Saururus chinensis, an herbaceous magnoliid without perianth, represents a clade of early-diverging angiosperms that have gone through woodiness-herbaceousness transition and pollination obstacles: the characteristic white leaves underneath inflorescence during flowering time are considered to be a substitute for perianth to attract insect pollinators. Here, using the newly sequenced S. chinensis genome, we revisited the phylogenetic position of magnoliids within mesangiosperms, and recovered a sister relationship for magnoliids and Chloranthales. By considering differentially expressed genes, we identified candidate genes that are involved in the morphogenesis of the white leaves in S. chinensis. Among those genes, we verified -in a transgenic experiment with Arabidopsis -that increasing the expression of the 'pseudo-etiolation in light' gene (ScPEL) can inhibit the biosynthesis of chlorophyll.ScPEL is thus likely being responsible for the switches between green and white leaves, suggesting that changes in gene expression may underlie the evolution of pollination strategies. Despite being an herbaceous plant, S. chinensis still has vascular cambium and maintains the potential for secondary growth as a woody plant, because the necessary machinery, i.e., the entire gene set involved in lignin biosynthesis, is well preserved. However, similar expression levels of two key genes (CCR and CAD) between the stem and other tissues in the lignin biosynthesis pathway are possibly associated with the herbaceous nature of S. chinensis. In conclusion, the S. chinensis genome provides valuable insights into the adaptive evolution of pollination in Saururaceae and reveals a possible mechanism for the evolution of herbaceousness in magnoliids.

MicroTom tomato has a short growth cycle and high transformation efficiency, and is a prospective model plant for studying organ development, metabolism, and plant-microbe interactions. Here, with a newly assembled reference genome for this tomato cultivar and abundant RNA-seq data derived from tissues of different organs/developmental stages/treatments, we constructed multiple gene co-expression networks, which will provide valuable clues for the identification of important genes involved in diverse regulatory pathways during plant growth, e.g., arbuscular mycorrhizal symbiosis and fruit development. Additionally, non-coding RNAs, including miRNAs, lncRNAs and circRNAs were also identified, together with their potential targets. Interacting networks between different types of non-coding RNAs (miRNA-lncRNA), and non-coding RNAs and genes (miRNA-mRNA and lncRNA-mRNA) were constructed as well. Our results and data will provide valuable information for the study of organ differentiation and development of this important fruit. Lastly, we established a database (http://eplant.njau.edu.cn/microTomBase/) with genomic and transcriptomic data, as well as details of gene co-expression and interacting networks on microTom, and this database should be of great value to those who wants to adopt microTom as a model plant for research.

Sequence discrepancy between genomic DNA and transcribed RNAs, namely RNA editing (RE), was reported to be extensive in metazoan nuclear genomes and plant organellar genomes, but largely unexplored in plant nuclear genomes. By comparing the tomato microTom RNA-seq data to its newly assembled genome, we, for the first time, detected extensive RE events (37,984 sites in 5,873 genes) on in the plant nuclear genome, which is supported by evidence from both experimental validation and proteomic data. Other than the prevalence of RE in the microTom genome, the biased pattern-transition overwhelmingly outnumbering transversion-rivals that in animals, and may imply an ancient and shared mechanism underlying RE across eukaryotes. We observed conserved RE sites that were always edited under all conditions, and could be considered as "fixed mutations" at the RNA level; also we detected conditional RE sites occurring only in specific organ/developmental stage/treatment, possibly suggesting distinct functional roles. Evolutionarily, RE results in sequence diversity at the RNA level and may lead to even functional innovation of proteins, hence may be considered as an additional mechanism to expand gene diversity other than gene duplications and alternative splicing.