Genome-Wide Identification of the AGC Protein Kinase Gene Family Related to Photosynthesis in Rice (Oryza sativa)

Jiang, Yue; Liu, Xuhui; Zhou, Mingao; Yang, Jian; Ke, Simin; Li, Yangsheng

doi:10.3390/ijms232012557

Cited by 8 publications

(6 citation statements)

References 58 publications

(74 reference statements)

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“…Based on the identification of the AGC gene family in Arabidopsis , Jiang Y et al. ( 5 ) successfully identified the ACG gene family in rice and validated its important regulatory role in photosynthesis . Moreover, gene families can provide insights into plant evolution.…”

Section: Introductionmentioning

confidence: 99%

CropGF: a comprehensive visual platform for crop gene family mining and analysis

Zhu

et al. 2023

Database

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A gene family refers to a group of genes that share a common ancestry and encode proteins or RNA molecules with similar functions or structural features. Gene families play a crucial role in determining the traits of plants and can be utilized to develop new crop varieties. Therefore, a comprehensive database of gene family is significant for gaining deep insight into crops. To address this need, we have developed CropGF (https://bis.zju.edu.cn/cropgf), a comprehensive visual platform that encompasses six important crops (rice, wheat, maize, barley, sorghum and foxtail millet) and one model plant (Arabidopsis), as well as genomics, transcriptomics and proteomics data for gene family mining and analysis, covering a total of 314 611 genes and 4399 types of domains. CropGF provides a versatile search system that allows for the identification of gene families and their members in a single crop or multiple crops. Users can customize their search based on gene family domains and/or homology using keywords or BLAST. To enhance usability, we have collected the corresponding ID information from various public databases for both genes and domains. Furthermore, CropGF comprises numerous downstream analysis modules, such as ka/ks analysis, phylogenetic tree construction, subcellular localization analysis and more. These visually-displayed modules provide intuitive insights into gene expression patterns, gene family expansion and functional relationships across different molecular levels and different species. We believe that CropGF will be a valuable resource for deep mining and analysis in future studies of crop gene families. Database URL https://bis.zju.edu.cn/cropgf

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Section: Introductionmentioning

confidence: 99%

CropGF: a comprehensive visual platform for crop gene family mining and analysis

Zhu

et al. 2023

Database

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“…In most cases, WGD events contributed more to gene expansion than SSD events in angiosperms. For example, WGD was demonstrated to be the predominant driving force for the expansion of P450, T6P, and WAK gene families in Arabidopsis [33][34][35], and VQ, AGC, and CSN families in rice [36][37][38]. We also proved that WGD mainly contributed to the large expansion of MADS, bHLH, and TCP families in B. napus [39][40][41].…”

Section: Small-scale Duplication Events Play An Important Role In Pur...mentioning

confidence: 61%

Genome-Wide Identification and Analysis of Phosphate Utilization Related Genes (PURs) Reveal Their Roles Involved in Low Phosphate Responses in Brassica napus L

Shen,

Chen,

Liu

et al. 2024

Preprint

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Background: Phosphorus (P) is an essential macronutrient for Brassica napus L. growth and development, and is mainly acquired from the soil as phosphate (Pi). However, there is no research on the system analysis of Pi utilization related genes (PURs) in B. napus yet. Results: In this study, 285 PURs were identified in B. napus genome, including 4 transcription factor (TF) families (83 genes) and 17 structural gene families (202 genes). Subcellular localization analysis showed that the proteins encoded by PURs were mainly located in the nucleus (~46.0%) and cell membrane (~36.5%). Chromosome localization analysis suggested that PURs were unequally distributed on the 19 chromosomes of B. napus, and tended to distribute on the Cn-subgenome (An:131, Cn:149). Collinearity analysis revealed that allopolyploidization and small-scale duplication events resulted in the large expansion of PURs. Expression and functional divergence of PURs may initially occur in the promoter region during evolution due to the lower sequence identity in the promoter than in CDS regions. A total of 362 genes were identified as PURs regulators, belonging to 32 TF families and 56 types of miRNAs. Spatiotemporal expression analysis demonstrated that PURs were widely expressed during the whole developmental stages, and most synteny-gene pairs (76.42%) shared conserved expression patterns. RNA-seq analyses revealed that most PURs were induced by LP stress, and the hub genes were generally the Pi transporter (PHT) family members. qRT-PCR analysis proved that the expression levels of four PURs were positively correlated with the root system architecture of three B. napus varieties under LP supply at the seedling stage. Conclusion: The 285 PURs were identified from B. napus with strong LP inducible expression profile. Our findings regarding the evolution, transcriptional regulation, and expression of PURs provide valuable information for further functional research.

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“…In recent years, the availability of the complete genome sequence of rice has facilitated the identification and functional analysis of various gene families, such as GH3, AGC, and GAox [27][28][29]. The CYP76 gene family is a member of the larger cytochrome P450 superfamily and plays important roles in various biological processes in plants, including biosynthesis of primary and secondary metabolites, hormone signaling, and response to environmental stresses [10][11][12][13].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Evolution Analysis of the CYP76 Subfamily in Rice (Oryza sativa)

Zhou

Jiang

Liu

et al. 2023

IJMS

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The CYP76 subfamily, a member of the CYP superfamily, plays crucial roles in the biosynthesis of phytohormones in plants, involving biosynthesis of secondary metabolites, hormone signaling, and response to environmental stresses. Here, we conducted a genome-wide analysis of the CYP76 subfamily in seven AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, and Oryza glumaepatula. These were identified and classified into three groups, and it was found that Group 1 contained the largest number of members. Analysis of cis-acting elements revealed a large number of elements related to jasmonic acid and light response. The gene duplication analysis revealed that the CYP76 subfamily expanded mainly in SD/WGD and tandem forms and underwent strong purifying selection during evolution. Expression pattern analysis of OsCYP76s in various developmental stages revealed that the majority of OsCYP76s exhibit relatively restricted expression patterns in leaves and roots. We further analyzed the expression of CYP76s in O. sativa, japonica, and O. sativa, indica under cold, flooding, drought, and salt abiotic stresses by qRT-PCR. We found that OsCYP76-11 showed a huge increase in relative expression after drought and salt stresses. After flooding stress, OsiCYP76-4 showed a greater increase in expression compared to other genes. CYP76 in japonica and indica showed different response patterns to the same abiotic stresses, revealing functional divergence in the gene family during evolution; these may be the key genes responsible for the differences in tolerance to indica japonica. Our results provide valuable insights into the functional diversity and evolutionary history of the CYP76 subfamily and pave the way for the development of new strategies for improving stress tolerance and agronomic traits in rice.

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Genome-Wide Identification of the AGC Protein Kinase Gene Family Related to Photosynthesis in Rice (Oryza sativa)

Cited by 8 publications

References 58 publications

CropGF: a comprehensive visual platform for crop gene family mining and analysis

CropGF: a comprehensive visual platform for crop gene family mining and analysis

Genome-Wide Identification and Analysis of Phosphate Utilization Related Genes (PURs) Reveal Their Roles Involved in Low Phosphate Responses in Brassica napus L

Genome-Wide Identification and Evolution Analysis of the CYP76 Subfamily in Rice (Oryza sativa)

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