GFAP: ultra-fast and accurate gene functional annotation software for plants

Xu, Dong; Jin, Kangming; Jiang, Huichuan; Gong, Desheng; Yang, Jason; Yu, Wenjuan; Yang, Yingxue; Li, Jihong; Pan, Weihua

doi:10.1101/2022.01.05.475154

Cited by 5 publications

(5 citation statements)

References 37 publications

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“…The above RNA-seq and bioinformatic analysis were carried out by BioMarker Technologies Illumina, Inc. (Shanghai, China). To further screen the differential genes in the transcriptome, all the differential genes were annotated using Gene Annotation Software for Plants (GFAP) (Xu et al, 2022 ), which quickly obtained the detailed information of candidate differential expressed genes in the transcriptome.…”

Section: Methodsmentioning

confidence: 99%

TCP Transcription Factors Involved in Shoot Development of Ma Bamboo (Dendrocalamus latiflorus Munro)

et al. 2022

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Ma bamboo (Dendrocalamus latiflorus Munro) is the most widely cultivated clumping bamboo in Southern China and is valuable for both consumption and wood production. The development of bamboo shoots involving the occurrence of lateral buds is unique, and it affects both shoot yield and the resulting timber. Plant-specific TCP transcription factors are involved in plant growth and development, particularly in lateral bud outgrowth and morphogenesis. However, the comprehensive information of the TCP genes in Ma bamboo remains poorly understood. In this study, 66 TCP transcription factors were identified in Ma bamboo at the genome-wide level. Members of the same subfamily had conservative gene structures and conserved motifs. The collinear analysis demonstrated that segmental duplication occurred widely in the TCP transcription factors of Ma bamboo, which mainly led to the expansion of a gene family. Cis-acting elements related to growth and development and stress response were found in the promoter regions of DlTCPs. Expression patterns revealed that DlTCPs have tissue expression specificity, which is usually highly expressed in shoots and leaves. Subcellular localization and transcriptional self-activation experiments demonstrated that the five candidate TCP proteins were typical self-activating nuclear-localized transcription factors. Additionally, the transcriptome analysis of the bamboo shoot buds at different developmental stages helped to clarify the underlying functions of the TCP members during the growth of bamboo shoots. DlTCP12-C, significantly downregulated as the bamboo shoots developed, was selected to further verify its molecular function in Arabidopsis. The DlTCP12-C overexpressing lines exhibited a marked reduction in the number of rosettes and branches compared with the wild type in Arabidopsis, suggesting that DlTCP12-C conservatively inhibits lateral bud outgrowth and branching in plants. This study provides useful insights into the evolutionary patterns and molecular functions of the TCP transcription factors in Ma bamboo and provides a valuable reference for further research on the regulatory mechanism of bamboo shoot development and lateral bud growth.

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Section: Methodsmentioning

confidence: 99%

TCP Transcription Factors Involved in Shoot Development of Ma Bamboo (Dendrocalamus latiflorus Munro)

et al. 2022

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“…Functional annotation was achieved by diamond program with e ‐values of 1e‐5 to compare predicted proteins against public databases by GFAP (v2.0.1) (Xu, Jin, et al., 2022). The results of best‐hit were considered as the gene functions.…”

Section: Methodsmentioning

confidence: 99%

The haplotype‐resolved genome of diploid Chrysanthemum indicum unveils new acacetin synthases genes and their evolutionary history

Hou,

Yang,

et al. 2024

The Plant Journal

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SUMMARYAcacetin, a flavonoid compound, possesses a wide range of pharmacological effects, including antimicrobial, immune regulation, and anticancer effects. Some key steps in its biosynthetic pathway were largely unknown in flowering plants. Here, we present the first haplotype‐resolved genome of Chrysanthemum indicum, whose dried flowers contain abundant flavonoids and have been utilized as traditional Chinese medicine. Various phylogenetic analyses revealed almost equal proportion of three tree topologies among three Chrysanthemum species (C. indicum, C. nankingense, and C. lavandulifolium), indicating that frequent gene flow among Chrysanthemum species or incomplete lineage sorting due to rapid speciation might contribute to conflict topologies. The expanded gene families in C. indicum were associated with oxidative functions. Through comprehensive candidate gene screening, we identified five flavonoid O‐methyltransferase (FOMT) candidates, which were highly expressed in flowers and whose expressional levels were significantly correlated with the content of acacetin. Further experiments validated two FOMTs (CI02A009970 and CI03A006662) were capable of catalyzing the conversion of apigenin into acacetin, and these two genes are possibly responsible acacetin accumulation in disc florets and young leaves, respectively. Furthermore, combined analyses of ancestral chromosome reconstruction and phylogenetic trees revealed the distinct evolutionary fates of the two validated FOMT genes. Our study provides new insights into the biosynthetic pathway of flavonoid compounds in the Asteraceae family and offers a model for tracing the origin and evolutionary routes of single genes. These findings will facilitate in vitro biosynthetic production of flavonoid compounds through cellular and metabolic engineering and expedite molecular breeding of C. indicum cultivars.

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“…The Pearson’s correlation coefficient threshold was set as 0.40 according to the FPKM values for each gene pair using the R (version 4.0.2) program ( Han et al, 2016 ). We screened for co-expression edge genes associated with the SpbZIP hub genes and performed Gene Ontology (GO) analyses using the Gene Annotation Software for Plants (GFAP) ( Xu et al, 2022 ). Subsequently, we classified the related genes according to their functions and visualized the relationships between nodes and edges using Cytoscape (version 3.6.1).…”

Section: Methodsmentioning

confidence: 99%

Identification and Analysis of bZIP Family Genes in Sedum plumbizincicola and Their Potential Roles in Response to Cadmium Stress

Qiu

Jin

et al. 2022

Front. Plant Sci.

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Sedum plumbizincicola (Crassulaceae), a cadmium (Cd)/zinc (Zn)/lead (Pb) hyperaccumulator native to Southeast China, is potentially useful for the phytoremediation of heavy metal-contaminated soil. Basic leucine zipper (bZIP) transcription factors play vital roles in plant growth, development, and abiotic stress responses. However, there has been minimal research on the effects of Cd stress on the bZIP gene family in S. plumbizincicola. In this study, 92 SpbZIP genes were identified in the S. plumbizincicola genome and then classified into 12 subgroups according to their similarity to bZIP genes in Arabidopsis. Gene structure and conserved motif analyses showed that SpbZIP genes within the same subgroup shared similar intron–exon structures and motif compositions. In total, eight pairs of segmentally duplicated SpbZIP genes were identified, but there were no tandemly duplicated SpbZIP genes. Additionally, the duplicated SpbZIP genes were mainly under purifying selection pressure. Hormone-responsive, abiotic and biotic stress-responsive, and plant development-related cis-acting elements were detected in the SpbZIP promoter sequences. Expression profiles derived from RNA-seq and quantitative real-time PCR analyses indicated that the expression levels of most SpbZIP genes were upregulated under Cd stress conditions. Furthermore, a gene co-expression network analysis revealed that most edge genes regulated by hub genes were related to metal transport, responses to stimuli, and transcriptional regulation. Because its expression was significantly upregulated by Cd stress, the hub gene SpbZIP60 was selected for a functional characterization to elucidate its role in the root response to Cd stress. In a transient gene expression analysis involving Nicotiana benthamiana leaves, SpbZIP60 was localized in the nucleus. The overexpression of SpbZIP60 enhanced the Cd tolerance of transgenic Arabidopsis plants by inhibiting ROS accumulation, protecting the photosynthetic apparatus, and decreasing the Cd content. These findings may provide insights into the potential roles of the bZIP family genes during the S. plumbizincicola response to Cd stress.

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GFAP: ultra-fast and accurate gene functional annotation software for plants

Cited by 5 publications

References 37 publications

TCP Transcription Factors Involved in Shoot Development of Ma Bamboo (Dendrocalamus latiflorus Munro)

TCP Transcription Factors Involved in Shoot Development of Ma Bamboo (Dendrocalamus latiflorus Munro)

The haplotype‐resolved genome of diploid Chrysanthemum indicum unveils new acacetin synthases genes and their evolutionary history

Identification and Analysis of bZIP Family Genes in Sedum plumbizincicola and Their Potential Roles in Response to Cadmium Stress

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