The jujube (Ziziphus jujuba Mill.), a member of family Rhamnaceae, is a major dry fruit and a traditional herbal medicine for more than one billion people. Here we present a high-quality sequence for the complex jujube genome, the first genome sequence of Rhamnaceae, using an integrated strategy. The final assembly spans 437.65 Mb (98.6% of the estimated) with 321.45 Mb anchored to the 12 pseudo-chromosomes and contains 32,808 genes. The jujube genome has undergone frequent inter-chromosome fusions and segmental duplications, but no recent whole-genome duplication. Further analyses of the jujube-specific genes and transcriptome data from 15 tissues reveal the molecular mechanisms underlying some specific properties of the jujube. Its high vitamin C content can be attributed to a unique high level expression of genes involved in both biosynthesis and regeneration. Our study provides insights into jujube-specific biology and valuable genomic resources for the improvement of Rhamnaceae plants and other fruit trees.

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Snapdragon (Antirrhinum majus L.), a member of the Plantaginaceae family, is an important model for plant genetics and molecular studies on plant growth and development, transposon biology and self-incompatibility. Here we report a near-complete genome assembly of A. majus cultivar JI7 (A. majus cv.JI7) comprising 510 Megabases (Mb) of genomic sequence and containing 37,714 annotated protein-coding genes. Scaffolds covering 97.12% of the assembled genome were anchored on eight chromosomes. Comparative and evolutionary analyses revealed that a whole-genome duplication event occurred in the Plantaginaceae around 46–49 million years ago (Ma). We also uncovered the genetic architectures associated with complex traits such as flower asymmetry and self-incompatibility, identifying a unique duplication of TCP family genes dated to around 46–49 Ma and reconstructing a near-complete ψS-locus of roughly 2 Mb. The genome sequence obtained in this study not only provides a representative genome sequenced from the Plantaginaceae but also brings the popular plant model system of Antirrhinum into the genomic age.

BackgroundPanax notoginseng (Burk.) F.H. Chen is one of the most highly valued medicinal plants in the world. The major bioactive molecules are triterpene saponins, which are also known as ginsenosides. However, its large genome size has hindered the assembly of a draft genome by whole genome sequencing. Hence, genomic and transcriptomic details about P. notoginseng, especially its biosynthetic pathways and gene expression in different parts of the plant, have remained largely unknown until now.ResultsIn this study, RNA sequencing of three different P. notoginseng tissues was performed using next generation DNA sequencing. After assembling the high quality sequencing reads into 107,340 unigenes, biochemical pathways were predicted and 9,908 unigenes were assigned to 135 KEGG pathways. Among them, 270 unigenes were identified to be involved in triterpene saponin biosynthesis. In addition, 350 and 342 unigenes were predicted to encode cytochrome P450s and glycosyltransferases, respectively, based on the annotation results, some of which encode enzymes responsible for the conversion of the triterpene saponin backbone into different ginsenosides. In particular, one unigene predominately expressed in the root was annotated as CYP716A53v2, which probably participates in the formation of protopanaxatriol from protopanaxadiol in P. notoginseng. The differential expression of this gene was further confirmed by real-time PCR.ConclusionsWe have established a global transcriptome dataset for P. notoginseng and provided additional genetic information for further genome-wide research and analyses. Candidate genes involved in ginsenoside biosynthesis, including putative cytochrome P450s and glycosyltransferases were obtained. The transcriptomes in different plant tissues also provide invaluable resources for future study of the differences in physiological processes and secondary metabolites in different parts of P. notoginseng.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1477-5) contains supplementary material, which is available to authorized users.

The use of dipyrido[3,2-d:2′,3′-f]quinoxaline (Dpq) combined with three structurally related benzene-dicarboxylic acid ligands [benzene-1,3-dicarboxylic acid (H 2 L 1 ), benzene-1,2-dicarboxylic acid (H 2 L 2 ), and biphenyl-4,4′-dicarboxylic acid (H 2 L 3 )] has allowed the rational design of three novel Cd(II) coordination polymers, [Cd 3 (Dpq) (2), and [Cd 2 (Dpq) 2 (L 3 ) 2 ]‚1.5H 2 O (3), which were hydrothermally synthesized and structurally determined by X-ray analysis.Compound 1 features a 1-D ribbonlike structure, compound 2 shows novel 2-D four-connected networks, and compound 3 possesses an interesting 6-connected 2-fold interpenetrated 3-D R-Po-related architecture. The Dpq ligand takes a chelating coordination mode while the other two nitrogen atoms did not coordinate to the Cd(II) ions. In these complexes, the three benzene-dicarboxylate ligands are able to link Cd(II) ions in various coordination modes, giving rise to 1-, 2-, and 3-dimensional Cd complexes, respectively. In addition, complexes 1-3 exhibit blue/green emission in the solid state at room temperature.

A conductive carbon paste electrode (CPE) comprised of a new copper-complex of [Cu 2 (Dpq) quinoxaline, Ac ¼ acetate) and carbon powder, was fabricated by the direct mixing method. The electrochemical behavior and electrocatalysis of the new copper-complex modified CPE (Cu-CPE) have been studied in detail. Cyclic voltammograms showed that the Cu-CPE had a favorable electrochemical response of a reversible redox couple of Cu(II)/Cu(I). The Cu-CPE showed good electrocatalytic activity toward the reduction of the bromate, nitrite and hydrogen peroxide. The electrocatalytic reduction peak current of KBrO 3 , KNO 2 and H 2 O 2 showed a linear dependent on their concentrations. All of the results revealed that the Cu-CPE had a good reproducibility, remarkable long term stability and especially good surface renewability by simple mechanical polishing in the event of surface fouling, which is important for practical application.

Two polyoxometalate-templated organic-inorganic hybrid porous frameworks, namely, [Cu2(H2O)2(bpp)2Cl][PM12O40].approximately 20H2O (for 1, M = W; for 2, M = Mo; bpp = 1,3-bis(4-pyridyl)propane), were self-assembly obtained and structurally determined by elemental analyses, inductively coupled plasma analyses, infrared spectroscopy, and single-crystal X-ray diffraction analyses. Single-crystal X-ray analysis of these crystals revealed that both of the structures are constructed from eight-connected three-dimensional coordination polymer hosts [Cu2(H2O)2(bpp)2Cl]n(3n+) and ball-shaped Keggin-type guests [PM12O40]n(3n-) as templates. The polymer hosts resulted from a bcc-type framework with nanotubes, and the nanotubes can be regarded as a tetra-stranded helix structure. Furthermore, compounds 1 and 2 exhibit photoluminescent properties at ambient temperature, and the compound 2 bulk-modified carbon paste electrode ( 2-CPE) displays good electrocatalytic activity toward the reduction of nitrite.

Ginger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger ‘Zhugen’, a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3’H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.