Genomic analyses provide comprehensive insights into the domestication of bast fiber crop ramie (Boehmeria nivea)

Ramie (Boehmeria nivea) is an economically important natural fiber-producing crop that has been cultivated for thousands of years in China; however, the evolution of this crop remains largely unknown. Here, we report a ramie domestication analysis based on genome assembly and resequencing of cultivated and wild accessions. Two chromosome-level genomes representing wild and cultivated ramie were assembled de novo. Numerous structural variations between two assemblies, together with the genetic variations from population resequencing, constituted a comprehensive genomic variation map for ramie. Domestication analysis identified 71 high-confidence selective sweeps comprising 320 predicted genes, and 29 genes from sweeps were associated with fiber growth in the expression. In addition, we identified seven genetic loci associated with the fiber yield trait in the segregated population derived from the crossing of two assembled accessions, and two of which showed an overlap with the selective sweeps. These findings indicated that bast fiber traits were focused on during the domestication history of ramie. This study sheds light on the domestication of ramie and provides a valuable resource for biological and breeding studies of this important crop.     

Draft genome sequence of ramie,Boehmeria nivea (L.) Gaudich

Ramie, Boehmeria nivea (L.) Gaudich, family Urticaceae, is a plant native to eastern Asia, and one of the world's oldest fibre crops. It is also used as animal feed and for the phytoremediation of heavy metal‐contaminated farmlands. Thus, the genome sequence of ramie was determined to explore the molecular basis of its fibre quality, protein content and phytoremediation. For further understanding ramie genome, different paired‐end and mate‐pair libraries were combined to generate 134.31 Gb of raw DNA sequences using the Illumina whole‐genome shotgun sequencing approach. The highly heterozygous B. nivea genome was assembled using the Platanus Genome Assembler, which is an effective tool for the assembly of highly heterozygous genome sequences. The final length of the draft genome of this species was approximately 341.9 Mb (contig N50 = 22.62 kb, scaffold N50 = 1,126.36 kb). Based on ramie genome annotations, 30,237 protein‐coding genes were predicted, and the repetitive element content was 46.3%. The completeness of the final assembly was evaluated by benchmarking universal single‐copy orthologous genes (BUSCO); 90.5% of the 1,440 expected embryophytic genes were identified as complete, and 4.9% were identified as fragmented. Phylogenetic analysis based on single‐copy gene families and one‐to‐one orthologous genes placed ramie with mulberry and cannabis, within the clade of urticalean rosids. Genome information of ramie will be a valuable resource for the conservation of endangered Boehmeria species and for future studies on the biogeography and characteristic evolution of members of Urticaceae.     

Proteomic analysis of leaves from a diploid cybrid produced by protoplast fusion between Satsuma mandarin and pummelo

Hypocotyls and cotyledons of three ramie (Boehmeria nivea Gaud.) cultivars (Zhongzhu No.1, Zhongsizhu No.1 and NC01), important plants for textile fiber, were pre-cultured on callus-inducing medium for 1 day before co-cultivation for 2 days with Agrobacterium tumefaciens strain LBA4404 harboring the plasmid pGBI4ABC carrying two insect resistance (CryIA and CpTI), gus, and neomycin phosphotransferase (npt II) genes. Calli were induced from both hypocotyl and cotyledon explants grown on a kanamycin selection medium. Regenerated shoots were obtained after two cycles of culture and transferred to rooting medium. Kanamycin-resistant plantlets were rooted in 2 weeks, and then transplanted to soil. Transgenic plants were subsequently confirmed by polymerase chain reaction, Southern blot hybridization, and GUS assays. More than 100 transgenic plants carrying insect-resistance genes were produced. A transformation frequency of 8.8 to 10.3% was obtained using hypocotyls as explants, which was higher than all previously reported transformation frequencies. The whole protocol, from transformation recovery of plants grown in soil, was completed within 2–4 months. Therefore, a simple, efficient, and robust Agrobacterium tumefaciens -mediated transformation system for ramie has been developed.     

In vitro plant regeneration from seedling-derived explants of ramie [Boehmeria nivea (L.) Gaud]

Ramie [Boehmeria nivea (L.) Gaud] is one of the most important perennial fiber crops in China. In vitro tissue culture of ramie could serve as an important means for its improvement through genetic transformation. To improve the regeneration capacity of ramie, the effects on plant regeneration of donor plant age, basal medium, plant growth regulators, and culture conditions were evaluated using explants derived from the cotyledon, hypocotyl, leaf, petiole, and stem of ramie seedlings. Cotyledons and hypocotyls excised from 4-d-old seedlings and leaves and petioles and stems from 15-d-old seedlings were optimal explants. The highest regeneration efficiency was obtained on Murashige and Skoog salts with Gamborg’s B₅ vitamins basal medium containing 2.27 μM thidiazuron (TDZ) and 0.054 μM naphthaleneacetic acid (NAA) for the five explant types tested. A photoperiod of 16:8 h (light/dark) was found to be superior than continuous darkness for regeneration of ramie using TDZ. The regenerated shoots were transferred to hormone-free medium for shoot elongation and successfully rooted on half-strength Murashige and Skoog supplemented with 0.134 μM NAA. The rooted plantlets with four to five leaves were transplanted to greenhouse for further growth.     

RETRACTED ARTICLE: Transgenic ramie [<Emphasis Type="Italic">Boehmeria nivea</Emphasis> (L.) Gaud.]: factors affecting the efficiency of <Emphasis Type="Italic">Agrobacterium</Emphasis><Emphasis Type="Italic">tumefaciens</Emphasis>-mediated transformation and regeneration

In the present study, an efficient Agrobacterium-mediated gene transformation system was developed for ramie [Boehmeria nivea (L.) Gaud.] based on the examinations of several factors affecting plant transformation efficiency. The effects of Agrobacterium cell density, acetosyringone, co-cultivation temperature, co-cultivation duration, co-cultivation photoperiod and pH on stable transformation were evaluated. Agrobacterium at a concentration of OD = 0.5–0.8 improved the efficiency of transformation. Concentration of acetosyringone at 50 mg/L during co-cultivation significantly increased transformation efficiency. Co-cultivation at 20°C, in comparison to 15, 25 and 28°C, consistently resulted in higher transformation frequencies. A relatively short co-cultivation duration (3 days) was optimal for ramie transformation. Co-cultivation medium at pH 5.9 and co-cultivation in darkness both improved the transformation efficiencies of ramie. An overall scheme for producing transgenic ramie is presented, through which an average transformation rate from 10.5 to 24.7% in five ramie varieties was obtained. Stable expression and integration of the transgenes were confirmed by histochemical GUS assay, kanamycin painting assay, PCR and Southern blotting. This optimized transformation system should be employed for efficient Agrobacterium-mediated transformation of ramie. An erratum to this article can be found at     

Morphological and physiological changes of ramie (Boehmeria nivea L. Gaud) in response to drought stress and GA3 treatment

Ramie (Boehmeria nivea L. Gaud) fibers extracted from the stem bast is one of the most important natural fibers. Ramie growth is severely hindered by drought stress but is promoted by gibberellins (GAs). In order to investigate ramie morphological and physiological responses to drought stress and GA₃ treatment, four groups of potted ramie (severe drought stress (DS), severe drought stress and spraying with GA₃ (DS + GA₃), normal watering and spraying with GA₃ (control + GA₃), and normal watering as a control) were tested. The result showed that, comparing with the ramie growing under well watering condition, a decrease in chlorophyll a (Chl a) and carotenoid and an increase in proline and soluble sugar contents were commonly observed in drought-stressed and GA₃-treated ramie. Different responses of the stem morphological traits, fiber yield, and seven physiological characteristics (relative water content, the activities of POD, SOD, and CAT enzymes, the contents of Chl b, endogenous GAs and MDA) were observed between drought-stressed and GA₃-treated plants. When the ramie suffering drought stress was sprayed with GA₃ (in (DS + GA₃) group), the responses of some physiological traits (POD, SOD, CAT, MDA, and endogenous GAs) and morphological traits (stem shape and fiber yield) to drought stress disappeared completely or partially, and the plant presented similar characteristics of well-watered ramie in these traits. These results suggested that the application of exogenous GA₃ can improve the drought tolerance of ramie.     

Byssochlamys nivea with patulin-producing capability has an isoepoxydon dehydrogenase gene (idh) with sequence homology to Penicillium expansum and P. griseofulvum

Nucleotide sequences of the isoepoxydon dehydrogenase gene (idh) for eight strains of Byssochlamys nivea were determined by constructing GenomeWalker libraries. A striking finding was that all eight strains of B. nivea examined had identical nucleotide sequences, including those of the two introns present. The length of intron 2 was nearly three times the size of introns in strains of Penicillium expansum and P. griseofulvum, but intron 1 was comparable in size to the number of nucleotides present in introns 1 and 2 of P. expansum and P. griseofulvum. A high degree of amino acid homology (88 %) existed for the idh genes of the strains of B. nivea when compared with sequences of P. expansum and P. griseofulvum. There were many nucleotide differences present, but they did not affect the amino acid sequence because they were present in the third position. The identity of the B. nivea isolates was confirmed by sequencing the ITS/partial LSU (28 S) rDNA genes. Four B. nivea strains were analysed for production of patulin, a mycotoxin found primarily in apple juice and other fruit products. The B. nivea strains produced patulin in amounts comparable to P. expansum strains. Interest in the genus Byssochlamys is related to the ability of its ascospores to survive pasteurization and cause spoilage of heat-processed fruit products worldwide.     

Higher expression of induced defenses in teosintes (Zea spp.) is correlated with greater resistance to fall armyworm,Spodoptera frugiperda

Selection for plant traits important for agriculture can come at a high cost to plant defenses. While selecting for increased growth rate and yield, domestication and subsequent breeding may lead to weakened defenses and greater susceptibility of plants to herbivores. We tested whether expression of defense genes differed among maize, Zea mays ssp. mays L. (Poaceae), and its wild relatives Zea mays ssp. parviglumis Iltis & Doebley and Zea diploperennis Iltis et al. We used two populations of Z. mays ssp. parviglumis: one expected to express high levels of an herbivore resistance gene, wound‐inducible protein (wip1), and another expected to have low expression of wip1. To test whether maize and wild Zea differed in induction of defenses against Spodoptera frugiperda (Smith) (Lepidoptera: Noctuidae), we quantified expression of several genes involved in plant defense: wip1, maize protease inhibitor (mpi), pathogenesis‐related protein (PR‐1), and chitinase. Moreover, we compared growth, development, and survival of caterpillars on maize and wild Zea plants. We found that maize expressed low levels of all but one of the genes when attacked by caterpillars, whereas the wild relatives of maize expressed induced defense genes at high levels. Expression of wip1, in particular, was much greater in the Z. mays ssp. parviglumis population that we expected to naturally express high levels of wip1, with expression levels 29‐fold higher than in herbivore‐free plants. Elevated expression of defenses in wild plants was correlated with higher resistance to caterpillars. Larvae were 15–20% smaller on wild Zea compared with maize, developed 20% slower, and only 22% of them survived to pupation on Z. mays ssp. parviglumis with high levels of wip1. Our results suggest that domestication has inadvertently reduced the resistance of maize, and it is likely that expression of wip1 and other genes associated with defenses play an important role in this reduction in resistance.     

Transgenic plants of ramie (Boehmeria nivea Gaud.) obtained by Agrobacterium mediated transformation

A regeneration and transformation protocol for ramie (Boehmeria nivea Gaud.) is presented. Regeneration was obtained from leaf discs placed on solid B-5 medium (Gamborg et al. 1968) containing adequate concentrations of auxin and cytokinin. Co-cultivation of leaf discs with Agrobacterium tumefaciens and subsequent regeneration resulted in transgenic plants as shown by Southern blot and analysis of expression of the GUS-marker gene.     

Characterization and overproduction of a thermo-alkaline pectate lyase from alkaliphilic Bacillus licheniformis with potential in ramie degumming

A thermo-alkaline pectate lyase (BliPelA) gene from an alkaliphilic Bacillus licheniformis strain was cloned and overexpressed in Escherichia coli. Mature BliPelA exhibited maximum activity at pH 11 and 70 °C, and demonstrated cleavage capability on a broad range of substrates such as polygalacturonic acid, pectins, and methylated pectins. The highest specific activity, of 320 U mg⁻¹, was towards polygalacturonic acid. Significant ramie (Boehmeria nivea) fiber weight loss (21.5%) was obtained following enzyme treatment and combined enzyme-chemical treatment (29.3%), indicating a high ramie degumming efficiency of BliPelA. The total activity of recombinant BliPelA reached 1450.1 U ml⁻¹ with a productivity of 48.3 U ml⁻¹ h⁻¹ under high-cell-density cultivation with a glycerol exponential feeding strategy for 30 h in 1-l fed-batch fermenter, and 1380.1 U ml⁻¹ with a productivity of 57.5 U ml⁻¹ h⁻¹ after 24 h under constant glucose feeding in a 20-l fermenter using E. coli as the host. The enzyme yields reached 4.5 and 4.3 g l⁻¹ in 1-l and 20-l fed-batch fermenters, respectively, which are higher than those of most reported alkaline Pels. Based on these promising properties and high-level production, BliPelA shows great potential for application in ramie degumming in textile industry.     

A Preformulation Study of a New Medicine for Chagas Disease Treatment: Physicochemical Characterization,Thermal Stability,and Compatibility of Benznidazole

This work aimed the studies of physicochemical characterization, thermal stability, and compatibility of benznidazole (BNZ) drug by spectroscopy (NMR, IR), thermoanalytical (differential thermal analysis, differential scanning calorimetry, and thermogravimetry), and chromatographic (HPLC) techniques, beyond the analytical tools of Van’t Hoff equation and Ozawa model. The compatibility study was conducted by binary mixtures (1:1, w/w) of the drug with microcrystalline cellulose 102 and 250, anhydrous lactose, and sodium starch glycolate. The physicochemical characterization confirmed data reported in scientific literature, guaranteeing authenticity of the analyzed raw material. The drug melts at 191.68°C (∆H, 119.71 J g⁻¹), characteristic of a non-polymorphic raw material, and a main stage decomposition at 233.76–319.35°C (∆m, 43.32%) occurred, ending the study with almost all mass volatilized. The quantification of drug purity demonstrated a correlation of 99.63% between the data obtained by chromatographic (99.20%) and thermoanalytical technique (99.56%). The Arrhenius equation and Ozawa model showed a zero-order kinetic behavior for the drug decomposition, and a calculated provisional validity time was 2.37 years at 25°C. The compatibility study evidenced two possible chemical incompatibilities between BNZ and the tested excipients, both associated by the authors to the reaction of the BNZ’s amine and a polymer carbohydrate’s carbonile, being maillard reactions. The BNZ reaction with anhydrous lactose is more pronounced than with the sodium starch glycolate because the lactose has more free hydroxyl groups to undergo reduction by the drug. In this sense, this work guides the development of a new solid pharmaceutical product for Chagas disease treatment, with defined quality control parameters and physicochemical stability.     

Domestication and geographic origin of Oryza sativa in China: insights from multilocus analysis of nucleotide variation of O. sativa and O. rufipogon

Previous studies have indicated that China is one of the domestication centres of Asian cultivated rice (Oryza sativa), and common wild rice (O. rufipogon) is the progenitor of O. sativa. However, the number of domestication times and the geographic origin of Asian cultivated rice in China are still under debate. In this study, 100 accessions of Asian cultivated rice and 111 accessions of common wild rice in China were selected to examine the relationship between O. sativa and O. rufipogon and thereby infer the domestication and evolution of O. sativa in China through sequence analyses of six gene regions, trnC‐ycf6 in chloroplast genomes, cox3 in mitochondrial genomes and ITS, Ehd1, Waxy, Hd1 in nuclear genomes. The results indicated that the two subspecies of O. sativa (indica and japonica) were domesticated independently from different populations of O. rufipogon with gene flow occurring later from japonica to indica; Southern China was the genetic diversity centre of O. rufipogon, and the Pearl River basin near the Tropic of Cancer was the domestication centre of O. sativa in China.