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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.

The Trehalose-6-Phosphate Synthase and Trehalose-6-Phosphate Phosphatase in Cocoa (Theobroma cacao L.): Genome-Wide Identification and Expression Analysis Nguyen, Quy Phuong; Cao, Phi Bang; Chu, Ngoc Thi Bich; Tran, Lan Thi Mai; Le, Man Thi; Luong, Hang Thi; Le, Quynh Thi Ngoc; Dong, Gioi Huy; Chu, Ha Duc
HAYATI Journal of Biosciences Vol. 32 No. 4 (2025): July 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.4.940-949

Cocoa (Theobroma cacao L.), a vital industrial crop renowned for its economic and nutritional significance, faces increasing challenges due to climate change-induced stresses. To enhance the understanding of cocoa's adaptive mechanisms, a comprehensive analysis was conducted on the trehalose-6-phosphate phosphatase (TPP) and trehalose-6-phosphate synthase (TPS) gene families, which play crucial roles in plant stress responses and development. Five TcTPP and eight TcTPS genes were identified using the latest cocoa genome assembly, distributed unevenly across nine of the ten chromosomes. Detailed physicochemical characterization revealed significant variability in amino acid length, molecular weight, isoelectric point, and hydrophilicity among these proteins, suggesting functional diversity. Phylogenetic analyses, performed using the maximum likelihood method, classified the TcTPP family into three distinct clades and the TcTPS family into two main groups. Gene structure examination uncovered variations in exon-intron organization, with TcTPP genes containing nine to twelve exons and TcTPS genes ranging from three to eighteen exons, indicating structural diversity within these families. Based on publicly available datasets, expression profiling demonstrated differential expression patterns of TcTPP and TcTPS genes during embryo development and under biotic stress conditions, such as pathogen infection by Phytophthora megakarya. Certain genes exhibited significant upregulation or downregulation in response to stress, implicating them in cocoa's defense mechanisms. Taken together, this study provides valuable insights into the TPP and TPS gene families in cocoa. It lays a foundation for developing strategies to enhance stress tolerance and sustainability in cocoa cultivation amidst changing climatic conditions.

Genomic Characterization and Transcriptomic Profiling of Phospholipase A Superfamily in Cocoa (Theobroma cacao): Genome-wide analysis of the phospholipase A genes in cocoa Nguyen, Quy Phuong; Vu, Xuan Duong; Chu, Ngoc Thi Bich; Tran, Lan Thi Mai; Chu, Ha Duc; La, Hong Viet; Dong, Huy Gioi; Tran, Huyen Thi Thanh; Cao, Phi Bang
Journal of Tropical Life Science Vol. 15 No. 2 (2025): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/res8c250

This study investigates the phospholipase A (PLA) superfamily in cocoa (Theobroma cacao), providing a comprehensive analysis of its genomic organization, structural diversity, and functional roles. A total of 19 PLA1 and 20 PLA2 genes were identified, with detailed assessments of their chromosomal locations, protein properties, and exon-intron structures. Phylogenetic analysis established evolutionary relationships with PLA proteins from other species, such as Arabidopsis thaliana and rice (Oryza sativa). Of our interest, transcriptomic profiling under biotic stress caused by Phytophthora megakarya infection and during embryo development revealed distinct expression patterns, demonstrating the involvement of PLA genes in stress responses and key developmental processes. Taken together, these findings provide valuable insights into the roles of PLA genes in cacao biology and offer a foundation for future applications to improve cacao’s resilience and productivity through genetic and biotechnological strategies.

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