Abstract
Auxin response factors (ARF) are important transcription factors which mediate the transcription of auxin responsive genes by binding directly to auxin response elements (AuxREs) found in the promoter regions of these genes. To date, no information has been available about the genome-wide organization of the ARF transcription factor family in physic nut. In this study, 17 ARF genes (JcARFs) are identified in the physic nut genome. A detailed investigation into the physic nut ARF gene family is performed, including analysis of the exon-intron structure, conserved domains, conserved motifs, phylogeny, chromosomal locations, potential small RNA targets and expression profiles under various conditions. Phylogenetic analysis suggests that the 17 JcARF proteins are clustered into 6 groups, and most JcARF proteins from the physic nut reveal closer relationships with those from Arabidopsis than those from rice. Of the 17 JcARF genes, eight are predicted to be the potential targets of small RNAs; most of the genes show differential patterns of expression among four tissues (root, stem cortex, leaf, and seed); and qRT-PCR indicates that the expression of all JcARF genes is inhibited or induced in response to exogenous auxin. Expression profile analysis based on RNA-seq data shows that in leaves, 11 of the JcARF genes respond to at least one abiotic stressor (drought and/or salinity) at, as a minimum, at least one time point. Our results provide valuable information for further studies on the roles of JcARF genes in regulating physic nut's growth, development and responses to abiotic stress.
Highlights
The plant hormone auxin plays a vital role in the regulation of plant growth during many developmental stages including vascular elongation, fruit development, lateral root initiation, leaf expansion and senescence, tissue and organ patterning, and flowering, and in response to abiotic stresses [1]
To identify the JcARF genes of physic nut, we performed BlastP searches against the physic nut genomics databases using the Auxin response factors (ARF) domain and all ARF proteins previously identified in rice and Arabidopsis
Genes encoding 17 putative ARF transcription factors were identified in physic nut, and these genes were provisionally named JcARF1 to JcARF17 based on their positions on physic nut linkage groups (LGs) 1 to 11
Summary
The plant hormone auxin plays a vital role in the regulation of plant growth during many developmental stages including vascular elongation, fruit development, lateral root initiation, leaf expansion and senescence, tissue and organ patterning, and flowering, and in response to abiotic stresses [1]. In the past few years, several studies have explored the rapid effects of auxin on gene expression and regulation [1,2].
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