Integrative analysis of the RNA interference toolbox in two Salicaceae willow species, and their roles in stress response in poplar (Populus trichocarpa Torr. & Gray)

Abstract Regulation of gene expression related to chromatin modification at the transcriptional silencing and RNA interference (RNAi) at the post-transcriptional level. RNA-dependent RNA polymerase (RDR) and Argonaute (AGO), along with Dicer-like (DCL) from the core components of RNAi, play integral roles in these processes. Here, 14 PtAGOs, 5 PtDCLs, and 9 PtRDRs were identified in P. trichocarpa and compared them with those of another Salicaceae willow (Salix suchowensis Cheng). Maximum-likelihood trees revealed that each AGO, DCL, and RDR family members were divided into four subfamilies. Forty-three orthologous pairs were identified between the P. trichocarpa and S. suchowensis RNAi-toolbox genes. Sixteen collinear gene pairs were detected in highly microsynteny regions with containing more than ten pairs of conserved flanking-genes, indicated that they were considered to have evolved from the large-scale duplication events. Many of the RNAi-toolbox genes were up-regulated, suggesting P. trichocarpa should have evolved specialized regulatory mechanisms in response to cold, salt, drought and heat stresses. Some RNAi-toolbox genes were most highly expressed in stem, suggesting these genes may function in the regulation of small RNAs during P. trichocarpa stem development. Our results provided the integrative analysis and highlighted the function and duplication of the RNAi-toolbox genes in P. trichocarpa.