Fig 1.
Distribution of ARF genes in the Brassica juncea genome.
Chromosomal distribution of ARF genes in B. juncea was determined, and the locations of closely linked genes are shown. The chromosome number is indicated on the top of each chromosome. Scale = megabases (Mb).
Fig 2.
Phylogenetic relationships of ARF genes from three different species (B. juncea, Arabidopsis thaliana, and Brassica napa).
The phylogenetic tree was constructed using MEGA 7.0 via the Neighbor-Joining method with 1,000 bootstraps. Different groups of the ARF family are represented in different colors.
Fig 3.
Phylogenetic tree of the ARF genes and genomic organization of ARF genes in B. juncea.
A. NJ tree of BjARFs; the Auxin_resp domain was identified and the phylogenetic tree was constructed using MEGA 7, via the Neighbor-Joining method with 1000 bootstraps. Different groups of the ARF family are shown in different colors. B. Exon and intron structures of BjARFs, CDSs are shown in green, black lines connecting two CDSs represent introns.
Fig 4.
Conserved motifs of BjARF proteins identified in this study.
The conserved motifs were identified using MEME (suite 4.11.4) based on BjARF protein sequences, and each motif is indicated with a colored box numbered 1 to 9 at the upper right corner.
Fig 5.
Analyze of cis-acting elements response to phytohormones in BjARFs promoters.
Value of x-axis means the number of cis-acting elements which founded in BjARFs promoters.
Fig 6.
miR160/167c-mediated post-transcriptional regulation of BjARFs.
(A-H). Prediction of the BjARFs regulated by Bj-miR160; (I-P). Prediction of the BjARFs regulated by Bj-miR167c. miRNA target sites (Black) with the nucleotide positions of BjARF transcripts are shown, and the Auxin_resp domain (Blue) with the nucleotide positions of BjARF transcripts are shown. The RNA sequences of each complementary site from 5′ to 3′ and the predicted miRNA sequence from 3′ to 5′ are indicated in the expanded regions.
Fig 7.
A. Expression profiles of BjARFs from RNA-seq in different tissues and cultivars. Color represents BjARF expression levels: Log2 (FPKM). The phylogenetic relationship is shown on the left. RNA expression data were selected as follows: leaf (L) of the seedling stage (SS), leaf and stem (S) of the flowing period (FP), leaf and stem of the mature period (MP) from YA1 (yonganxiaoye1), YA2 (yonganxiaoye2) and YA3 (yonganxiaoye3), respectively. B–M. Validation of candidate BjARFs using qRT-PCR, based on altered expression levels. From left to right representing seedling, leaf (VP), tumor stem (VP), tumor stem (FP), flower, and legume. Error bars show the standard error calculated from three biological replicates. Values are presented as the mean ± SEM.
Fig 8.
Fold induction of BjARF genes in response to exogenous auxin.
For B. juncea Yonganxiaoye 1, 20-day-old seedling and a 60-day-old leaf and tumor stem were collected following treatment with 50 μM IAA and water as a control. Values represent the mean ± standard error of the mean (SEM). Paired-samples t-test (one-tail) for 50 μM IAA treatment with a negative control to detect significant differences, ** p < 0.01 and * p < 0.05.