, Huyen; Chu, Ha Duc; Vu, Quyen Thi Xuan; Tran, Lan Thi Mai; La, Hong Viet; Le, Chi Toan; Cao, Phi Bang
Journal of Tropical Life Science Vol. 14 No. 3 (2024): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.02

Heat shock transcription factors (Hsf-s) have been considered one of the major regulatory proteins that play important roles in various biological processes during the growth and development of plants. Unfortunately, no comprehensive studies of the Hsf family in papaya (Carica papaya), a popular tropical fruit crop, have been performed, even the papaya genome assembly has been released recently. In this study, a total of 18 members of the Hsf family, namely CpHsf-s have been identified in papaya. Based on various computational tools, a systematic characterization of the CpHsf family, such as gene structure, physic-chemical features, categorization, and protein-protein interaction, has been conducted. We found that the physic-chemical properties of the CpHsf proteins were highly variable, while all proteins were hydrophilic and localized in the nucleus. Our classification indicated that the CpHsf proteins could be categorized into three groups, including HsfA, HsfB, and HsfC, and members in the same clade share similar gene structure. According to the previous RNA-Seq datasets, our re-analysis revealed that the CpHsf genes exhibited different expressions in various major organs or tissues during fruit ripening and under the ultra-low temperature stress. Taken together, our study could provide a list of candidate genes for further functional characterization towards the improvement of stress tolerance in papaya.

Mining GATA Transcription Factor Encoding Genes in The Cocoa Tree (Theobroma cacao L.) Suggests Their Potential Roles in Embryo Development and Biotic Stress Response Chu, Ngoc Thi Bich; Le, Thi Man; Chu, Ha Duc; Tran, Huyen Thi Thanh; Tran, Lan Thi Mai; La, Hong Viet; Vu, Quyen Thi Xuan; Phung, Huynh Huy; Cao, Phi Bang
Journal of Tropical Biodiversity and Biotechnology Vol 9, No 3 (2024): September
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.88015

GATA transcription factors (TFs) are widely recognized as significant regulators, characterized by a DNA-binding domain that consists of a type IV zinc finger motif. This TF family has been widely investigated in numerous higher plant species. The purpose of the present work was to comprehensively analyze the GATA TF in cocoa plant (Theobroma cacao L.) by using various bioinformatics tools. As a result, a total of 24 members of the GATA TFs have been identified and annotated in the assembly of the cocoa plant. According to phylogenetic analysis, these TcGATA proteins were classified into four distinct groups, including groups I (10 members), II (seven members), III (five members), and IV (two members). Next, our investigation indicated that the TcGATA proteins in different groups exhibited a high variation in their physic-chemical features due to their different protein lengths, gene structures, and conserved motif distributions, whereas the TcGATA proteins in the same clade might share the common conserved motifs. Additionally, the gene duplication of the TcGATA genes in the cocoa plant was also investigated. Of our interest, the relative expression levels of the TcGATA genes were investigated according to available transcriptome databases. The results exhibited differential expression patterns of all TcGATA genes in various developmental stages of zygotic and somatic embryogenesis, indicating that these TcGATA genes divergently function during various developmental stages of the zygotic and somatic embryos. Moreover, TcGATA genes were differently expressed under Phytophthora megakarya treatment across different points of treatment and cocoa varieties. To sum up, our findings could provide a basis for a further deep understanding of the GATAs in the cocoa plant.

Genome-wide investigation and characterization of heat shock transcription factors in papaya (Carica papaya): Mining of the HSF transcription factor in papaya Le, Thi Man; Azar, Sahar; Thi Thanh Tran, Huyen; Chu, Ha Duc; Vu, Quyen Thi Xuan; Tran, Lan Thi Mai; La, Hong Viet; Le, Chi Toan; Cao, Phi Bang
Journal of Tropical Life Science Vol. 14 No. 3 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.02

Heat shock transcription factors (Hsf-s) have been considered one of the major regulatory proteins that play important roles in various biological processes during the growth and development of plants. Unfortunately, no comprehensive studies of the Hsf family in papaya (Carica papaya), a popular tropical fruit crop, have been performed, even the papaya genome assembly has been released recently. In this study, a total of 18 members of the Hsf family, namely CpHsf-s have been identified in papaya. Based on various computational tools, a systematic characterization of the CpHsf family, such as gene structure, physic-chemical features, categorization, and protein-protein interaction, has been conducted. We found that the physic-chemical properties of the CpHsf proteins were highly variable, while all proteins were hydrophilic and localized in the nucleus. Our classification indicated that the CpHsf proteins could be categorized into three groups, including HsfA, HsfB, and HsfC, and members in the same clade share similar gene structure. According to the previous RNA-Seq datasets, our re-analysis revealed that the CpHsf genes exhibited different expressions in various major organs or tissues during fruit ripening and under the ultra-low temperature stress. Taken together, our study could provide a list of candidate genes for further functional characterization towards the improvement of stress tolerance in papaya.

Comprehensive Characterization of Phospholipase C and D Families in Cocoa (Theobroma cacao L.): Identification, Phylogenetics, Gene Structure, and Transcriptomic Insights Nguyen, Quy Phuong; Tran, Huyen Thi Thanh; Nguyen, Huong Thi Thanh; Dong, Gioi Huy; Ha, Quyen Thi; Vu, Quyen Thi Xuan; Le, Chi Toan; Cao, Phi Bang; Chu, Ha Duc
HAYATI Journal of Biosciences Vol. 32 No. 3 (2025): May 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.3.768-780

This study provides a detailed investigation of the phospholipase C (PLC) and phospholipase D (PLD) gene families in cocoa (Theobroma cacao), focusing on their identification, characterization, and expression patterns. A total of 10 PLC and 12 PLD genes was identified and systematically annotated based on their sequence homology, conserved domains, and functional classification, adhering to established nomenclature. Analysis of physicochemical properties revealed diversity in molecular weights, isoelectric points, and stability parameters, reflecting their structural and functional variability. Phylogenetic analysis classified the genes into distinct subfamilies and highlighted their evolutionary relationships with homologs in Arabidopsis thaliana and rice (Oryza sativa). Gene structure analysis demonstrated significant variation in exon-intron organization, indicating functional specialization and regulatory complexity within these gene families. Expression profiling during cocoa embryo development showed that certain genes, such as TcNPC2, TcPI-PLC5, and TcPLDα1, were highly expressed, while others exhibited stage-specific activity. In response to Phytophthora megakarya infection, several PLC and PLD genes displayed significant changes in expression across different time points and genotypes, including the upregulation of TcPI-PLC2, TcPLDα5, and TcPLDζ2, suggesting their roles in cocoa's stress responses and defense mechanisms. These findings offer new insights into the biological roles of PLC and PLD gene families in cocoa, particularly in growth, development, and stress adaptation, providing a solid foundation for further functional research and potential applications in cocoa improvement programs.

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