Genomic imprinting is an epigenetic phenomenon leading to parent-of-origin specific differential expression of maternally and paternally inherited alleles. In plants, genomic imprinting has mainly been observed in the endosperm, an ephemeral triploid tissue derived after fertilization of the diploid central cell with a haploid sperm cell. In an effort to identify novel imprinted genes in Arabidopsis thaliana, we generated deep sequencing RNA profiles of F1 hybrid seeds derived after reciprocal crosses of Arabidopsis Col-0 and Bur-0 accessions. Using polymorphic sites to quantify allele-specific expression levels, we could identify more than 60 genes with potential parent-of-origin specific expression. By analyzing the distribution of DNA methylation and epigenetic marks established by Polycomb group (PcG) proteins using publicly available datasets, we suggest that for maternally expressed genes (MEGs) repression of the paternally inherited alleles largely depends on DNA methylation or PcG-mediated repression, whereas repression of the maternal alleles of paternally expressed genes (PEGs) predominantly depends on PcG proteins. While maternal alleles of MEGs are also targeted by PcG proteins, such targeting does not cause complete repression. Candidate MEGs and PEGs are enriched for cis-proximal transposons, suggesting that transposons might be a driving force for the evolution of imprinted genes in Arabidopsis. In addition, we find that MEGs and PEGs are significantly faster evolving when compared to other genes in the genome. In contrast to the predominant location of mammalian imprinted genes in clusters, cluster formation was only detected for few MEGs and PEGs, suggesting that clustering is not a major requirement for imprinted gene regulation in Arabidopsis.

Wood originates from cell proliferation of the vascular cambium. Xylem (i.e. wood) is produced inside and phloem outside of the cambium 1. Morphogenesis in plants is typically coordinated by organiser cells which direct the adjacent stem cells to undergo programmed cell division and differentiation. It is unknown where the vascular cambium stem cells are located and whether the organiser concept applies to the cambium 2. Here, we combine lineage tracing and molecular genetic studies in Arabidopsis thaliana roots to show that cells with xylem identity direct adjacent vascular cambial cells to divide and function as stem cells. Thus, these xylem identity cells constitute an organiser. A local maximum of the phytohormone auxin and consequent expression of class III homeodomain-leucine zipper (HD-ZIP III) transcription factors promote xylem identity and cellular quiescence of the organiser cells. Additionally, the organiser maintains phloem identity cell nonautonomously. Consistent with this dual function of the organiser cells, xylem and phloem originate from a single, bifacial stem cell in each radial cell file, thus confirming the classical theory of a uniseriate vascular cambium 3. Ectopically activated high auxin signalling clones differentiate as xylem vessels, and induce cell divisions and expression of cambial and phloem markers in the adjacent cells, suggesting that local auxin signalling maximum is sufficient to specify a stem cell organiser. Although vascular cambium has a unique function among plant meristems, its stem cell organiser shares features with the root and shoot meristem organisers.

While apical growth in plants initiates upon seed germination, radial growth is only primed during early ontogenesis in procambium cells and activated later by the vascular cambium 1 . Although it is not known how radial growth is organized and regulated in plants, this system resembles the developmental competence observed in some animal systems, in which pre-existing patterns of developmental potential are established early on 2,3 . Here we show that the initiation of radial growth occurs around early protophloem sieve element (PSE) cell files of the root procambial tissue in Arabidopsis. In this domain cytokinin signalling promotes expression of a pair of novel mobile transcription factors, PHLOEM EARLY DOF (PEAR1, PEAR2) and their four homologs (DOF6, TMO6, OBP2 and HCA2), collectively called PEAR proteins. The PEAR proteins form a short-range concentration gradient peaking at PSE and activating gene expression that promotes radial growth. The expression and function of PEAR proteins are antagonized by well-established polarity transcription factors, HD-ZIP III 4 , whose expression is concentrated in the more internal domain of radially non-dividing procambial cells by the function of auxin and mobile miR165/166. The PEAR proteins locally promote transcription of their inhibitory HD-ZIP III genes, thereby establishing a negative feedback loop that forms a robust boundary demarking the zone of cell divisions. Taken together, we have established a network, in which the PEAR -HD-ZIP III module integrates spatial information of the hormonal domains and miRNA gradients during root procambial development, to provide adjacent zones of dividing and more quiescent cells as a foundation for further radial growth. Cambial growth in plants is initiated within the procambial tissues of the apical meristems through periclinal (i.e. longitudinal) divisions associated with formation of the vascular tissues xylem and phloem 1 (Extended Data Fig. 1a). It has been established that during procambial development in Arabidopsis roots there are distinct domains for high auxin and cytokinin signalling, which mark the regions for further development of xylem and phloem/procambium, respectively 5-8 . To accurately map the spatial distribution of the periclinal divisions, we established a new nomenclature for the root procambial cells, including PSE-lateral neighbours (PSE-LN) as cells directly contacting both PSE and the pericycle, the outer procambial cells (OPC) as procambial cells adjacent to the pericycle but not contacting PSE, and SE-internal neighbours (PSE-IN) as cells located internal to and directly contacting PSE (Fig. 1a). Both the PSE cell and PSE-LN showed higher activity of periclinal cell division than the OPC and PSE-IN (Fig. 1b, Extended Data Fig. 1b-d and Supplementary Information).We observed virtually no periclinal divisions in metaxylem (MX) and internal procambial cells (IPC) (Fig. 1b). Furthermore, blocking symplastic transport genetically 9 between the PSE and the surrounding cells results in a dramatic reduct...