Genome-wide identification of Aux/IAA gene family and their expression analysis in Prunus mume

Abstract

AUXIN/INDOLE ACETIC ACIDs (Aux/IAAs), an early auxin-responsive gene family, is important for plant growth and development. To fully comprehend the character of Aux/IAA genes in woody plants, we identified 19 PmIAA genes in Prunus mume and dissected their protein domains, phylogenetic relationship, gene structure, promoter, and expression patterns during floral bud flushing, auxin response, and abiotic stress response. The study showed that PmIAA proteins shared conserved Aux/IAA domain, but differed in protein motif composition. 19 PmIAA genes were divided into six groups (Groups Ⅰ to Ⅵ) based on phylogenetic analysis. The gene duplication analysis showed that segmental and dispersed duplication greatly influenced the expansion of PmIAA genes. Moreover, we identified and classified the cis-elements of PmIAA gene promoters and detected elements that are related to phytohormone responses and abiotic stress responses. With expression pattern analysis, we observed the auxin-responsive expression of PmIAA5, PmIAA17, and PmIAA18 in flower bud, stem, and leaf tissues. PmIAA5, PmIAA13, PmIAA14, and PmIAA18 were possibly involved in abiotic stress responses in P. mume. In general, these results laid the theoretical foundation for elaborating the functions of Aux/IAA genes in perennial woody plant development.

Keywords: Aux/IAA gene family; Prunus mume; auxin-responsive genes; evolutionary analysis; expression pattern analysis.

FIGURE 1

Sequence alignment and conserved domains analysis between PmIAA proteins and PpIAA proteins. Domain I to domain IV of the PmIAA proteins are indicated with black words and red lines. Similar and conserved amino acid residues were represented by the color shading.

FIGURE 2

Construction of Phylogenetic tree for Aux/IAA proteins among mei, peach, poplar, Arabidopsis, and rice. Protein sequences were aligned by the ClustalW and the phylogenetic tree was constructed with MEGA 11 software through the ML method. The six Aux/IAA groups (Ⅰ–Ⅵ) were colored differently.

FIGURE 3

The phylogenetic relationship, protein motif, and gene structure analysis of PmIAAs in mei. The ML tree on the left includes 19 PmIAA proteins. The schematic in the middle represents different protein motifs identified using MEME. The gene structure of PmIAAs was displayed on the right.

FIGURE 4

Promoter sequence analysis reveals the functional cis-acting elements involved in stress-responsive and hormonal signaling. The x-axis represents PmIAA genes and the y-axis indicates the number of each kind of cis-acting element within each PmIAA gene.

FIGURE 5

Expression pattern analysis of PmIAAs during five organs and floral bud development (A) The gene expression pattern of PmIAA genes in root, stem, leaf, floral bud, and fruit tissues (B) Expression pattern of PmIAA genes during floral bud flush. Expression trends of PmIAA in the dormancy release of floral bud. ED one and ED two represent different degrees of endodormancy, ED three represents eco-dormancy, and NF represents flower bud break.

FIGURE 6

Expression pattern analysis of PmIAAs in IAA response (A) The relative gene expression level of PmIAAs after IAA treatment in buds (B) The relative gene expression level of PmIAAs after IAA treatment in stems. The mean ± standard error of three replicates is shown. The letters above the error bars are marked with significance for expression levels.

FIGURE 7

Expression pattern analysis of PmIAAs in abiotic stress responses (A) The relative gene expression level of PmIAAs after drought treatment in stems (B) The relative gene expression level of PmIAAs after salt treatment in stems. The mean ± standard error of three replicates is shown. The letters above the error bars are marked with significance for expression levels.

FIGURE 8

The synteny analysis of IAA genes from mei, Arabidopsis, peach, poplar, and rice. The gray lines in the background represent the collinear blocks among five species, the blue lines emphasize the syntenic Aux/IAA gene pairs and the red triangle represents Aux/IAA genes.