Contrasting origins, expression patterns and functions of circRNAs between salt-sensitive and salt-tolerant poplars

•We developed a pipeline that obviously improves the efficiency of plant circRNA identification.•Approximately 36.7 % of circRNAs were highly conserved among three poplars and expressed at higher levels.•Differentiation of circRNAs provided a plastic strategy for poplars to respond to stresses.•15 circRNAs with miRNA-binding sites were recovered to response salt stress by “sponge” function in P. euphratica. CircRNAs play a crucial role in regulating gene functions; however, our knowledge of circRNAs’ roles in plants remains limited, especially considering the difficulty of accurate identification and interspecific differences. Here, using Find_circ software, we developed a new pipeline that obviously improves the efficiency of plant circRNA identification. We used this pipeline to identify circRNAs and identify their differences from 108 stand-specific transcriptomes from four tissues of three poplar species with and without salt stress. We found that most circRNAs in poplars were derived from exon regions, induced by large flanking intron sequences and expressed in specific tissues/species at low levels. Moreover, the origin of most circRNAs is species-specific or moderately conserved with regard to their parental genes, even generated from different loci of orthologous genes. Furthermore, the expression patterns and functions of most circRNAs also vary greatly between salt-sensitive and salt-tolerant poplars. Finally, 15 circRNAs with miRNA-binding sites in P. euphratica were recovered to response salt stress. These results suggest that circRNAs may regulate the gene expression of woody poplars very finely and highlight the potential regulatory functions of circRNAs in salt tolerance of different poplars.