Genome-Wide Identification and Evolutionary Analysis of Functional Genes in Plant Species

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2025 Jan 8

PMID 39766881

Authors

Zhengyuan Hong

Linghong Zhu

Chaolei Liu

Kejian Wang

Yuchun Rao

Hongwei Lu

Affiliations

Soon will be listed here.

Abstract

: BABY BOOM (BBM), a transcription factor from the APETALA2 (AP2) protein family, plays a critical role in somatic embryo induction and apomixis. has now been widely applied to induce apomixis or enhance plant transformation and regeneration efficiency through overexpression or ectopic expression. However, the structural and functional evolutionary history of genes in plants is still not well understood. : The protein sequences of 10 selected plant species were used to locate the branch of BBM-Like by key domain identification and phylogenetic tree construction. The identified genes were used for further conserved motif identification, gene structural analysis, miRNA binding site prediction, cis-acting element prediction, collinear analysis, protein-protein interaction network construction, three-dimensional structure modeling, molecular docking, and expression pattern analysis. : A total of 24 BBML proteins were identified from 10 representative plant species. Phylogenetic relationship analysis displayed that BBML proteins from eudicots and monocots were divided into two clusters, with monocots exhibiting a higher number of BBMLs. Gene duplication events indicated that whole genome/segmental duplication were the primary drivers of genes' evolution in the tested species, with purifying selection playing a key role during evolution processes. Comparative analysis of motif, domains, and gene structures revealed that most BBMLs were highly evolutionarily conserved. The expression patterns of genes revealed significant tissue specificity, particularly in the root and embryo. We also constructed protein-protein interaction networks and molecular docking models to identify functional pathways and key amino acid residues of BBML proteins. The functions of BBMLs may differ between monocots and eudicots, as suggested by the functional enrichment of interacting proteins. : Our research delved into the molecular mechanism, evolutionary relationships, functional differentiation, and expression patterns of genes across plants, laying the groundwork for further investigations into the molecular properties and biological roles of .

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