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All Journal HAYATI Journal of Biosciences Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Journal of Tropical Biodiversity and Biotechnology
Tran, Huyen Thi Thanh
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Environmental Science Immunology & microbiology

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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

Abstract

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.  
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

Abstract

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.
Genome-wide Analysis of CONSTANS-like (CqCOL) Transcription Factors in Quinoa (Chenopodium quinoa): Structural Diversity, Phylogeny, and Stress-Responsive Expression Tran, Huyen Thi Thanh; Dong, Gioi Huy; Chu, Ha Duc; Cao, Phi Bang
HAYATI Journal of Biosciences Vol. 32 No. 5 (2025): September 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.5.1135-1146

Abstract

Quinoa (Chenopodium quinoa) is an ancient grain renowned for its remarkable nutritional value and remarkable adaptability to diverse environmental conditions, making it a valuable crop for enhancing food security. Understanding the molecular mechanisms triggering its development and stress responses is crucial for crop improvement. This study conducted a comprehensive analysis of the CONSTANS-like (CqCOL) transcription factors in quinoa, which play a pivotal role in photoperiodic flowering regulation. We identified and characterized 20 CqCOL genes, analyzing their physicochemical properties, phylogenetic relationships, gene structures, and promoter regions. Our findings revealed significant diversity among the CqCOL proteins and suggested potential functional specialization within the family. Promoter analysis uncovered various stress-responsive and phytohormone-responsive cis-regulatory elements, revealing that CqCOL genes may be associated with stress adaptation and hormonal signaling pathways. Transcriptomic analyses under different conditions supported these insights, highlighting the importance of CqCOL genes in quinoa's developmental processes and stress responses. Specifically, most CqCOL genes exhibited stable expression under heat stress, except CqCOL02 and CqCOL12, which were induced in roots by 1.85- and 1.91-fold, respectively. Under normal conditions, CqCOL01, CqCOL11, and CqCOL18 showed organ-specific expression, particularly in flowers and leaves, with no expression detected in roots. This study enhances our understanding of the CqCOL transcription factor family. It provides a foundation for future functional studies and breeding strategies aimed at improving stress tolerance and optimizing flowering time in quinoa.
Bioinformatics study of GATA family in Amaranthus hypochondriacus: Identification, Characterization, and Expression Profiles: Investigation of the GATA family in grain amaranth at the genome-wide scale Vu, Xuan Duong; Le, Man Thi; Le, Quynh Thi Ngoc; Chu, Ha Duc; La, Hong Viet; Huy Gioi, Dong; Tran, Huyen Thi Thanh; Cao, Phi Bang
Journal of Tropical Life Science Vol. 15 No. 1 (2025)
Publisher : Journal of Tropical Life Science

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

Abstract

GATA transcription factors (TFs) play critical roles in regulating various physiological and biochemical processes in plants. However, their functions in grain amaranth (Amaranthus hypochondriacus) remain unexplored. This study identified and characterized 23 GATA TFs (AhGATAs) in grain amaranth through genome-wide bioinformatics analysis. The gene structure, gene duplication, phylogenetic analysis, and protein features were performed. As a result, the AhGATA TF family in grain amaranth exhibited diverse gene structures, including variations in exon-intron organization, with the number of exons ranging from one to eleven. We also found that the AhGATA TF family in grain amaranth could be grouped into four different clades as similar to other higher plant species. Next, the recent RNA-Seq dataset was explored to re-analyze the transcriptional changes of the AhGATA genes in several main organs during the growth and development of grain amaranth plants. We proposed four AhGATA genes, including AhGATA01, 05, 13, and 19, which were exclusively expressed in at least one major organ, such as stems, roots, leaves, maturing seeds, flowers, immature seeds, and green cotyledons. In summary, this current study could provide the basis for further exploration of the GATA gene family functions in plants and enhance our understanding of cellular regulation in plant defense mechanisms.
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

Abstract

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.
Co-Authors Cao, Phi Bang Chu, Ha Duc Chu, Ngoc Thi Bich Dong, Gioi Huy Dong, Huy Gioi Ha, Quyen Thi Huy Gioi, Dong La, Hong Viet Le, Chi Toan Le, Man Thi Le, Quynh Thi Ngoc Le, Thi Man Nguyen, Huong Thi Thanh Nguyen, Quy Phuong Phung, Huynh Huy Tran, Lan Thi Mai Vu, Quyen Thi Xuan Vu, Xuan Duong