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All Journal HAYATI Journal of Biosciences Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences
Le, Quynh Thi Ngoc
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Agriculture, Biological Sciences & Forestry Earth & Planetary Sciences Environmental Science

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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.
Comprehensive Analysis of the Aldehyde Dehydrogenase Gene Superfamily in Cassava (Manihot esculenta): Genome-Wide Identification and Transcriptional Insights: Genome-wide analysis of the ALDH genes in cassava Tran, Vinh Thanh; Le, Man Thi; Nguyen, Anh Thi Ngoc; Dong, Huy Gioi; Le, Quynh Thi Ngoc; Cao, Phi Bang; Chu, Ha Duc
Journal of Tropical Life Science Vol. 15 No. 2
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/qc82wn93

Abstract

Aldehyde dehydrogenases (ALDHs) are a vital enzyme superfamily involved in cellular detoxification, metabolism, and stress responses in plants. Despite their known roles in various species, a comprehensive genome-wide analysis of the ALDH gene superfamily in cassava (Manihot esculenta), a key drought-tolerant crop, remains limited. This study systematically identified and characterized 29 ALDHs in the cassava genome, classifying them into distinct families based on sequence similarity and phylogenetic relationships. Structural and physicochemical analysis revealed notable variations in gene length, exon-intron organization, and protein properties, indicating functional diversity within the family. Of our interest, expression profiling across 11 different organs/tissues showed that several ALDHs exhibit tissue-specific expression patterns, suggesting their potential roles in diverse physiological processes. Moreover, transcriptomic analysis under drought stress conditions revealed significant changes in ALDH gene expression, with specific members being strongly up-regulated and down-regulated, implying their involvement in drought tolerance mechanisms. The findings provide new insights into the potential roles of ALDHs in cassava's ability to mitigate oxidative stress and enhance drought resilience. This study serves as a foundation for further functional characterization of ALDHs and offers valuable genetic resources for breeding programs aimed at improving cassava’s adaptation to environmental stresses. Understanding these genetic mechanisms will contribute to developing stress-resistant cultivars, ensuring sustainable cassava production in drought-prone regions.
In silico Analysis of Phospholipase C Proteins Revealed Role During the Growth and Development of Peanut (Arachis hypogaea): Genome-wide analysis of the phospholipase C genes in peanut Chu, Ha Duc; Tran, Huyen Thi Thanh; Le, Quynh Thi Ngoc; La, Hong Viet; Le, Thuy Thi; Cao, Phi Bang
Journal of Tropical Life Science Vol. 15 No. 3
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.15.03.06

Abstract

Phospholipase C (PLC) enzymes, including phosphatidylinositol-specific PLC (PI-PLC) and non-specific PLC (NPC), play central roles in plant lipid signalling, although their genomic features and expression patterns in peanut (Arachis hypogaea) are still insufficiently characterized. This study aimed to identify all PLC family members in the peanut genome and to analyze their structural properties, phylogenetic relationships, and expression profiles across major tissues. Through homology-based searches and domain validation, we identified a total of 10 and 16 ArahyNPC and ArahyPI-PLC genes within the peanut genome, respectively. Phylogenetic analysis classified these PLC proteins into two distinct clades, including NPC and PI-PLC. Gene structure and physicochemical assessment indicated conserved organization and similar protein characteristics within each subfamily. Re-analysis of publicly available RNA-Seq datasets revealed clear tissue-specific expression patterns. Interestingly, ArahyNPC-02 and ArahyNPC-09 showed predominant expression in nodules, while ArahyPI-PLC-15 was expressed mainly in roots. These findings indicate functional diversification among PLC genes in peanut and highlight several candidates that may regulate key developmental processes. The results provide a comprehensive genomic resource that supports future functional studies on PLC-mediated signalling and contributes to breeding strategies aimed at enhancing stress resilience in peanut cultivars. This genome-wide characterization, combined with transcriptomic re-analysis, provides a systematic resource for understanding PLC-mediated lipid signalling in peanut. The identified tissue-preferential PLC candidates offer promising targets for future functional studies aimed at elucidating their roles in development and stress-responsive pathways.
Co-Authors Azar, Sahar Cao, Phi Bang Chu, Ha Duc Chu, Ngoc Thi Bich Dong, Gioi Huy Dong, Huy Gioi Huy Gioi, Dong La, Hong Viet Le, Man Thi Le, Thuy Thi Luong, Hang Thi Nguyen, Anh Thi Ngoc Nguyen, Dinh Van Nguyen, Quy Phuong Nguyen, Thanh Xuan Tran, Huyen Thi Thanh Tran, Lan Thi Mai Tran, Vinh Thanh Vu, Xuan Duong