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<p>The <i>homeobox (HB)</i> genes encode transcription factors that play a significant role in various growth and developmental processes, as well as in stress responses. However, the identification and functional analysis of the entire <i>HB</i> gene family in orchids has rarely been reported. In our research, we identified a total of 87&#xa0;<i>HB</i> genes in <i>Phalaenopsis equestris</i>. Based on domain organization and phylogenetic analysis, these genes were grouped into 13 subclasses, with HD-ZIP showing the highest number of genes (34) compared to the other subclasses. Characteristic differences were observed during multiple sequence alignment within the homeodomain sequences among various classes of the <i>HB</i> gene family. The exon–intron arrangement exhibited high variation across all classes. Members of the <i>HB</i> gene family showed differential expression in various developmental tissues, indicating that these genes play a role in diverse developmental processes. The role of the <i>HB</i> gene family in stress responses, plant growth, and development was further supported by the prediction of specific <i>cis</i>-regulatory elements and co-expression analysis. Homology modelling analysis revealed that most protein sequences were dominated by alpha helices. This study, which includes genome-wide identification, comprehensive gene expression profiling, and co-expression analysis of <i>HB</i> gene family members in <i>P. equestris</i>, aims to facilitate the functional characterization of <i>HB</i> genes in orchids.</p>

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Deciphering the role of HOMEOBOX (HB) genes in growth and development of orchids: a genome-wide study in Phalaenopsis equestris

  • 期刊论文

  • 发表日期：

    2025年2月27日

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  • Madhvi Kanchan,
  • Himani,
  • Jaspreet K. Sembi

摘要

The homeobox (HB) genes encode transcription factors that play a significant role in various growth and developmental processes, as well as in stress responses. However, the identification and functional analysis of the entire HB gene family in orchids has rarely been reported. In our research, we identified a total of 87 HB genes in Phalaenopsis equestris. Based on domain organization and phylogenetic analysis, these genes were grouped into 13 subclasses, with HD-ZIP showing the highest number of genes (34) compared to the other subclasses. Characteristic differences were observed during multiple sequence alignment within the homeodomain sequences among various classes of the HB gene family. The exon–intron arrangement exhibited high variation across all classes. Members of the HB gene family showed differential expression in various developmental tissues, indicating that these genes play a role in diverse developmental processes. The role of the HB gene family in stress responses, plant growth, and development was further supported by the prediction of specific cis-regulatory elements and co-expression analysis. Homology modelling analysis revealed that most protein sequences were dominated by alpha helices. This study, which includes genome-wide identification, comprehensive gene expression profiling, and co-expression analysis of HB gene family members in P. equestris, aims to facilitate the functional characterization of HB genes in orchids.