Genome-wide identification, isolation and expression analysis of auxin response factor(ARF) gene family in sweet orange (Citrus sinensis)

• Main Authors: si-bei eli, wei-zhi eouyang, xiao-jin ehou, liang-liang eXie, chun-gen ehu, Jin-Zhi eZhang
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2015-03-01
• Series: Frontiers in Plant Science
• Subjects: Citrus; auxin; phylogenetic analysis; expression analysis; sweet orange; ARF gene
• Online Access: http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00119/full

Auxin response factors (ARFs) are an important family of proteins in auxin-mediated response, with key roles in various physiological and biochemical processes. To date, a genome-wide overview of the ARF gene family in citrus was not available. A systematic analysis of this gene family in citrus was begun by carrying out a genome-wide search for the homologues of auxin response genes. A total of 19 non-redundant ARF genes (CiARF) were identified and validated from the sweet orange genome. A comprehensive overview of the CiARF gene family was undertaken, including the gene structures, phylogeny, chromosome locations, conserved motifs, and cis-elements in promoter sequences. Furthermore, expression profiling using real-time PCR revealed many CiARF genes, albeit with different patterns depending on types of tissues and/or developmental stages. Comprehensive expression analysis of these genes was also performed under two hormone treatments using real-time PCR. Indole-3-acetic acid and N-1-napthylphthalamic acid treatment experiments revealed differential up-regulation and down-regulation, respectively, of the 19 citrus ARF genes in the callus of sweet orange. Our comprehensive analysis of ARF genes further elucidates the roles of CiARF family members in citrus growth and development.