Genome-Wide Analysis of Aux/IAA Gene Family in Artemisia argyi: Identification, Phylogenetic Analysis, and Determination of Response to Various Phytohormones

Abstract

Artemisia argyi is a traditional herbal medicine plant, and its folium artemisia argyi is widely in demand due to moxibustion applications globally. The Auxin/indole-3-acetic acid (Aux/IAA, or IAA) gene family has critical roles in the primary auxin-response process, with extensive involvement in plant development and stresses, controlling various essential traits of plants. However, the systematic investigation of the Aux/IAA gene family in A. argyi remains limited. In this study, a total of 61 Aux/IAA genes were comprehensively identified and characterized. Gene structural analysis indicated that 46 Aux/IAA proteins contain the four typical domains, and 15 Aux/IAA proteins belong to non-canonical IAA proteins. Collinear prediction and phylogenetic relationship analyses suggested that Aux/IAA proteins were grouped into 13 distinct categories, and most Aux/IAA genes might experience gene loss during the tandem duplication process. Promoter cis-element investigation indicated that Aux/IAA promoters contain a variety of plant hormone response and stress response cis-elements. Protein interaction prediction analysis demonstrated that AaIAA26/29/7/34 proteins are possibly core members of the Aux/IAA family interaction. Expression analysis in roots and leaves via RNA-seq data indicated that the expression of some AaIAAs exhibited tissue-specific expression patterns, and some AaIAAs were involved in the regulation of salt and saline-alkali stresses. In addition, RT-qPCR results indicated that AaIAA genes have differential responses to auxin, with complex response patterns in response to other hormones, indicating that Aux/IAA may play a role in connecting auxin and other hormone signaling pathways. Overall, these findings shed more light on AaIAA genes and offer critical foundational knowledge toward the elucidation of their function during plant growth, stress response, and hormone networking of Aux/IAA family genes in A. argyi.

Keywords: Artemisia argyi; Aux/IAA family; expression pattern; function prediction.

Figure 1

Chromosome distribution mapping of Aux/IAA gene family in A. argyi.

Figure 2

Collinear prediction and sequence similarity analysis of the Aux/IAA genes in A. argyi. (A): Mapping of collinear prediction of the AaIAA family genes in A. argyi. Black lines show AaIAA paralogs, red maths indicates chromosome numbers. (B): Visualising sequence similarity of the AaIAA genes in A. argyi. Different colored ribbons represent different levels of similarity, blue ≤ 50%, green ≤ 75%, orange ≤ 99%, red > 99%. (C): Collinear prediction of the Aux/IAA family genes between A. thaliana and A. argyi. Red lines show the collinear events.

Figure 3

Gene structure, conserved motif, conserved domains, and promoter cis-element analysis of the Aux/IAA family genes in A. argyi. (A) Exon–intron organization of A. argyi Aux/IAA genes. (B) Conserved motif analysis of A. argyi Aux/IAA proteins. (C) The amino acid sequence of four typical conserved domains. (D) Cis-element analysis in the promoters of A. argyi Aux/IAA genes.

Figure 4

GO annotation of the Aux/IAA gene family in A. argyi.

Figure 5

Phylogenetic investigation of Aux/IAA proteins in A. argyi and A. thaliana. The phylogenetic tree was developed using MEGA software (Version: 6.06) and the neighbor-joining method with 1000 bootstraps. Each Aux/IAA group (1 to 13) is indicated by a specific color. AaIAAs in A. argyi are indicated by a solid circle dot, and AtIAAs in Arabidopsis are indicated by a star.

Figure 6

Prediction analysis of Aux/IAA protein interaction in A. argyi. Different line colors indicate the type of interaction evidence.

Figure 7

Expression profiles of AaIAA genes in the leaves and roots of A. argyi in response to salt and saline-alkali stresses based on RNA-seq data. (A) The expression profiles of AaIAA genes in the leaves and roots of A. argyi; FPKM data were normalized by Z-score; the bar chart shows the log₂FC values of root vs. leaf. (B) Expression profiles of AaIAA genes in response to salt and saline–alkali stresses in leaves. (C) Expression profiles of AaIAA genes in response to salt and saline–alkali stresses in roots. The log₂(FPKM values) data were normalized by Z-score. R: root, L: leaf, CK: control group, ST: salt treatment, SAT: saline–alkali treatment. Each set had three replicates.

Figure 8

Expression profiles of AaIAA genes under various hormonal treatments. (A) IAA treatment. (B) ABA treatment. (C) SA treatment. (D) MeJA treatment. Error bars represent standard error of the mean; data shown are means ± SE. Letters “a,b,c…” indicate significant differences at p < 0.05.