Genome-wide characterization, evolutionary analysis, and expression pattern analysis of the trihelix transcription factor family and gene expression analysis under MeJA treatment in Panax ginseng

• Published in: BMC plant biology Vol. 23; no. 1; p. 376
• Main Authors: Hu, Jian, Liu, Tao, Huo, Huimin, Liu, Sizhang, Liu, Mingming, Liu, Chang, Zhao, Mingzhu, Wang, Kangyu, Wang, Yi, Zhang, Meiping
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 01.08.2023; BioMed Central; BMC
• Subjects: Abiotic stress; Alternative splicing; Bioinformatics; Botanical research; Chromosomes; Cultivars; DNA binding proteins; Functional genomics; Gene duplication; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes; Genetic aspects; Genetic resources; Genomes; Genomics; Ginseng; GT factors; Herbal medicine; Identification and classification; Localization; Medicinal plants; Medicine, Botanic; Medicine, Herbal; Metabolites; Methyl jasmonate; Methyl jasmonate treatment; Network analysis; Panax - genetics; Panax - metabolism; Panax ginseng; Pattern analysis; Phylogenetics; Phylogeny; Physiological aspects; Plant genetics; Plant Proteins - genetics; Plant Proteins - metabolism; Proteins; Questioning; Roots; Subgroups; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Transcriptomes; Trihelix transcription factor family; China; GT factors; Methyl jasmonate treatment; Panax ginseng; Trihelix transcription factor family; Functional genomics
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-023-04390-w

Panax ginseng is a well-known medicinal plant with several pharmacological uses in China. The trihelix family transcription factors, also known as GT factors, can be involved in the regulation of growth and developmental processes in plants. There have been no in-depth reports or systematic studies about the trihelix transcription factor in ginseng. In this study, the structure, chromosomal localization, gene duplication, phylogeny, functional differentiation, expression patterns and coexpression interactions of trihelix transcripts were analysed using bioinformatics methods based on the ginseng transcriptome database. Thirty-two trihelix transcription factor genes were identified in ginseng, and these genes were alternatively spliced to obtain 218 transcripts. These transcripts were unevenly distributed on different chromosomes of ginseng, and phylogenetic analysis classified the PgGT transcripts into five subgroups. Gene Ontology (GO) analysis classified PgGT transcripts into eight functional subclasses, indicating that they are functionally diverse. The expression pattern analysis of 218 PgGT transcripts revealed that their expression was tissue-specific and spatiotemporally-specific in 14 different tissues of 4-year-old ginseng, 4 different ages of ginseng roots, and 42 farmers' cultivars of 4-year-old ginseng roots. Despite the differences in the expression patterns of these transcripts, coexpression network analysis revealed that these transcripts could be expressed synergistically in ginseng. In addition, two randomly selected PgGT transcripts in each of the five different subfamilies were subjected to methyl jasmonate treatment at different times, and PgGT was able to respond to the regulation of methy1 jasmonate. These results provide a theoretical basis and gene resources for an in-depth study of the function of trihelix genes in other plants.