Transcriptome-wide characterization, evolutionary analysis, and expression pattern analysis of the NF-Y transcription factor gene family and salt stress response in Panax ginseng. 2022

Mingming Liu, and Zhaoxi Pan, and Jie Yu, and Lei Zhu, and Mingzhu Zhao, and Yanfang Wang, and Ping Chen, and Chang Liu, and Jian Hu, and Tao Liu, and Kangyu Wang, and Yi Wang, and Meiping Zhang
College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China.

Jilin ginseng (Panax ginseng C. A. Meyer) has a long history of medicinal use worldwide. The quality of ginseng is governed by a variety of internal and external factors. Nuclear factor Y (NF-Y), an important transcription factor in eukaryotes, plays a crucial role in the plant response to abiotic stresses by binding to a specific promoter, the CCAAT box. However, the NF-Y gene family has not been reported in Panax ginseng. In this study, 115 PgNF-Y transcripts with 40 gene IDs were identified from the Jilin ginseng transcriptome database. These genes were classified into the PgNF-YA (13), PgNF-YB (14), and PgNF-YC (13) subgroups according to their subunit types, and their nucleotide sequence lengths, structural domain information, and amino acid sequence lengths were analyzed. The phylogenetic analysis showed that the 79 PgNF-Y transcripts with complete ORFs were divided into three subfamilies, NF-YA, NF-YB, and NF-YC. PgNF-Y was annotated to eight subclasses under three major functions (BP, MF, and CC) by GO annotation, indicating that these transcripts perform different functions in ginseng growth and development. Expression pattern analysis of the roots of 42 farm cultivars, 14 different tissues of 4-year-old ginseng plants, and the roots of 4 different-ages of ginseng plants showed that PgNF-Y gene expression differed across lineages and had spatiotemporal specificity. Coexpression network analysis showed that PgNF-Ys acted synergistically with each other in Jilin ginseng. In addition, the analysis of the response of PgNF-YB09, PgNF-YC02, and PgNF-YC07-04 genes to salt stress treatment was investigated by fluorescence quantitative PCR. The expression of these genes increased after salt stress treatment, indicating that they may be involved in the regulation of the response to salt stresses in ginseng. These results provide important functional genetic resources for the improvement and gene breeding of ginseng in the future.Conclusions: This study fills a knowledge gap regarding the NF-Y gene family in ginseng, provides systematic theoretical support for subsequent research on PgNF-Y genes, and provides data resources for resistance to salt stress in ginseng.

UI MeSH Term Description Entries
D010802 Phylogeny The relationships of groups of organisms as reflected by their genetic makeup. Community Phylogenetics,Molecular Phylogenetics,Phylogenetic Analyses,Phylogenetic Analysis,Phylogenetic Clustering,Phylogenetic Comparative Analysis,Phylogenetic Comparative Methods,Phylogenetic Distance,Phylogenetic Generalized Least Squares,Phylogenetic Groups,Phylogenetic Incongruence,Phylogenetic Inference,Phylogenetic Networks,Phylogenetic Reconstruction,Phylogenetic Relatedness,Phylogenetic Relationships,Phylogenetic Signal,Phylogenetic Structure,Phylogenetic Tree,Phylogenetic Trees,Phylogenomics,Analyse, Phylogenetic,Analysis, Phylogenetic,Analysis, Phylogenetic Comparative,Clustering, Phylogenetic,Community Phylogenetic,Comparative Analysis, Phylogenetic,Comparative Method, Phylogenetic,Distance, Phylogenetic,Group, Phylogenetic,Incongruence, Phylogenetic,Inference, Phylogenetic,Method, Phylogenetic Comparative,Molecular Phylogenetic,Network, Phylogenetic,Phylogenetic Analyse,Phylogenetic Clusterings,Phylogenetic Comparative Analyses,Phylogenetic Comparative Method,Phylogenetic Distances,Phylogenetic Group,Phylogenetic Incongruences,Phylogenetic Inferences,Phylogenetic Network,Phylogenetic Reconstructions,Phylogenetic Relatednesses,Phylogenetic Relationship,Phylogenetic Signals,Phylogenetic Structures,Phylogenetic, Community,Phylogenetic, Molecular,Phylogenies,Phylogenomic,Reconstruction, Phylogenetic,Relatedness, Phylogenetic,Relationship, Phylogenetic,Signal, Phylogenetic,Structure, Phylogenetic,Tree, Phylogenetic
D010940 Plant Proteins Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which PLANT PROTEINS, DIETARY is available. Plant Protein,Protein, Plant,Proteins, Plant
D010944 Plants Multicellular, eukaryotic life forms of kingdom Plantae. Plants acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations. It is a non-taxonomical term most often referring to LAND PLANTS. In broad sense it includes RHODOPHYTA and GLAUCOPHYTA along with VIRIDIPLANTAE. Plant
D005894 Panax An araliaceous genus of plants that contains a number of pharmacologically active agents used as stimulants, sedatives, and tonics, especially in traditional medicine. Sometimes confused with Siberian ginseng (ELEUTHEROCOCCUS). Ginseng,Korean Ginseng,Korean Red Ginseng,Panax ginseng,Jen Shen,Ninjin,Renshen,Schinseng,Shinseng,Ginseng, Korean,Ginseng, Korean Red,Ginsengs,Jen Shens,Korean Ginsengs,Korean Red Ginsengs,Ninjins,Red Ginseng, Korean,Renshens,Schinsengs,Shen, Jen,Shinsengs
D000069600 Plant Breeding The purposeful manipulation of plant species with the goal of creating desired genotypes and phenotypes, using techniques such as controlled pollination and or genetic engineering, followed by artificial selection of progeny. Breeding, Plant
D000077323 Salt Stress The condition that results from ion toxicity due to ion imbalances (e.g., excessive Na+ and deficiency in Mg++). Salinity Stress,Salinity Stress Reaction,Salinity Stress Reponse,Salt Stress Reaction,Salt Stress Response,Reaction, Salinity Stress,Reaction, Salt Stress,Reponse, Salinity Stress,Response, Salt Stress,Salinity Stress Reactions,Salinity Stress Reponses,Salinity Stresses,Salt Stress Reactions,Salt Stress Responses,Salt Stresses,Stress Reaction, Salinity,Stress Reaction, Salt,Stress Reponse, Salinity,Stress Response, Salt,Stress, Salinity,Stress, Salt
D014157 Transcription Factors Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process. Transcription Factor,Factor, Transcription,Factors, Transcription
D059467 Transcriptome The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells. Transcriptomes,Gene Expression Profiles,Gene Expression Signatures,Transcriptome Profiles,Expression Profile, Gene,Expression Profiles, Gene,Expression Signature, Gene,Expression Signatures, Gene,Gene Expression Profile,Gene Expression Signature,Profile, Gene Expression,Profile, Transcriptome,Profiles, Gene Expression,Profiles, Transcriptome,Signature, Gene Expression,Signatures, Gene Expression,Transcriptome Profile
D018506 Gene Expression Regulation, Plant Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants. Plant Gene Expression Regulation,Regulation of Gene Expression, Plant,Regulation, Gene Expression, Plant
D023081 CCAAT-Binding Factor A heterotrimeric DNA-binding protein that binds to CCAAT motifs in the promoters of eukaryotic genes. It is composed of three subunits: A, B and C. CCAAT-Binding Factor, A-Subunit,CCAAT-Binding Factor, B-Subunit,CCAAT-Binding Factor, C-Subunit,CBF Protein, CCAAT-Binding,CBF-A Protein, CCAAT-Binding,CBF-B Protein, CCAAT-Binding,CBF-C Protein, CCAAT-Binding,CCAAT-Binding Protein, CP1,CCAAT-Binding Transcription Factor,CCAAT-Binding-Factor,NF-Y Protein,CBF A Protein, CCAAT Binding,CBF B Protein, CCAAT Binding,CBF C Protein, CCAAT Binding,CBF Protein, CCAAT Binding,CCAAT Binding Factor,CCAAT Binding Factor, A Subunit,CCAAT Binding Factor, B Subunit,CCAAT Binding Factor, C Subunit,CCAAT Binding Protein, CP1,CCAAT Binding Transcription Factor,CCAAT-Binding CBF Protein,CCAAT-Binding CBF-A Protein,CCAAT-Binding CBF-B Protein,CCAAT-Binding CBF-C Protein,CP1 CCAAT-Binding Protein,Factor, A-Subunit CCAAT-Binding,Factor, B-Subunit CCAAT-Binding,Factor, C-Subunit CCAAT-Binding,NF Y Protein,Protein, CCAAT-Binding CBF-A,Protein, CCAAT-Binding CBF-B,Protein, NF-Y,Transcription Factor, CCAAT-Binding

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