Genome-wide identification and expression analysis of growth-regulating factors in Dendrobium officinale and Dendrobium chrysotoxum

• Published in: PeerJ (San Francisco, CA) CA), 2023-12, Vol.11, p.e16644-e16644, Article e16644
• Main Authors: Zhu, Shuying, Wang, Hongman, Xue, Qiqian, Zou, Huasong, Liu, Wei, Xue, Qingyun, Ding, Xiao-Yu
• Format: Article
• Language: English
• Subjects: Analysis; Bioinformatics; Conserved sequence; Dendrobium; Dendrobium - genetics; Dendrobium chrysotoxum; Dendrobium officinale; Evolutionary genetics; Expression profiles; Gene expression; Gene family; Genera; Genes; Genes, Plant; Genomes; Genomics; Growth; Growth-regulating factor; Jasmonic acid; Medicinal plants; Methyl jasmonate; Molecular Biology; Phylogenetics; Phylogeny; Plant growth; Plant Science; Proteins; Software; Somatotropin releasing hormone; Transcriptome; Transcriptomes
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.16644

, one of the largest genera in Orchidaceae, is popular not only for its aesthetic appeal but for its significant medicinal value. Growth-regulating factors (GRFs) play an essential role in plant growth and development. However, there is still a lack of information about the evolution and biological function analysis of the gene family among species. Growth-regulating factors from Kimura et Migo and Lindl. were identified by HMMER and BLAST. Detailed bioinformatics analysis was conducted to explore the evolution and function of gene family in and using genomic data, transcriptome data and qRT-PCR technology. Here, we evaluated the evolution of the gene family based on the genome sequences of and . Inferred from phylogenetic trees, the genes were classified into two clades, and each clade contains three subclades. Sequence comparison analysis revealed relatively conserved gene structures and motifs among members of the same subfamily, indicating a conserved evolution of genes within species. However, considering the distribution of orthologous s and s, and the differences in the number of s among species, we suggest that the gene family has undergone different evolutionary processes. A total of 361 -elements were detected, with 33, 141, and 187 related to plant growth and development, stress, and hormones, respectively. The tissue-specific expression of s showed that may have a significant function in the stem elongation of . Moreover, four genes were up-regulated under Methyl-jasmonic acid/methyl jasmonate (MeJA) treatment, showing that s and s play a crucial role in stress response. These findings provide valuable information for further investigations into the evolution and function of genes in and .