Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants

Abstract

The NGATHA (NGA) transcription factor (TF) belongs to the ABI3/VP1 (RAV) transcriptional subfamily, a subgroup of the B3 superfamily, which is relatively well-studied in Arabidopsis. However, limited data are available on the contributions of NGA TF in other plant species. In this study, 207 NGA gene family members were identified from a genome-wide search against Arabidopsis thaliana in the genome data of 18 dicots and seven monocots. The phylogenetic and sequence alignment analyses divided NGA genes into different clusters and revealed that the numbers of genes varied depending on the species. The phylogeny was followed by the characterization of the Solanaceae (tomato, potato, capsicum, tobacco) and Poaceae (Brachypodium distachyon, Oryza sativa L. japonica, and Sorghum bicolor) family members in comparison with A. thaliana. The gene and protein structures revealed a similar pattern for NGA and NGA-like sequences, suggesting that both are conserved during evolution. Promoter cis-element analysis showed that phytohormones such as abscisic acid, auxin, and gibberellins play a crucial role in regulating the NGA gene family. Gene ontology analysis revealed that the NGA gene family participates in diverse biological processes such as flower development, leaf morphogenesis, and the regulation of transcription. The gene duplication analysis indicates that most of the genes are evolved due to segmental duplications and have undergone purifying selection pressure. Finally, the gene expression analysis implicated that the NGA genes are abundantly expressed in lateral organs and flowers. This analysis has presented a detailed and comprehensive study of the NGA gene family, providing basic knowledge of the gene, protein structure, function, and evolution. These results will lay the foundation for further understanding of the role of the NGA gene family in various plant developmental processes.

AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding

“…Sequence variation among the orthologs of various species may induce subtle, or even substantial, changes in protein structure, which may lead to proteins with similar sequence showing different functions [ 45 – 47 ]. This leads to great difficulty in functional annotations for orthologous proteins [ 48 ], and it is therefore of great interests to compare the capacities of AnnoPRO and the state-of-the-art methods/tools ( DeepGOPlus , PFmulDL and NetGO3 ) from this perspective.…”

Genetic Analyses of Seed Longevity in Capsicum annuum L. in Cold Storage Conditions

“…Similarly, phosphatidylinositol 4-kinase gamma 2 is known to play a role in the phosphorylation of phosphatidylinositol (PI) to PI 4-phosphate, which is one of the key reactions in the production of phosphoinositides, which are lipid regulators of several cellular functions [ 29 ]. NGA transcription factors are involved mainly in developing pistils; they are also involved in regulating the shape and size of lateral organs such as leaves and petals and the regulation of seed size [ 30 ].…”

A Rapid and Simplified Method to Isolate Specific Regulators Based on Biotin–Avidin Binding Affinities in Crops

“…Genome-wide identification for TFs involved in stress conditions has gained increasing attention in recent years. 6,45 Also, the candidate TF genes were identified using the oligo-DNA macroarray technique in plants. 46 Furthermore, transcriptomic analysis was used to identify the TFs in response to different abiotic and biotic stresses in plants.…”

“…The identification and characterization of TFs involved in response to hormones, biotic and abiotic factors, and stress signaling pathways are significant for understanding the gene regulation network in plants. Genome-wide identification for TFs involved in stress conditions has gained increasing attention in recent years. , Also, the candidate TF genes were identified using the oligo-DNA macroarray technique in plants . Furthermore, transcriptomic analysis was used to identify the TFs in response to different abiotic and biotic stresses in plants. ,,,, Additionally, the Y1H assay is a robust genetic method to identify the regulators for targeted DNA fragment; however, the whole procedure is complicated and time-consuming for screening. − On the other hand, the Y1H assay has a major limitation, and the quality of the cDNA library affects the screening results directly. , …”

“…A fundamental question in plant growth and development is how the complex patterns of gene expression are regulated in response to environmental changes. Transcription factors (TFs) are critical components of transcriptional regulatory pathways controlling the expression of genes involved in intrinsic and external signal transduction. − Genome-wide approaches for TF identification provided new insights into the mechanisms of gene regulation controlled by transcriptional key regulators in plants. − Several previous studies have used inducible versions of TFs, and the global analysis of gene expression changes on induction to deduce the functions of key regulators involved in stress responses . Furthermore, genome-wide identification and characterization of cis-regulatory elements (CREs) and cis-regulatory modules (CRMs) are crucial for regulating the protein-coding genes and noncoding RNA genes, which would be valuable to address the issue in gene expression regulation by TFs in plants. , Although key regulators have been identified in plant development and stress responses in recent years, their function and specific regulatory networks involving hundreds of genes are yet to be explored.…”