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Genome-Wide Analysis of GATA Transcription Factor Family in Quinoa (Chenopodium quinoa): Identification, Characterization, and Expression Profiles: Genome Survey of the GATA Transcription Factor in Quinoa Le, Thi Man; La, Hong Viet; Chu, Ha Duc; Pham, Chau Thuy; Ha, Quyen Thi; Le, Thi Ngoc Quynh; Tran, Thi Thanh Huyen; Tran, Van Tien; Dong, Huy Gioi; Pham, Minh Hong; Tran, Vinh Thanh; Chu, Thi Bich Ngoc; Cao, Phi Bang
Journal of Tropical Life Science Vol. 14 No. 2 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.02.02

GATA-binding factor (GATA) proteins are the transcription factor (TF) family that are commonly involved in plant growth and development. The GATA TF family has been successfully identified and characterized for various higher plant species, but there is little research on the GATA TF family in quinoa (Chenopodium quinoa). In this present study, a total of 32 CqGATA genes were identified and analyzed in the quinoa genome. While the general features of the CqGATA TFs in quinoa were slightly variable, the majority of genes encoding the CqGATA TFs contained two and three exons. Our phylogenetic analysis demonstrated that the CqGATA TFs could be classified into four different groups. Gene expression analysis indicated that the expression profiles of the CqGATA genes varied in different tissues. Overall, our study could provide a reference for further functional characterization of the CqGATA genes in quinoa.

Identification of Two Enzymes for Trehalose Synthesis and Their Potential Function in Growth and Development in Peanut (Arachis hypogaea): Genome Analysis of the Encoding Trehalose Synthesis Enzymes in Peanut Chu, Ha Duc; Tran, Yen Thi Hai; Pham, Chau Thuy; Le, Thi Ngoc Quynh; Tran, Thi Thanh Huyen; Nguyen, Trung Quoc; Dong, Huy Gioi; Tran, Van Tien; Cao, Phi Bang
Journal of Tropical Life Science Vol. 14 No. 1 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.01.10

Plant trehalose has been regarded to play a key role in various biological processes during the growth and development stages. Trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) are two important enzymes for the synthesis of plant trehalose. Up till now, the TPS and TPP gene families have been identified and characterized in numerous higher plant species, but are rarely recorded in peanuts (Arachis hypogaea). In this study, a comprehensive search was performed to identify all putative TPS and TPP proteins in the peanut genome using Arabidopsis TPS and TPP proteins as queries. We then analyzed the characteristics of TPS and TPP members, including physic-chemical parameters, subcellular localization, phylogeny relationships, gene duplication, and expression patterns by various computational tools. As a result, a total of 17 ArahyTPS and 15 ArahyTPP genes were identified and annotated in the peanut genome, which was expanded by segmental duplication events. Our Neighbor-Joining based phylogenetic tree indicated that the ArahyTPS and ArahyTPP proteins could be categorized into three and two major branches. Gene structures and protein features analysis exhibited that the ArahyTPS and ArahyTPP proteins shared high structural and functional similarities. Based on previous RNA-Seq datasets, a majority of the ArahyTPS and ArahyTPP genes were found to specifically express in at least one major organ/tissue during the growth and development. This work will not only lead to a solid foundation on reveal the potential roles of ArahyTPS and ArahyTPP gene families in peanuts but also provide evidence to related trehalose research in other higher plant species.

Genome-Wide Analysis of GATA Transcription Factor Family in Quinoa (Chenopodium quinoa): Identification, Characterization, and Expression Profiles: Genome Survey of the GATA Transcription Factor in Quinoa Le, Thi Man; La, Hong Viet; Chu, Ha Duc; Pham, Chau Thuy; Ha, Quyen Thi; Le, Thi Ngoc Quynh; Tran, Thi Thanh Huyen; Tran, Van Tien; Dong, Huy Gioi; Pham, Minh Hong; Tran, Vinh Thanh; Chu, Thi Bich Ngoc; Cao, Phi Bang
Journal of Tropical Life Science Vol. 14 No. 2 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.02.02

GATA-binding factor (GATA) proteins are the transcription factor (TF) family that are commonly involved in plant growth and development. The GATA TF family has been successfully identified and characterized for various higher plant species, but there is little research on the GATA TF family in quinoa (Chenopodium quinoa). In this present study, a total of 32 CqGATA genes were identified and analyzed in the quinoa genome. While the general features of the CqGATA TFs in quinoa were slightly variable, the majority of genes encoding the CqGATA TFs contained two and three exons. Our phylogenetic analysis demonstrated that the CqGATA TFs could be classified into four different groups. Gene expression analysis indicated that the expression profiles of the CqGATA genes varied in different tissues. Overall, our study could provide a reference for further functional characterization of the CqGATA genes in quinoa.

Identification of Two Enzymes for Trehalose Synthesis and Their Potential Function in Growth and Development in Peanut (Arachis hypogaea): Genome Analysis of the Encoding Trehalose Synthesis Enzymes in Peanut Chu, Ha Duc; Tran, Yen Thi Hai; Pham, Chau Thuy; Le, Thi Ngoc Quynh; Tran, Thi Thanh Huyen; Nguyen, Trung Quoc; Dong, Huy Gioi; Tran, Van Tien; Cao, Phi Bang
Journal of Tropical Life Science Vol. 14 No. 1 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.01.10

Plant trehalose has been regarded to play a key role in various biological processes during the growth and development stages. Trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) are two important enzymes for the synthesis of plant trehalose. Up till now, the TPS and TPP gene families have been identified and characterized in numerous higher plant species, but are rarely recorded in peanuts (Arachis hypogaea). In this study, a comprehensive search was performed to identify all putative TPS and TPP proteins in the peanut genome using Arabidopsis TPS and TPP proteins as queries. We then analyzed the characteristics of TPS and TPP members, including physic-chemical parameters, subcellular localization, phylogeny relationships, gene duplication, and expression patterns by various computational tools. As a result, a total of 17 ArahyTPS and 15 ArahyTPP genes were identified and annotated in the peanut genome, which was expanded by segmental duplication events. Our Neighbor-Joining based phylogenetic tree indicated that the ArahyTPS and ArahyTPP proteins could be categorized into three and two major branches. Gene structures and protein features analysis exhibited that the ArahyTPS and ArahyTPP proteins shared high structural and functional similarities. Based on previous RNA-Seq datasets, a majority of the ArahyTPS and ArahyTPP genes were found to specifically express in at least one major organ/tissue during the growth and development. This work will not only lead to a solid foundation on reveal the potential roles of ArahyTPS and ArahyTPP gene families in peanuts but also provide evidence to related trehalose research in other higher plant species.

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.

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

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.

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