Genome-wide identification and expression profiling of the auxin response factor (ARF) gene family in physic nut

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.

Auxin Response Factor 2A Is Part of the Regulatory Network Mediating Fruit Ripening Through Auxin-Ethylene Crosstalk in Durian

“…Auxin signaling is known to regulate the expression of early/primary auxin response genes through ARFs. Previous studies have already identified members of the ARF family in crops with economic values ( Wang et al., 2007 ; Kumar et al., 2011 ; Xing et al., 2011 ; Luo et al., 2014 ; Wan et al., 2014 ; Shen et al., 2015 ; Hu et al., 2015 ; Liu et al., 2015 ; Singh et al., 2017 ; Tang et al., 2018 ). According to the Plant Transcription Factor Database ( ), 4,578 members of the ARF gene family exist in the genomes of different plant species in varying numbers; papaya (10), tomato (22), Arabidopsis (37), banana (50), and durian (77).…”

“…The domain architecture of ARFs is known to play a key role in their specificity. Since the identification and characterization of the first Arabidopsis ARF ( AtARF1 ) ( Ulmasov et al., 1997 ), numerous studies have identified members of the ARF gene family in plant species, such as tomato ( Kumar et al., 2011 ), rice ( Wang et al., 2007 ), Medicago ( Shen et al., 2015 ), banana ( Hu et al., 2015 ), apple ( Luo et al., 2014 ), maize ( Xing et al., 2011 ), chickpea ( Singh et al., 2017 ), physic nut ( Tang et al., 2018 ), grape ( Wan et al., 2014 ), and papaya ( Liu et al., 2015 ). Functional characterization of some ARFs based on the phenotypes of the loss-of-function and gain-of-function mutants have also been carried out.…”

Down Regulation and Loss of Auxin Response Factor 4 Function Using CRISPR/Cas9 Alters Plant Growth, Stomatal Function and Improves Tomato Tolerance to Salinity and Osmotic Stress

“…Since ARF1, the first Arabidopsis ARF gene, was cloned and its function investigated [6], the ARF gene family has been identified and well characterized in many crop species, including tomato (Solanum lycopersicum), maize (Zea mays), rice (Oryza sativa), poplar (Populus trichocarpa), Chinese cabbage (Brassica rapa), banana (Musa sp.) and physic nut (Jatropha curcas L.) [4,[7][8][9][10].…”

Genome-Wide Identification of the YABBY Gene Family in Seven Species of Magnoliids and Expression Analysis in Litsea

“…Exon/intron analysis could provide some valuable information regarding the evolutionary relationships among plant taxa [ 36 ]. Therefore, this study investigated and compared the exon/intron structures of YABBY genes among these seven magnoliids species.…”

“…YABBY genes are small and essential key regulators that are specifically related to the evolution of leaves in seed plants that encode a C2C2 zinc-finger domain at the N-terminal region and a conserved YABBY domain in the C-terminal region with a helix–loop–helix motif [ 37 , 38 ]. In terms of basal angiosperms, five YABBY genes have been identified in Amborella , Cabomba, and Nymphaea [ 36 ]. In addition, six YABBY genes have been described in the model plant Arabidopsis , and eight have been identified in Oryza [ 20 , 21 , 22 , 37 ].…”