title: Genome-wide analysis of auxin response factor gene family members in medicinal model plant Salvia miltiorrhiza.
abstract: Auxin response factors (ARFs) can function as transcriptional activators or repressors to regulate the expression of auxin response genes by specifically binding to auxin response elements (AuxREs) during plant development. Based on a genome-wide strategy using the medicinal model plant Salvia miltiorrhiza, 25 S. miltiorrhiza ARF (SmARF) gene family members in four classes (class Ia, IIa, IIb and III) were comprehensively analyzed to identify characteristics including gene structures, conserved domains, phylogenetic relationships and expression patterns. In a hybrid analysis of the phylogenetic tree, microRNA targets, and expression patterns of SmARFs in different organs, root tissues, and methyl jasmonate or indole-3-acetic acid treatment conditions, we screened for candidate SmARFs involved in various developmental processes of S. miltiorrhiza Based on this analysis, we predicted that SmARF25, SmARF7, SmARF16 and SmARF20 are involved in flower, leaf, stem and root development, respectively. With the further insight into the targets of miR160 and miR167, specific SmARF genes in S. miltiorrhiza might encode products that participate in biological processes as described for ARF genes in Arabidopsis Our results provide a foundation for understanding the molecular basis and regulatory mechanisms of SmARFs in S. miltiorrhiza.
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100193, China Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing 100193, China.
authors.forename: Zhichao
authors.initials: Z
authors.lastname: Xu
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100193, China Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing 100193, China.
authors.forename: Aijia
authors.initials: A
authors.lastname: Ji
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100193, China Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing 100193, China jysong@implad.ac.cn slchen@icmm.ac.cn.
authors.forename: Jingyuan
authors.identifier: http://orcid.org/0000-0003-2733-0416
authors.initials: J
authors.lastname: Song
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100193, China Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing 100193, China Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Science, Beijing 100700, China jysong@implad.ac.cn slchen@icmm.ac.cn.
authors.forename: Shilin
authors.initials: S
authors.lastname: Chen
keywords: Auxin response elements; Auxin response factors; Developmental processes; MicroRNA; Salvia miltiorrhiza