Aux/IAA and ARF Gene Families in Salix suchowensis: Identification, Evolution, and Dynamic Transcriptome Profiling During the Plant Growth Process

Abstract

The phytohormone auxin plays a pivotal role in the regulation of plant growth and development, including vascular differentiation and tree growth. The auxin/indole-3-acetic acid (Aux/IAA) and auxin response transcription factor (ARF) genes are key components of plant auxin signaling. To gain more insight into the regulation and functional features of Aux/IAA and ARF genes during these processes, we identified 38 AUX/IAA and 34 ARF genes in the genome of Salix suchowensis and characterized their gene structures, conserved domains, and encoded amino acid compositions. Phylogenetic analysis of some typical land plants showed that the Aux/IAA and ARF genes of Salicaceae originated from a common ancestor and were significantly amplified by the ancestral eudicot hexaploidization event and the "salicoid" duplication that occurred before the divergence of poplar and willow. By analyzing dynamic transcriptome profiling data, some Aux/IAA and ARF genes were found to be involved in the regulation of plant growth, especially in the initial plant growth process. Additionally, we found that the expression of several miR160/miR167-ARFs was in agreement with canonical miRNA-ARF interactions, suggesting that miRNAs were possibly involved in the regulation of the auxin signaling pathway and the plant growth process. In summary, this study comprehensively analyzed the sequence features, origin, and expansion of Aux/IAA and ARF genes, and the results provide useful information for further studies on the functional involvement of auxin signaling genes in the plant growth process.

Keywords: Aux/IAA and ARF gene families; auxin signaling; dynamic transcriptome profiling; plant growth process; polyploidization events.

FIGURE 1

Genomic distribution of SuIAA and SuARF genes on the Salix suchowensis genome. The SuIAA genes and SuARF genes on each chromosome are plotted in purple and blue, respectively. Gray ribbons indicate collinear relationships among the blocks in whole genome; meanwhile, purple and blue links indicate the syntenic pairs of SuIAA genes and SuARF genes, respectively. The willow chromosomes and Contig694 are arranged with arcs with different colors, and the size of each arc is displayed in Mb.

FIGURE 2

The phylogenetic relationships and conserved domain architecture of the SuIAA and SuARF proteins. (A) The phylogenetic tree of SuIAA proteins is divided into three subfamilies, which are represented by blue, cyan, and orange arcs. Domains I–IV are shaped with ellipse, vertical hexagon, horizontal hexagon, and rhombus from inside to outside. (B) The phylogenetic tree of SuARF proteins is also divided into three subfamilies, and canonical domains DBD (DNA-binding domain), MR (middle region), and CTD (C-terminal dimerization domain) are separately drawn with octagon, pentagram, and eclipse. Three dashed concentric circles of different colors are used to indicate the scale of the SuIAA and SuARF proteins length.

FIGURE 3

Phylogenetic relationships of auxin/indole-3-acetic acid (Aux/IAA) proteins in nine typical land plants. The neighbor-joining tree was constructed with one MpoIAA, two PpaIAA, seven SmoIAA, 13 AtrIAA, 31 OsaIAA, 23 VviIAA, 36 PtrIAA, 38 SuIAA, and 29 AthIAA proteins. The colored solid circles indicate duplicated genes in different species, and the colored rings indicate non-duplicated genes in different species. The colored dashed links represent paralog duplicated pairs. Mpo, M. polymorpha; Ppa, P. patens; Smo, S. moellendorffii; Atr, A. trichopoda; Osa, O. sativa; Vvi, V. vinifera; Ptr, P. trichocarpa; Su, S. suchowensis; Ath, A. thaliana.

FIGURE 4

The time-sequential transcriptome profilings of some SuIAA and SuARF genes in two contrasting clones “S328” and “S3412.” The X-axis shows the different sampling time points (t1: 45 days after planting; t2: 75 days after planting; t3: 135 days after planting; t4: 195 days after planting; t5: 240 days after planting; and t6: 270 days after planting). The Y-axis represents the fragments per kilobase of transcript per million fragments mapped (FPKM) value, which are the mean ± SD of three replicates, and the P-values are shown as *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001.