Project description:Spirodela polyrhiza (9509) was grown under replete conditions for 10d, subject to media without phosphate or control for 24h, and then sequenced.
Project description:In flowering plants, silencing of transposable elements (TEs) is achieved by the installation of DNA methylation and histone modifications. 24-nt long small-interfering RNAs (siRNAs) guide the deposition of DNA methylation through RNA-directed DNA methylation (RdDM), which can be maintained independently of siRNAs in coordination with H3K9me2. In most angiosperms, RdDM is ubiquitously expressed in vegetative and sexual reproductive tissues. Spirodela polyrhiza (Lemnaceae), represents an exception with low levels of DNA methylation, very low expression of RdDM and near absence of 24-nt siRNAs during its clonal vegetative propagation. Moreover, some components of RdDM, DNA methylation maintenance and RNA silencing are absent from the genome. By investigating the distribution of epigenetic marks on TEs, we show that Spirodela epigenome is shaped by the loss of DNA methylation and H3K9me2 as TEs decay. Nonetheless, such abundant TE remnants remain silenced and marked by H3K9me1. In contrast, scarce, relatively intact TEs display high levels of DNA methylation, H3K9me2 and siRNAs whose patterns resemble those of TEs subjected to RdDM in other angiosperms. Furthermore, despite the absence of DCL2 in duckweeds, Spirodela can produce 22-nt siRNAs, not only from TEs, but from diverse sources of double-stranded (ds)RNA. Our data suggests that RdDM might still be functional during vegetative clonal growth, albeit tissue or developmentally regulated, and highlights the use of alternative models to further understand and explore the diversity of silencing pathways in plants.
Project description:We performed RNA-seq on microdissected regions of Lemna minor (clone 8263) and Spirodela polyrhiza (clone 9509) fronds, alongside the related aroid Colocasia esculenta (taro), to define region-specific transcriptomes and compare organ-identity programmes across species. Transcript abundance was quantified with Salmon v1.10.0 and cross-species comparisons were performed on 7,480 one-to-one orthologues identified by OrthoFinder v3.0.1b1.
