Whole genome identification and expression analysis of AUX/IAA gene family in Populus wilsonii

Abstract

This study will use bioinformatics technology and combine genomic data of Populus wilsonii to systematically investigate the characteristics of members within the AUX/IAA gene family of Populus wilsonii. Based on Hidden Markov Model (HMM) and homologous sequence alignment, 35 AUX/IAA gene members (named PwiAUX/IAA1 to PwiAUX/IAA35) were identified from the entire genome of Populus wilsonii. Chromosomal localization analysis reveals that members exhibit uneven distribution across 12 chromosomes. By employing the adjacency method to construct a phylogenetic tree, members of the family can be categorized into four subfamilies (Group A-D). Among them, the structural domain of Group B gene (such as Motif 10 representing specificity) suggests its special function in response to abiotic stress. Conservative motif analysis showed that all members carry core functional domains involved in auxin signaling (Motif 2 and Motif 3), while subfamily specific motifs (such as Motif 4/8 enriched in Group A associated with hormone response and Motif 6 enriched in Group C associated with light response) reveal the molecular basis of functional differentiation. 20 types of cis acting elements were identified through promoter region analysis, covering important pathways such as plant hormone regulation, stress response, and growth and development. Organizational expression profiling analysis showed that PwiAUX/IAA14 and PwiAUX/IAA31 exhibited sustained high expression in multiple tissues such as xylem and phloem. The expression levels of PwiAUX/IAA6 and PwiAUX/IAA15 in root meristem tissue were significantly increased compared to other tissues. Protein interaction network analysis shows that core genes (such as PwiAUX/IAA1, PwiAUX/IA9) form regulatory hubs through "one to many" or "many to many" interaction patterns, while the interaction range of edge genes is limited, suggesting that their functions may be tissue-specific. This study comprehensively analyzed the phylogenetic relationships, spatiotemporal expression patterns, and protein interaction networks of the AUX/IAA gene family in Populus wilsonii for the first time, providing important theoretical basis for elucidating the molecular mechanisms of this family in auxin signaling, tissue differentiation, and stress adaptation. It has reference value for the study of forest gene families and genetic improvement of Populus wilsonii.