The ARF gene family in the medicinal plant Macleaya cordata: genome-wide survey and gene expression profiling

Abstract Auxin response factors (ARFs) are a class of transcription factor that direct plant gene responses to auxin, and which is critical for plant growth and development. Macleaya cordata, a medicinal plant species from the Papaveraceae family, has not yet been subjected to a genome-wide investigation of the ARF gene family. We identified ARFs in Macleaya cordata using bioinformatic approaches and studied their structure, chromosome distribution, conserved protein domains, phylogenetic trees, and expression profiles. As a result, 17 ARFs in Macleaya cordata were discovered, all of which had the Auxin-resp domain and B3 DNA binding domain. In Macleaya cordata, fragment replication events were discovered in four gene pairs, but no tandem repeats of the ARF genes were observed. ARF5, ARF3, ARF8, and ARF16 were all substantially expressed in the roots, which suggested they might be involved in plant stress responses. Furthermore, the expression of ARF8 and ARF16 altered significantly when exposed to salt and cold stress. This result adds further evidence that these two ARF genes may have a function in plant stress tolerance. Our findings lay the groundwork for understanding the molecular basis and regulatory mechanisms of ARFs in Macleaya cordata.