New technologies accelerate the exploration of non-coding RNAs in horticultural plants.

Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs

Identification of a male-specific amplified fragment length polymorphism (AFLP) marker in Broussonetia papyrifera

The present study exhibits amplified fragment length polymorphism (AFLP) molecular marker for sex identification in Broussonetia papyrifera. Based on nine selective amplification primer combinations, 230 bands were produced and the E-AGG/M-CAA combination was found to be a male-specific AFLP marker. Subsequently, this male-specific AFLP fragment was sequenced and converted into a sequence tagged site (STS) marker. Based on STS sequence, two primers, MADB-1 and MADB-2 (Male-Associated DNA from B. papyrifera), were designed to verify the specificity of the fragment. The results indicate that common homology sequence is existed in both male and female plants while one of the bands amplified via MADB-2 primer was solely present in male individuals at high annealing temperature up to 66°C. Finally, MADB-2 primer was introduced to amplify another 16 plants and it revealed that this primer could be used as a convenient, efficient, reliable, and low-cost molecular marker for sex identification in B. papyrifera.Keywords: Broussonetia papyrifera, AFLP, STS, male-specific marke

The Giant Chalukou Porphyry Mo Deposit, Northeast China: The Product of a Short-Lived, High Flux Mineralizing Event

Whether giant porphyry ore deposits are the products of single, short-lived magmatic-hydrothermal events or multiple events over a prolonged interval is a topic of considerable debate. Previous studies, however, have all been devoted to porphyry Cu and Cu-Mo deposits. In this paper, we report high-precision isotope dilution-negative-thermal ionization mass spectrometric (ID-N-TIMS) molybdenite Re-Os ages for the newly discovered, world-class Chalukou porphyry Mo deposit (reserves of 2.46 Mt @ 0.087 wt % Mo) in NE China. Samples were selected based on a careful evaluation of the relative timing of the different vein types (i.e., A, B, and D veins), thereby ensuring that the suite of samples analyzed could be used to reliably determine the age and duration of mineralization. The molybdenite Re-Os geochronology reveals that hydrothermal activity at Chalukou involved two magmatic-hydrothermal events spanning an interval of 6.92 ± 0.16 m.y. The first event (153.96 ± 0.08/0.63/0.79 Ma, molybdenite ID-N-TIMS Re-Os age) was associated with the emplacement of a granite porphyry dated at 152.1 ± 2.2 Ma (zircon laser ablation-inductively coupled plasma-microscopic [LA-ICP-MS] U-Pb ages), and led to only minor Mo mineralization, accounting for 90%) was deposited in less than 650 kyr, between 147.67 ± 0.10/0.60/0.76 and 147.04 ± 0.12/0.72/0.86 Ma (molybdenite ID-N-TIMS Re-Os ages), coincident with the emplacement of a fine-grained porphyry at 148.1 ± 2.6 Ma (zircon LA-ICP-MS U-Pb ages). The high-precision Re-Os age determinations presented here show, contrary to the finding of a number of studies of porphyry Cu and Cu-Mo systems, that the giant Chalukou porphyry Mo deposit primarily formed in a single, short-lived (<650 kyr) hydrothermal event, suggesting that this may also have been the case for other giant porphyry Mo deposits

De Novo

Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop worldwide. The orange-fleshed sweet potato is considered to be an important source of beta-carotene. In this study, the transcriptome profiles of an orange-fleshed sweet potato cultivar “Weiduoli” and its mutant “HVB-3” with high carotenoid content were determined by using the high-throughput sequencing technology. A total of 13,767,387 and 9,837,090 high-quality reads were produced from Weiduoli and HVB-3, respectively. These reads were de novo assembled into 58,277 transcripts and 35,909 unigenes with an average length of 596 bp and 533 bp, respectively. In all, 874 differentially expressed genes (DEGs) were obtained between Weiduoli and HVB-3, 401 of which were upregulated and 473 were downregulated in HVB-3 compared to Weiduoli. Of the 697 DEGs annotated, 316 DEGs had GO terms and 62 DEGs were mapped onto 50 pathways. The 22 DEGs and 31 transcription factors involved in carotenoid biosynthesis were identified between Weiduoli and HVB-3. In addition, 1,725 SSR markers were detected. This study provides the genomic resources for discovering the genes involved in carotenoid biosynthesis of sweet potato and other plants

Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism.

BackgroundCrassulacean acid metabolism (CAM), a specialized mode of photosynthesis, enables plant adaptation to water-limited environments and improves photosynthetic efficiency via an inorganic carbon-concentrating mechanism. Kalanchoë fedtschenkoi is an obligate CAM model featuring a relatively small genome and easy stable transformation. However, the molecular responses to light quality and intensity in CAM plants remain understudied.ResultsHere we present a genome-wide expression atlas of K. fedtschenkoi plants grown under 12&nbsp;h/12&nbsp;h photoperiod with different light quality (blue, red, far-red, white light) and intensity (0, 150, 440, and 1,000 μmol m-2 s-1) based on RNA sequencing performed for mature leaf samples collected at dawn (2 h before the light period) and dusk (2 h before the dark period). An eFP web browser was created for easy access of the gene expression data. Based on the expression atlas, we constructed a light-responsive co-expression network to reveal the potential regulatory relationships in K. fedtschenkoi. Measurements of leaf titratable acidity, soluble sugar, and starch turnover provided metabolic indicators of the magnitude of CAM under the different light treatments and were used to provide biological context for the expression dataset. Furthermore, CAM-related subnetworks were highlighted to showcase genes relevant to CAM pathway, circadian clock, and stomatal movement. In comparison with white light, monochrome blue/red/far-red light treatments repressed the expression of several CAM-related genes at dusk, along with a major reduction in acid accumulation. Increasing light intensity from an intermediate level (440 μmol m-2 s-1) of white light to a high light treatment (1,000 μmol m-2 s-1) increased expression of several genes involved in dark CO2 fixation and malate transport at dawn, along with an increase in organic acid accumulation.ConclusionsThis study provides a useful genomics resource for investigating the molecular mechanism underlying the light regulation of physiology and metabolism in CAM plants. Our results support the hypothesis that both light intensity and light quality can modulate the CAM pathway through regulation of CAM-related genes in K. fedtschenkoi

A donor-chromophore-catalyst assembly for solar CO2 reduction

We describe here the preparation and characterization of a photocathode assembly for CO2 reduction to CO in 0.1 M LiClO4 acetonitrile. The assembly was formed on 1.0 μm thick mesoporous films of NiO using a layer-by-layer procedure based on Zr(IV)–phosphonate bridging units. The structure of the Zr(IV) bridged assembly, abbreviated as NiO|-DA-RuCP22+-Re(I), where DA is the dianiline-based electron donor (N,N,N′,N′-((CH2)3PO3H2)4-4,4′-dianiline), RuCP2+ is the light absorber [Ru((4,4′-(PO3H2CH2)2-2,2′-bipyridine)(2,2′-bipyridine))2]2+, and Re(I) is the CO2 reduction catalyst, ReI((4,4′-PO3H2CH2)2-2,2′-bipyridine)(CO)3Cl. Visible light excitation of the assembly in CO2 saturated solution resulted in CO2 reduction to CO. A steady-state photocurrent density of 65 μA cm−2 was achieved under one sun illumination and an IPCE value of 1.9% was obtained with 450 nm illumination. The importance of the DA aniline donor in the assembly as an initial site for reduction of the RuCP2+ excited state was demonstrated by an 8 times higher photocurrent generated with DA present in the surface film compared to a control without DA. Nanosecond transient absorption measurements showed that the expected reduced one-electron intermediate, RuCP+, was formed on a sub-nanosecond time scale with back electron transfer to the electrode on the microsecond timescale which competes with forward electron transfer to the Re(I) catalyst at t1/2 = 2.6 μs (kET = 2.7 × 105 s−1)

Plant biosystems design research roadmap 1.0

Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they are still not able to meet the ever-increasing needs, in terms of both quantity and quality, resulting from the rapid increase in world population and expected standards of living. A step change that may address these challenges would be to expand the potential of plants using biosystems design approaches. This represents a shift in plant science research from relatively simple trial-and-error approaches to innovative strategies based on predictive models of biological systems. Plant biosystems design seeks to accelerate plant genetic improvement using genome editing and genetic circuit engineering or create novel plant systems through de novo synthesis of plant genomes. From this perspective, we present a comprehensive roadmap of plant biosystems design covering theories, principles, and technical methods, along with potential applications in basic and applied plant biology research. We highlight current challenges, future opportunities, and research priorities, along with a framework for international collaboration, towards rapid advancement of this emerging interdisciplinary area of research. Finally, we discuss the importance of social responsibility in utilizing plant biosystems design and suggest strategies for improving public perception, trust, and acceptance

The Kalanchoe genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that convergent evolution of protein sequence and temporal gene expression underpins the independent emergences of CAM from C3 photosynthesis. To test this hypothesis, we generate a de novo genome assembly and genome-wide transcript expression data for Kalanchoë fedtschenkoi, an obligate CAM species within the core eudicots with a relatively small genome (~260 Mb). Our comparative analyses identify signatures of convergence in protein sequence and re-scheduling of diel transcript expression of genes involved in nocturnal CO2 fixation, stomatal movement, heat tolerance, circadian clock, and carbohydrate metabolism in K. fedtschenkoi and other CAM species in comparison with non-CAM species. These findings provide new insights into molecular convergence and building blocks of CAM and will facilitate CAM-into-C3 photosynthesis engineering to enhance water-use efficiency in crops