Aberrant METTL14 gene expression contributes to malignant transformation of benzene-exposed myeloid cells.

Benzene is a known contributor to human leukaemia through its toxic effects on bone marrow cells, and epigenetic modification is believed to be a potential mechanism underlying benzene pathogenesis. However, the specific roles of N6-methyladenosine (m6A), a newly discovered RNA post-transcriptional modification, in benzene-induced hematotoxicity remain unclear. In this study, we identified self-renewing malignant proliferating cells in the bone marrow of benzene-exposed mice through in vivo bone marrow transplantation experiments and Competitive Repopulation Assay. Subsequent analysis using whole transcriptome sequencing and RNA m6A methylation sequencing revealed a significant upregulation of RNA m6A modification levels in the benzene-exposed group. Moreover, RNA methyltransferase METTL14, known as a pivotal player in m6A modification, was found to be aberrantly overexpressed in Lin-Sca-1+c-Kit+ (LSK) cells of benzene-exposed mice. Further analysis based on the GEO database showed a positive correlation between the expression of METTL14, mTOR, and GFI and benzene exposure dose. In vitro cellular experiments, employing experiments such as western blot, q-PCR, m6A RIP, and CLIP, validated the regulatory role of METTL14 on mTOR and GFI1. Mechanistically, continuous damage inflicted by benzene exposure on bone marrow cells led to the overexpression of METTL14 in LSK cells, which, in turn, increased m6A modification on the target genes' (mTOR and GFI1) RNA. This upregulation of target gene expression activated signalling pathways such as mTOR-AKT, ultimately resulting in malignant proliferation of bone marrow cells. In conclusion, this study offers insights into potential early targets for benzene-induced haematologic malignant diseases and provides novel perspectives for more targeted preventive and therapeutic strategies.

The haplotype-resolved genome assembly of autotetraploid rhubarb Rheum officinale provides insights into its genome evolution and massive accumulation of anthraquinones.

Rheum officinale, a member of the Polygonaceae family, is an important medicinal plant that is widely used in traditional Chinese medicine. Here, we report a 7.68-Gb chromosome-scale assembly of R. officinale with a contig N50 of 3.47 Mb, which was clustered into 44 chromosomes across four homologous groups. Comparative genomics analysis revealed that transposable elements have made a significant contribution to its genome evolution, gene copy number variation, and gene regulation and expression, particularly of genes involved in metabolite biosynthesis, stress resistance, and root development. We placed the recent autotetraploidization of R. officinale at ∼0.58 mya and analyzed the genomic features of its homologous chromosomes. Although no dominant monoploid genomes were observed at the overall expression level, numerous allele-differentially-expressed genes were identified, mainly with different transposable element insertions in their regulatory regions, suggesting that they functionally diverged after polyploidization. Combining genomics, transcriptomics, and metabolomics, we explored the contributions of gene family amplification and tetraploidization to the abundant anthraquinone production of R. officinale, as well as gene expression patterns and differences in anthraquinone content among tissues. Our report offers unprecedented genomic resources for fundamental research on the autopolyploid herb R. officinale and guidance for polyploid breeding of herbs.

Subchronic feeding study of glyphosate-tolerant maize GG2 with the gr79-epsps and gat genes in Wistar Han RCC rats.

The genetically modified (GM) maize GG2 contains gr79-epsps and gat genes, conferring glyphosate tolerance. The present study aimed to investigate potential effects of maize GG2 in a 90-day subchronic feeding study on Wistar Han RCC rats. Maize grains from GG2 or non-GM maize were incorporated into diets at concentrations of 25% and 50% and administered to Wistar Han RCC rats (n = 10/sex/group) for 90 days. The basal-diet group of rats (n = 10/sex/group) were fed with common commercialized rodent diet. Compared with rats fed with the corresponding non-GM maize and the basal-diet, no biologically relevant differences were observed in rats fed with the maize GG2, according to the results of body weight/gain, feed consumption/utilization, clinical signs, mortality, ophthalmology, clinical pathology (hematology, prothrombin time, urinalysis, serum chemistry), organ weights, and gross and microscopic pathology. Under the conditions of this study, these results indicated that maize GG2 is as safe as the non-GM maize in this 90-day feeding study.

A 90-day feeding study of genetically modified maize LP007-1 in wistar han RCC rats.

LP007-1 is a variety of insect-resistant and herbicide-tolerant maize containing the modified cry1Ab, cry2Ab, vip3Aa and cp4-epsps genes. The food safety assessment of the maize LP007-1 was conducted in Wistar Han RCC rats by a 90-days feeding study. Maize grains from both LP007-1 or its corresponding non-genetically modified control maize AX808 were incorporated into rodent diets at 25% and 50% concentrations by mass and administered to rats (n = 10/sex/group) for 90 days. A commercialized rodent diet was fed to an additional group as the basal-diet group. The diets of all groups were nutritionally balanced. No biologically relevant differences were observed in rats fed with maize LP007-1 compared to rats fed with AX808 and the basal-diet with respect to body weight/gain, food consumption/utilization, clinical signs, mortality, ophthalmology, clinical pathology (hematology, prothrombin time, activation of partial thrombin time, serum chemistry, urinalysis), organ weights, and gross and microscopic pathology. Considering the circumstances of this study, the results provided evidence that LP007-1 maize did not exhibit toxicity in the 90-day feeding study.

Pharmacokinetics, pharmacodynamics, and safety of prandial oral insulin (N11005) in healthy subjects.

Aims: To verify whether the oral insulin N11005 is administered as a prandial insulin by assessing the pharmacokinetics (PK), pharmacodynamics (PD), and safety profiles of N11005 with a short-acting biosynthetic human insulin (Novolin R) as reference. Methods: This was a randomized, open-label, single-dose, crossover hyperinsulinemic-euglycemic clamp study in healthy Chinese male subjects. A total of 12 subjects were enrolled in the test (T) group (N11005, 300 IU, p.o.) and the reference (R) group (Novolin R, 0.1 IU/Kg, i.h.) with a washout period of 14 days. All subjects were administered on the same day of the clamp study. Glucose Infusion Rates (GIR), serum insulin, and C-peptide concentration were determined during every 8-hour clamp cycle. Trial registration: Clinicaltrials.gov identifier NCT04975022. Results: After administration, the ratios of mean serum C-peptide concentration to baseline concentration in both T and R groups were lower than 50%, which confirmed the stability of the clamp platform. T group (N11005) showed a more rapid onset of action (tGIR10%max≈11 min) and a comparable duration of action to the R group, which was basically in line with the characteristics of prandial insulins. No adverse events (AEs) occurred throughout the study, which demonstrated that N11005 and Novolin R are safe and well-tolerated. Conclusions: The PD profiles of the single-dose N11005 in the human body are similar to those of prandial insulins, with an excellent safety profile. Clinical trial registration: Clinicaltrials.gov, identifier NCT04975022.

Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum.

BACKGROUND: Pennisetum giganteum (AABB, 2n = 4x = 28) is a C4 plant in the genus Pennisetum with origin in Africa but currently also grown in Asia and America. It is a crucial forage and potential energy grass with significant advantages in yield, stress resistance, and environmental adaptation. However, the mechanisms underlying these advantageous traits remain largely unexplored. Here, we present a high-quality genome assembly of the allotetraploid P. giganteum aiming at providing insights into biomass accumulation. RESULTS: Our assembly has a genome size 2.03 Gb and contig N50 of 88.47 Mb that was further divided into A and B subgenomes. Genome evolution analysis revealed the evolutionary relationships across the Panicoideae subfamily lineages and identified numerous genome rearrangements that had occurred in P. giganteum. Comparative genomic analysis showed functional differentiation between the subgenomes. Transcriptome analysis found no subgenome dominance at the overall gene expression level; however, differentially expressed homoeologous genes and homoeolog-specific expressed genes between the two subgenomes were identified, suggesting that complementary effects between the A and B subgenomes contributed to biomass accumulation of P. giganteum. Besides, C4 photosynthesis-related genes were significantly expanded in P. giganteum and their sequences and expression patterns were highly conserved between the two subgenomes, implying that both subgenomes contributed greatly and almost equally to the highly efficient C4 photosynthesis in P. giganteum. We also identified key candidate genes in the C4 photosynthesis pathway that showed sustained high expression across all developmental stages of P. giganteum. CONCLUSIONS: Our study provides important genomic resources for elucidating the genetic basis of advantageous traits in polyploid species, and facilitates further functional genomics research and genetic improvement of P. giganteum.

Cultivation pattern affects starch structure and physicochemical properties of yam (Dioscorea persimilis).

Yam (Dioscorea spp.) is a major food source in many countries due to its tuber rich in starch (60 %-89 % of the dry weight) and various important micronutrients. Orientation Supergene Cultivation (OSC) pattern is a simple and efficient cultivation mode developed in China in recent years. However, little is known about its effect on yam tuber starch. In this study, the starchy tuber yield, starch structure and physicochemical properties were compared and analyzed in detail between OSC and Traditional Vertical Cultivation (TVC) with Dioscorea persimilis "zhugaoshu", a widely cultivated variety. The results proved that OSC significantly increased tuber yield (23.76 %-31.86 %) and commodity quality (more smooth skin) compared with TVC in three consecutive years of field experiments. Moreover, OSC increased amylopectin content, resistant starch content, granule average diameter and average degree of crystallinity by 2.7 %, 5.8 %, 14.7 % and 9.5 %, respectively, while OSC decreased starch molecular weight (Mw). These traits resulted in starch with lower thermal properties (To, Tp, Tc, ΔHgel), but higher pasting properties (PV, TV). Our results indicated that cultivation pattern affected the yam production and starch physicochemical properties. It would not only provide a practical basis for OSC promotion, but also provide valuable information on how to guide the yam starch end use in food and non-food industries.

Antihepatoma peptide, scolopentide, derived from the centipede scolopendra subspinipes mutilans.

BACKGROUND: Centipedes have been used to treat tumors for hundreds of years in China. However, current studies focus on antimicrobial and anticoagulation agents rather than tumors. The molecular identities of antihepatoma bioactive components in centipedes have not yet been extensively investigated. It is a challenge to isolate and characterize the effective components of centipedes due to limited peptide purification technologies for animal-derived medicines. AIM: To purify, characterize, and synthesize the bioactive components with the strongest antihepatoma activity from centipedes and determine the antihepatoma mechanism. METHODS: An antihepatoma peptide (scolopentide) was isolated and identified from the centipede scolopendra subspinipes mutilans using a combination of enzymatic hydrolysis, a Sephadex G-25 column, and two steps of high-performance liquid chromatography (HPLC). Additionally, the CCK8 assay was used to select the extracted fraction with the strongest antihepatoma activity. The molecular weight of the extracted scolopentide was characterized by quadrupole time of flight mass spectrometry (QTOF MS), and the sequence was matched by using the Mascot search engine. Based on the sequence and molecular weight, scolopentide was synthesized using solid-phase peptide synthesis methods. The synthetic scolopentide was confirmed by MS and HPLC. The antineoplastic effect of extracted scolopentide was confirmed by CCK8 assay and morphological changes again in vitro. The antihepatoma effect of synthetic scolopentide was assessed by the CCK8 assay and Hoechst staining in vitro and tumor volume and tumor weight in vivo. In the tumor xenograft experiments, qualified model mice (male 5-week-old BALB/c nude mice) were randomly divided into 2 groups (n = 6): The scolopentide group (0.15 mL/d, via intraperitoneal injection of synthetic scolopentide, 500 mg/kg/d) and the vehicle group (0.15 mL/d, via intraperitoneal injection of normal saline). The mice were euthanized by cervical dislocation after 14 d of continuous treatment. Mechanistically, flow cytometry was conducted to evaluate the apoptosis rate of HepG2 cells after treatment with extracted scolopentide in vitro. A Hoechst staining assay was also used to observe apoptosis in HepG2 cells after treatment with synthetic scolopentide in vitro. CCK8 assays and morphological changes were used to compare the cytotoxicity of synthetic scolopentide to liver cancer cells and normal liver cells in vitro. Molecular docking was performed to clarify whether scolopentide tightly bound to death receptor 4 (DR4) and DR5. qRT-PCR was used to measure the mRNA expression of DR4, DR5, fas-associated death domain protein (FADD), Caspase-8, Caspase-3, cytochrome c (Cyto-C), B-cell lymphoma-2 (Bcl-2), Bcl-2-associated X protein (Bax), x-chromosome linked inhibitor-of-apoptosis protein and Cellular fas-associated death domain-like interleukin-1ß converting enzyme inhibitory protein in hepatocarcinoma subcutaneous xenograft tumors from mice. Western blot assays were used to measure the protein expression of DR4, DR5, FADD, Caspase-8, Caspase-3, and Cyto-C in the tumor tissues. The reactive oxygen species (ROS) of tumor tissues were tested. RESULTS: In the process of purification, characterization and synthesis of scolopentide, the optimal enzymatic hydrolysis conditions (extract ratio: 5.86%, IC50: 0.310 mg/mL) were as follows: Trypsin at 0.1 g (300 U/g, centipede-trypsin ratio of 20:1), enzymolysis temperature of 46 °C, and enzymolysis time of 4 h, which was superior to freeze-thawing with liquid nitrogen (IC50: 3.07 mg/mL). A peptide with the strongest antihepatoma activity (scolopentide) was further purified through a Sephadex G-25 column (obtained A2) and two steps of HPLC (obtained B5 and C3). The molecular weight of the extracted scolopentide was 1018.997 Da, and the peptide sequence was RAQNHYCK, as characterized by QTOF MS and Mascot. Scolopentide was synthesized in vitro with a qualified molecular weight (1018.8 Da) and purity (98.014%), which was characterized by MS and HPLC. Extracted scolopentide still had an antineoplastic effect in vitro, which inhibited the proliferation of Eca-109 (IC50: 76.27 µg/mL), HepG2 (IC50: 22.06 µg/mL), and A549 (IC50: 35.13 µg/mL) cells, especially HepG2 cells. Synthetic scolopentide inhibited the proliferation of HepG2 cells (treated 6, 12, and 24 h) in a concentration-dependent manner in vitro, and the inhibitory effects were the strongest at 12 h (IC50: 208.11 µg/mL). Synthetic scolopentide also inhibited the tumor volume (Vehicle vs Scolopentide, P = 0.0003) and weight (Vehicle vs Scolopentide, P = 0.0022) in the tumor xenograft experiment. Mechanistically, flow cytometry suggested that the apoptosis ratios of HepG2 cells after treatment with extracted scolopentide were 5.01% (0 µg/mL), 12.13% (10 µg/mL), 16.52% (20 µg/mL), and 23.20% (40 µg/mL). Hoechst staining revealed apoptosis in HepG2 cells after treatment with synthetic scolopentide in vitro. The CCK8 assay and morphological changes indicated that synthetic scolopentide was cytotoxic and was significantly stronger in HepG2 cells than in L02 cells. Molecular docking suggested that scolopentide tightly bound to DR4 and DR5, and the binding free energies were-10.4 kcal/mol and-7.1 kcal/mol, respectively. In subcutaneous xenograft tumors from mice, quantitative real-time polymerase chain reaction and western blotting suggested that scolopentide activated DR4 and DR5 and induced apoptosis in SMMC-7721 Liver cancer cells by promoting the expression of FADD, caspase-8 and caspase-3 through a mitochondria-independent pathway. CONCLUSION: Scolopentide, an antihepatoma peptide purified from centipedes, may inspire new antihepatoma agents. Scolopentide activates DR4 and DR5 and induces apoptosis in liver cancer cells through a mitochondria-independent pathway.

A 90-day rodent feeding study with grain for genetically modified maize L4 conferring insect resistance and glyphosate tolerance.

A 90-day rat feeding study was performed to conduct a safety assessment on L4, a multi-gene genetically modified maize, conferring "Bt" insect resistance and glyphosate tolerance. A total of 140 Wistar rats were assigned to seven groups, 10 animals/group/sex, which comprised three genetically modified groups fed diets containing different concentrations of L4, three corresponding non-genetically modified groups fed diets containing different concentrations of zheng58 (parent plants), and a basal diet group fed the standard basal diet for 13 weeks. The fed diets contained L4 and Zheng58 at w/w% percentages of 12.5%, 25.0%, and 50% of the total. Animals were evaluated on some research parameters, including general behaviour, body weight/gain, feed consumption/efficiency, ophthalmology, clinical pathology, organ weights, and histopathology. Throughout the feeding trial, all animals were in good condition. No mortality and no biologically relevant effects or toxicologically significant alterations were observed in the total research parameters of the rats in the genetically modified groups compared with those in the basal diet group or their corresponding non-genetically modified groups. No adverse effects were observed in any of the animals. The results indicated that L4 is as safe and wholesome as conventional, non-genetically modified control maize.

Uptake, Translocation, and Distribution of Cyantraniliprole in a Wheat Planting System.

Cyantraniliprole uptake, translocation, and distribution in wheat plants grown in hydroponics and soil conditions were investigated. The hydroponics experiment indicated that cyantraniliprole was prone to be absorbed by wheat roots mainly through the apoplastic pathway and predominately distributed in the cell-soluble fraction (81.4-83.6%) and ultimately transferred upward to leaves (TFleave/stem = 4.84 > TFstem/root = 0.67). In wheat-soil systems, the uptake of cyantraniliprole was similar to that in hydroponics. The accumulation of cyantraniliprole in wheat tissues was mainly affected by the content of soil organic matter and clay, resulting in the increased adsorption of cyantraniliprole onto soils (R2 > 0.991, P < 0.01), and was positively related to the concentration of cyantraniliprole in soil pore water (R2 > 0.991, P < 0.001). Besides, the absorption of cyantraniliprole by wheat was predicted well by the partition-limited model. These results increased our understanding of the absorption and accumulation of cyantraniliprole in wheat and were also helpful for guiding the practical application and risk evaluation of cyantraniliprole.

High-quality Fagopyrum esculentum genome provides insights into the flavonoid accumulation among different tissues and self-incompatibility.

Common buckwheat (Fagopyrum esculentum) and Tartary buckwheat (Fagopyrum tataricum), the two most widely cultivated buckwheat species, differ greatly in flavonoid content and reproductive mode. Here, we report the first high-quality and chromosome-level genome assembly of common buckwheat with 1.2 Gb. Comparative genomic analysis revealed that common buckwheat underwent a burst of long terminal repeat retrotransposons insertion accompanied by numerous large chromosome rearrangements after divergence from Tartary buckwheat. Moreover, multiple gene families involved in stress tolerance and flavonoid biosynthesis such as multidrug and toxic compound extrusion (MATE) and chalcone synthase (CHS) underwent significant expansion in buckwheat, especially in common buckwheat. Integrated multi-omics analysis identified high expression of catechin biosynthesis-related genes in flower and seed in common buckwheat and high expression of rutin biosynthesis-related genes in seed in Tartary buckwheat as being important for the differences in flavonoid type and content between these buckwheat species. We also identified a candidate key rutin-degrading enzyme gene (Ft8.2377) that was highly expressed in Tartary buckwheat seed. In addition, we identified a haplotype-resolved candidate locus containing many genes reportedly associated with the development of flower and pollen, which was potentially related to self-incompatibility in common buckwheat. Our study provides important resources facilitating future functional genomics-related research of flavonoid biosynthesis and self-incompatibility in buckwheat.

Antifungal active ingredient from the twigs and leaves of Clausena lansium Lour. Skeels (Rutaceae).

Two novel amides, named clauphenamides A and B, and twelve other known compounds were isolated from the twigs and leaves of Clausena lansium Lour. Skeels (Rutaceae). Their structures were elucidated on the basis of extensive spectroscopic analysis and comparison with data reported in the literature. Clauphenamide A (1) featured in the unit of N-2-(4,8-dimethoxyfuro [2,3-b]quinolin-7-yl)vinyl, and clauphenamide B (2) was a unprecedented N-phenethyl cinnamide dimer. Other known compounds belong to pyrrolidone amides (3 and 4), furacoumarins (7-10), simple coumarins (11-14), lignan (5) and sesquiterpene (6). Compounds 5, 6, 10 and 12 were separated from the genus (Clausena) for the first time, while 13 was isolated in the species (C. lansium) for the first time. The antifungal activities of the isolated compounds were assayed. As a result, at the concentration of 100 µg/ml, compared with the control (chlorothalonil, inhibition rate of 83.67%), compounds 1 and 2 were found to exhibit moderate antifungal activity against B. dothidea with inhibition rates of 68.39% and 52.05%, respectively. Compounds 11-14 also exhibited moderate activity against B. dothidea and F. oxysporum, with inhibition rates greater than 40%. In addition, compared with the control (chlorothalonil, inhibition rate of 69.02%), compounds 11-14 showed strong antifungal activity to P. oryzae, with inhibition rates greater than 55%. Among them, compound 14 has the strongest antifungal activity against P. oryzae, and the inhibition rate (65.44%) is close to that of the control chlorothalonil. Additionally, the structure-activity relationships of the separated compounds are also discussed preliminarily in this paper.

First Report of Fusarium oxysporum and F. proliferatum Causing Postharvest Corm Rot on Taro in China.

Taro (Colocasia esculenta), a perennial tuberous herb of the family Araceae, is cultivated widely in southern China. In December 2020, postharvest corm rot occurred on taro of 5 tons with approximately 70% incidence in a 18 square meter cellar in the Qingshanhu District (115°83'E, 28°76'N) of Nanchang City, Jiangxi Province, China. Infected corms had round, soft and slightly sunken lesions covered with white mycelia. The lesions gradually expanded, causing part or whole corm to become soft and shrink, and the inner corm tissue turned brown and rotten. To isolate the pathogen, a total of 30 diseased corm samples were collected. The corms were surface-disinfected by wiping them with 70% ethanol and then passing them over flame back and forth for 5 s. After epidermal tissue of the corms was removed using a sterilized scalpel, small portions of the inner tissue were transferred onto potato dextrose agar (PDA) and incubated at 25°C in the dark. A total of 27 isolates forming Fusarium-like colonies were obtained using monosporic isolation, of which 11 isolates were identified as F. oxysporum and 16 isolates were identified as F. proliferatum based on the colony characteristics and conidial morphology (Leslie and Summerell, 2006). Colonies of F. oxysporum isolates produced dense whitish to light purple mycelia with dark red pigments. Macroconidia were sickle-shaped, straight to slightly curved, 3-5 septa, measuring 25.6 to 45.8 × 3.3 to 6.1 µm. Microconidia were hyaline, oval or ellipsoid, aseptate, and measured 5.2 to 11.8 × 2.2 to 3.5 µm. Chlamydospores were round, 3.5 to 7.6 µm in diameter. Colonies of F. proliferatum isolates were whitish with abundant aerial mycelia and orange pigments. Numerous oval unicellular microconidia were 4.5 to 11.8 × 1.9 to 4.2 µm, and sparse falcate macroconidia with 3-4 septa were 19.4 to 39.2 × 1.9 to 5.2 µm in size. No chlamydospores were observed. Genomic DNA of two representative isolates (F. oxysporum isolate YTU1 and F. proliferatum isolate YTH1) was extracted, and the internal transcribed spacer (ITS) region and translation elongation factor 1-α (TEF1-α) gene were amplified and sequenced using primers ITS1/ITS4 and EF-1H/EF-2T (White et al., 1990; Zhang et al., 2014) respectively. Using BLAST analysis, the ITS sequences of isolates YTU1 (506 bp) and YTH1 (508 bp) exhibited 100% homology with F. oxysporum (MN633363) and F. proliferatum (MT534188), respectively, and the TEF1-α sequences of YTU1 (712 bp) and YTH1 (703 bp) shared 100% homology with F. oxysporum (MN507110) and F. proliferatum (MK952799), respectively. Sequences were deposited in GenBank with the Accession Nos. MZ157124 and MZ310443 for ITS, and MZ383814 and MZ383815 for TEF1-α. The pathogenicity of each isolate was determined on six healthy taro corms. All the taro corms were surface-disinfected with 70% alcohol and two locations from each corm were inoculated. One location was inoculated with 20 µl of conidial suspension (1×105 conidia/ml) and the other was inoculated with sterilized water as a control. All corms were incubated in a growth chamber at 25℃ and 95% relative humidity in the dark. After 15 days, all inoculated corms developed brown rot symptoms, while the non-inoculated control corms remained symptomless. The original isolates were successfully reisolated from all symptomatic corms and identified by sequencing, fulfilling Koch's postulates. F. oxysporum has been reported causing postharvest corm rot of taro in Bogor, Japan, and British Solomon Islands (Widodo et al., 2011). However, to our knowledge, this is the first report of F. oxysporum causing postharvest corm rot of taro in China and F. proliferatum causing postharvest corm rot of taro in the world. The disease poses a potential threat to taro production and should be timely assessed and properly managed.

Integration of GWAS and transcriptome analyses to identify SNPs and candidate genes for aluminum tolerance in rapeseed (Brassica napus L.).

BACKGROUND: The exchangeable aluminum (Al), released from the acid soils, is another addition to the environmental stress factors in the form of Al toxicity stress. Al stress affects the normal crop development and reduces the overall yield of rapeseed (Brassica napus L.). The response mechanism of plants to Al toxicity is complicated and difficult to understand with few QTL related studies in rapeseed under Al toxicity stress. RESULT: Using 200,510 SNPs developed by SLAF-seq (specific-locus amplified fragment sequencing) technology, we carried out the genome-wide association analysis (GWAS) in a population of 254 inbred lines of B. napus with large genetic variation and Al-tolerance differences. There were 43 SNPs significantly associated with eight Al-tolerance traits in the seedling stage were detected on 14 chromosomes, and 777 candidate genes were screened at the flanking 100 kb region of these SNPs. Moreover, RNA-seq detected 8291 and 5341 DEGs (the differentially expressed gene) in the Al -tolerant line (ATL) and -sensitive line (ASL), respectively. Based on integration of GWAS and RNA-seq analysis, 64 candidate genes from GWAS analysis differentially expressed at least once in 6 h vs 0 h or 24 h vs 0 h conditions in ATL or ASL. Moreover, four out of sixty-four candidate genes (BnaA03g30320D, BnaA10g11500D, BnaC03g38360D and BnaC06g30030D) were differentially expressed in both 6 h and 24 h compared to 0 h (control) conditions in both lines. The proposed model based on the candidate genes excavated in this study highlighted that Al stress disturb the oxidation-redox balance, causing abnormal synthesis and repair of cell wall and ABA signal transduction, ultimately resulting in inhibition of root elongation. CONCLUSIONS: The integration of GWAS and transcriptome analysis provide an effective strategy to explore the SNPs and candidate genes, which has a potential to develop molecular markers for breeding Al tolerant rapeseed varieties along with theoretical basis of molecular mechanisms for Al toxicity response of Brassica napus plants.

Complete chloroplast genome sequences of three aroideae species (Araceae): lights into selective pressure, marker development and phylogenetic relationships.

BACKGROUND: Colocasia gigantea, Caladium bicolor and Xanthosoma sagittifolium are three worldwide famous ornamental and/or vegetable plants in the Araceae family, these species in the subfamily Aroideae are phylogenetically perplexing due to shared interspecific morphological traits and variation. RESULT: This study, for the first time ever, assembled and analyzed complete chloroplast genomes of C. gigantea, C. bicolor and X. sagittifolium with genome sizes of 165,906 bp, 153,149 bp and 165,169 bp in length, respectively. The genomes were composed of conserved quadripartite circular structures with a total of 131 annotated genes, including 8 rRNA, 37 tRNA and 86 protein-coding genes. A comparison within Aroideae showed seven protein-coding genes (accD, ndhF, ndhK, rbcL, rpoC1, rpoC2 and matK) linked to environmental adaptation. Phylogenetic analysis confirmed a close relationship of C. gigantea with C. esculenta and S. colocasiifolia, and the C. bicolor with X. sagittifolium. Furthermore, three DNA barcodes (atpH-atpI + psaC-ndhE, atpH-atpI + trnS-trnG, atpH-atpI + psaC-ndhE + trnS-trnG) harbored highly variable regions to distinguish species in Aroideae subfamily. CONCLUSION: These results would be beneficial for species identification, phylogenetic relationship, genetic diversity, and potential of germplasm resources in Aroideae.

Molecular Characterization of Mg-Chelatase CHLI Subunit in Pea (Pisum sativum L.).

As a rate-limiting enzyme for chlorophyll biosynthesis, Mg-chelatase is a promising target for improving photosynthetic efficiency. It consists of CHLH, CHLD, and CHLI subunits. In pea (Pisum sativum L.), two putative CHLI genes (PsCHLI1 and PsCHLI2) were revealed recently by the whole genome sequencing, but their molecular features are not fully characterized. In this study, PsCHLI1 and PsCHLI2 cDNAs were identified by PCR-based cloning and sequencing. Phylogenetic analysis showed that PsCHLIs were derived from an ancient duplication in legumes. Both PsCHLIs were more highly expressed in leaves than in other organs and downregulated by abscisic acid and heat treatments, while PsCHLI1 was more highly expressed than PsCHLI2. PsCHLI1 and PsCHLI2 encode 422- and 417-amino acid proteins, respectively, which shared 82% amino acid identity and were located in chloroplasts. Plants with a silenced PsCHLI1 closely resembled PsCHLI1 and PsCHLI2 double-silenced plants, as both exhibited yellow leaves with barely detectable Mg-chelatase activity and chlorophyll content. Furthermore, plants with a silenced PsCHLI2 showed no obvious phenotype. In addition, the N-terminal fragment of PsCHLI1 (PsCHLI1N, Val63-Cys191) and the middle fragment of PsCHLI1 (PsCHLI1M, Gly192-Ser336) mediated the formation of homodimers and the interaction with CHLD, respectively, while active PsCHLI1 was only achieved by combining PsCHLI1N, PsCHLI1M, and the C-terminal fragment of PsCHLI1 (Ser337-Ser422). Taken together, PsCHLI1 is the key CHLI subunit, and its peptide fragments are essential for maintaining Mg-chelatase activity, which can be used to improve photosynthetic efficiency by manipulating Mg-chelatase in pea.

Genome-wide analysis of valine-glutamine motif-containing proteins related to abiotic stress response in cucumber (Cucumis sativus L.).

BACKGROUND: Cucumber (Cucumis sativus L.) is one of the most important economic crops and is susceptible to various abiotic stresses. The valine-glutamine (VQ) motif-containing proteins are plant-specific proteins with a conserved "FxxhVQxhTG" amino acid sequence that regulates plant growth and development. However, little is known about the function of VQ proteins in cucumber. RESULTS: In this study, a total of 32 CsVQ proteins from cucumber were confirmed and characterized using comprehensive genome-wide analysis, and they all contain a conserved motif with 10 variations. Phylogenetic tree analysis revealed that these CsVQ proteins were classified into nine groups by comparing the CsVQ proteins with those of Arabidopsis thaliana, melon and rice. CsVQ genes were distributed on seven chromosomes. Most of these genes were predicted to be localized in the nucleus. In addition, cis-elements in response to different stresses and hormones were observed in the promoters of the CsVQ genes. A network of CsVQ proteins interacting with WRKY transcription factors (CsWRKYs) was proposed. Moreover, the transcripts of CsVQ gene were spatio-temporal specific and were induced by abiotic adversities. CsVQ4, CsVQ6, CsVQ16-2, CsVQ19, CsVQ24, CsVQ30, CsVQ32, CsVQ33, and CsVQ34 were expressed in the range of organs and tissues at higher levels and could respond to multiple hormones and different stresses, indicating that these genes were involved in the response to stimuli. CONCLUSIONS: Together, our results reveal novel VQ resistance gene resources, and provide critical information on CsVQ genes and their encoded proteins, which supplies important genetic basis for VQ resistance breeding of cucumber plants.

Arginine methylation by PRMT2 promotes IFN-ß production through TLR4/IRF3 signaling pathway.

A balance between the positive and negative regulation of toll-like receptor (TLR) signaling pathways is required to avoid detrimental and inappropriate inflammatory responses. Although some protein post-translational modifications (PTMs) such as phosphorylation and ubiquitination have been demonstrated to potently modulate innate immune responses, the role of methylation, an important PTM, control of TLR4 signaling pathway remains unclear. In this study, we found that protein arginine methyltransferase 1, 2 and 3 (PRMT1, 2 and 3) were recruited to methylate TLR4-CD (cytoplasmic domain) after lipopolysaccharide (LPS) stimulation respectively, but the effect of PRMT2 on arginine methylation of TLR4-CD is the most significant among above three PRMTs, which prompted us to focus on PRMT2. Reduction of PRMT2 expression down-regulated arginine (R) methylation level of TLR4 with or without LPS treatment. Methionine 115 (M115) mediated PRMT2 catalyzed-arginine methylation of TLR4 on R731 and R812. Furthermore, PRMT1, 2 and 3 was recruited to methylate interferon regulatory factor 3 (IRF3) after LPS stimulation respectively, but the effect of PRMT2 on arginine methylation of IRF3 is the most significant among the above three PRMTs. Arginine methylation of TLR4 on R812 or arginine methylation of IRF3 on R285 mediated the interaction between TLR4 and IRF3 respectively. Arginine methylation of IRF3 on R285 induced by LPS led to its dimerization and promoted its translocation from the cytoplasm to the nucleus. In addition, the enhancement of arginine methylation of TLR4 induced by PRMT1 or 2 increased IRF3 transcription activity with or without LPS treatment, while PRMT2 with histidine 112 glutamine (H112Q) or methionine 115 isoleucine (M115I) mutation and TLR4 with arginine 812 lysine (R812K) mutation decreased it. Arginine methylation of TLR4 on R812 or PRMT2 enhanced interferon-ß (IFN-ß) production. Our study reveals a critical role for PRMT2 and protein arginine methylation in the enhancement of IFN-ß production via TLR4/IRF3 signaling pathway and may provide a therapeutic strategy to control endotoxemia.

Uncovering the genetic diversity of yams (Dioscorea spp.) in China by combining phenotypic trait and molecular marker analyses.

Yam is an important edible tuber and root plant worldwide; China as one of the native places of yams has many diverse local resources. The goal of this study was to clarify the genetic diversity of the commonly cultivated yam landraces and the genetic relationship between the main yam species in China. In this study, 26 phenotypic traits of 112 yam accessions from 21 provinces in China were evaluated, and 24 simple sequence repeat (SSR) and 29 sequence-related amplified polymorphism (SRAP) markers were used for the genetic diversity analysis. Phenotypic traits revealed that Dioscorea opposita had the highest genetic diversity, followed by D. alata, D. persimilis, D. fordii, and D. esculenta. Among the 26 phenotypic traits, the Shannon diversity indexes of leaf shape, petiole color, and stem color were high, and the range in the variation of tuber-related traits in the underground part was higher than that in the aboveground part. All accessions were divided into six groups by phenotypic trait clustering, which was also supported by principal component analysis (PCA). Molecular marker analysis showed that SSR and SRAP markers had good amplification effects and could effectively and accurately evaluate the genetic variation of yam. The unweighted pair-group method with arithmetic means analysis based on SSR-SRAP marker data showed that the 112 accessions were also divided into six groups, similar to the phenotypic trait results. The results of PCA and population structure analysis based on SSR-SRAP data also produced similar results. In addition, the analysis of the origin and genetic relationship of yam indicated that the species D. opposita may have originated from China. These results demonstrate the genetic diversity and distinctness among the widely cultivated species of Chinese yam and provide a theoretical reference for the classification, breeding, germplasm innovation, utilization, and variety protection of Chinese yam resources.

Iodine monitoring models contribute to avoid adverse birth outcomes related more than adequate iodine intake.

BACKGROUND: Iodine plays an important role in pregnancy. How to maintain adequate iodine intake amongst pregnant women in each trimester of pregnancy to prevent adverse birth outcomes in central China is a challenge for clinical practice. METHODS: 870 pregnant women and their infants were enrolled in the study. Urinary iodine concentration (UIC) was measured using an inductively coupled plasma mass spectrometry (ICP-MS). Maternal and newborn information were obtained during follow-up. Multinomial logistic regression models were established. RESULTS: Median UIC of pregnant women was 172 ± 135 µg/L which is currently considered to be sufficient. Multivitamin supplements containing iodine, iodized salt intake and frequent milk intake were significantly associated with higher UIC. Multivariate logistic regression analysis showed that multivitamin supplements containing iodine and milk consumption were risk factors for more than adequate iodine (UIC ≥ 250 µg/L). Iodine-rich diet was significantly related to heavier birthweight, larger head circumference and longer femur length of the newborns while more than adequate iodine intake (UIC ≥ 250 µg/L) was a risk factor for macrosomia. Logistic regression models based on potential risk factors involving iodine containing supplements and iodine-rich diet were established to predict and screen pregnant women with high risk of more than adequate iodine intake among local pregnant women in different trimesters and guide them to supplement iodine reasonably to prevent the risk. CONCLUSIONS: Multivitamin supplements containing iodine and milk consumption were risk factors for maternal UIC ≥ 250 µg/L which was a risk factor for macrosomia. Iodine monitoring models were established to provide guidance for pregnant women to reduce the risk of more than adequate iodine intake, thereby contributing to reduce the risk of having a macrosomia.