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Epigenomics is the study of molecular signatures associated with discrete regions within genomes, many of which are important for a wide range of nuclear processes. The ability to profile the epigenomic landscape associated with genes, repetitive regions, transposons, transcription, differential expression, cis-regulatory elements, and 3D chromatin interactions has vastly improved our understanding of plant genomes. However, many epigenomic and single-cell genomic assays are challenging to perform in plants, leading to a wide range of data quality issues; thus, the data require rigorous evaluation prior to downstream analyses and interpretation. In this commentary, we provide considerations for the evaluation of plant epigenomics and single-cell genomics data quality with the aim of improving the quality and utility of studies using those data across diverse plant species.

Trans -species RNA interference (RNAi) occurs naturally when small RNAs (sRNAs) silence genes in species different from their origin. This phenomenon has been observed between plants and various organisms including fungi, animals and other plant species. Understanding the mechanisms used in natural cases of trans- species RNAi, such as sRNA processing and movement, will enable more effective development of crop protection methods using host-induced gene silencing (HIGS). Recent progress has been made in understanding the mechanisms of cell-to-cell and long-distance movement of sRNAs within individual plants. This increased understanding of endogenous plant sRNA movement may be translatable to trans -species sRNA movement. Here, we review diverse cases of natural trans- species RNAi focusing on current theories regarding intercellular and long-distance sRNA movement. We also touch on trans -species sRNA evolution, highlighting its research potential and its role in improving the efficacy of HIGS. [ABSTRACT FROM AUTHOR]

Amborella trichopoda is strongly supported as the single living species of the sister lineage to all other extant flowering plants, providing a unique reference for inferring the genome content and structure of the most recent common ancestor (MRCA) of living angiosperms. Sequencing the Amborella genome, we identified an ancient genome duplication predating angiosperm diversification, without evidence of subsequent, lineage-specific genome duplications. Comparisons between Amborella and other angiosperms facilitated reconstruction of the ancestral angiosperm gene content and gene order in the MRCA of core eudicots. We identify new gene families, gene duplications, and floral protein-protein interactions that first appeared in the ancestral angiosperm. Transposable elements in Amborella are ancient and highly divergent, with no recent transposon radiations. Population genomic analysis across Amborella's native range in New Caledonia reveals a recent genetic bottleneck and geographic structure with conservation implications.

Author(s): Saima Shahid [1, 2]; Gunjune Kim [3]; Nathan R. Johnson [1, 2]; Eric Wafula [2]; Feng Wang [1, 2]; Ceyda Coruh [1, 2]; Vivian Bernal-Galeano [3]; Tamia Phifer [4]; [...]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2006.10.040 Byline: J. Graham Ruby (1)(2), Calvin Jan (1)(2), Christopher Player (1), Michael J. Axtell (1), William Lee (3), Chad Nusbaum (3), Hui Ge (1), David P. Bartel (1)(2) Abstract: We sequenced [approximately equal to]400,000 small RNAs from Caenorhabditis elegans. Another 18 microRNA (miRNA) genes were identified, thereby extending to 112 our tally of confidently identified miRNA genes in C. elegans. Also observed were thousands of endogenous siRNAs generated by RNA-directed RNA polymerases acting preferentially on transcripts associated with spermatogenesis and transposons. In addition, a third class of nematode small RNAs, called 21U-RNAs, was discovered. 21U-RNAs are precisely 21 nucleotides long, begin with a uridine 5'-monophosphate but are diverse in their remaining 20 nucleotides, and appear modified at their 3'-terminal ribose. 21U-RNAs originate from more than 5700 genomic loci dispersed in two broad regions of chromosome IV -- primarily between protein-coding genes or within their introns. These loci share a large upstream motif that enables accurate prediction of additional 21U-RNAs. The motif is conserved in other nematodes, presumably because of its importance for producing these diverse, autonomously expressed, small RNAs (dasRNAs). Author Affiliation: (1) Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA (2) Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA (3) Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Article History: Received 16 June 2006; Revised 23 September 2006; Accepted 27 October 2006 Article Note: (miscellaneous) Published: December 14, 2006

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2006.09.032 Byline: Michael J. Axtell (1)(2), Calvin Jan (1)(2), Ramya Rajagopalan (1)(2), David P. Bartel (1)(2) Abstract: In Arabidopsis, microRNA-directed cleavage can define one end of RNAs that then generate phased siRNAs. However, most miRNA-targeted RNAs do not spawn siRNAs, suggesting the existence of additional determinants within those that do. We find that in moss, phased siRNAs arise from regions flanked by dual miR390 cleavage sites. AtTAS3, an siRNA locus important for development and conserved among higher plants, also has dual miR390 complementary sites. Both sites bind miR390 in vitro and are functionally required in Arabidopsis, but cleavage is undetectable at the 5' site -- demonstrating that noncleavable sites can be functional in plants. Phased siRNAs also emanate from the bounded regions of every Arabidopsis gene with two known microRNA/siRNA complementary sites, but only rarely from genes with single sites. Therefore, two 'hits,' -- often, but not always, two cleavage events -- constitute a conserved trigger for siRNA biogenesis, a finding with implications for recognition and silencing of aberrant RNA. Author Affiliation: (1) Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA (2) Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA Article History: Received 21 March 2006; Revised 7 July 2006; Accepted 25 September 2006 Article Note: (miscellaneous) Published: November 2, 2006

Parasitic plants pose a major biotic threat to plant growth and development and lead to losses in crop productivity of billions of USD annually. By comparison with "normal" autotrophic plants, parasitic plants live a heterotrophic lifestyle and rely on water, solutes and to a greater (holoparasitic plants) or lesser extent (hemiparasitic plants) on sugars from other host plants. Most hosts are unable to detect an infestation by plant parasites or unable to fend off these parasitic invaders. However, a few hosts have evolved defense strategies to avoid infestation or protect themselves actively post-attack often leading to full or partial resistance. Here, we review the current state of our understanding of the defense strategies to plant parasitism used by host plants with emphasis on the active molecular resistance mechanisms. Furthermore, we outline the perspectives and the potential of future studies that will be indispensable to develop and breed resistant crops. [ABSTRACT FROM AUTHOR]