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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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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