Article Per Year (5 Year)
p-Index From 2021 - 2026
0.751
P-Index
This Author published in this journals
All Journal HAYATI Journal of Biosciences Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences
Le, Quynh Thi Ngoc
Unknown Affiliation
Agriculture, Biological Sciences & Forestry Earth & Planetary Sciences Environmental Science

Published : 4 Documents Claim Missing Document
Claim Missing Document
Check
Articles

Found 4 Documents
Search

 1 
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

Abstract

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.
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 (2025): In Press
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.
Genome-Scale Screening, Characterization, and Expression Analysis of Grain Amaranth Small Auxin-Up RNA Gene Family in Response to Drought Stress Vu, Xuan Duong; Azar, Sahar; Chu, Ha Duc; Le, Quynh Thi Ngoc; Nguyen, Quy Phuong; Nguyen, Thanh Xuan; Nguyen, Dinh Van
HAYATI Journal of Biosciences Vol. 33 No. 2 (2026): March 2026
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.33.2.518-528

Abstract

The Small Auxin-Up RNA (SAUR) gene family represents a class of early auxin-responsive genes that are widely involved in regulating plant cell elongation, tissue differentiation, and environmental adaptation. In this study, we performed a genome-wide analysis of the SAUR gene family in grain amaranth (Amaranthus hypochondriacus), a nutrient-rich pseudocereal. A total of 80 SAUR genes were identified based on the conserved PF02519 domain and were systematically characterized in terms of protein properties, gene structure, and phylogenetic relationships. Most SAUR genes in grain amaranth encode small, basic, and hydrophilic proteins, and gene structure analysis revealed that the majority are intronless. Phylogenetic analysis grouped AhSAURs into ten clades alongside Arabidopsis SAURs. Transcriptomic profiling across seven tissues and drought-treated samples showed that although many SAUR genes had low or no expression, several genes, including AhSAUR76, AhSAUR71, AhSAUR65, AhSAUR54, and AhSAUR73, were highly expressed in a tissue-preferential manner and showed responsiveness to drought. These findings highlight the potential regulatory roles of selected SAUR genes in growth and stress adaptation, offering a valuable resource for future genetic and functional studies aimed at enhancing agronomic traits in grain amaranth.
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 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