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Background  Auxin response factors (ARFs) in auxin signaling pathway are an important component that can regulate the transcription of auxin-responsive genes involved in almost all aspects of plant growth and development. To our knowledge, the comprehensive and systematic characterization of  ARF  genes has never been reported in  Prunus sibirica , a novel woody biodiesel feedstock in China.    Results  In this study, we identified 14  PsARF  genes with a perfect open reading frame (ORF) in  P. sibirica  by using its previous transcriptomic data. Conserved motif analysis showed that all identified PsARF proteins had typical DNA-binding and ARF domain, but 5 members (PsARF3, 8 10, 16 and 17) lacked the dimerization domain. Phylogenetic analysis of the ARF proteins generated from various plant species indicated that ARFs could be categorized into 4 major groups (Class I, II, III and IV), in which all identified ARFs from  P. sibirica  showed a closest relationship with those from  P. mume . Comparison of the expression profiles of 14  PsARF  genes in different developmental stages of Siberian apricot mesocarp (SAM) and kernel (SAK) reflected distinct temporal or spatial expression patterns for  PsARF  genes. Additionally, based on the expressed data from fruit and seed development of multiple plant species, we identified 1514  ARF -correlated genes using weighted gene co-expression network analysis (WGCNA). And the major portion of  ARF -correlated gene was characterized to be involved in protein, nucleic acid and carbohydrate metabolic, transport and regulatory processes.    Conclusions  In summary, we systematically and comprehensively analyzed the structure, expression pattern and co-expression network of  ARF  gene family in  P. sibirica . All our findings provide theoretical foundation for the  PsARF  gene family and will pave the way for elucidating the precise role of  PsARF  genes in SAM and SAK development.    Electronic supplementary material  The online version of this article (10.1186/s12870-017-1220-2) contains supplementary material, which is available to authorized users.

Identification of AUXIN RESPONSE FACTOR gene family from Prunus sibirica and its expression analysis during mesocarp and kernel development