Wei F

References (11)

Title : Lipase-Catalyzed Preparation and Optimization of Structured Phosphatidylcholine Containing Nervonic Acid - Ang_2024_Molecules_29_
Author(s) : Ang X , Chen H , Xiang J , Wei F , Quek SY
Ref : Molecules , 29 : , 2024
Abstract : This study investigated the incorporation of nervonic acid into the chemical structure of phosphatidylcholine via a lipase-catalyzed acidolysis reaction to obtain a functional phospholipid. Lipase immobilization was conducted, and Amberlite XAD7-HP was selected as a carrier to immobilize phospholipase A(1) (PLA(1)) for subsequent experiments. The main acidolysis reaction parameters, including enzyme load, substrate ratio, temperature, and water content, were studied against the reaction time. The optimum reaction conditions obtained were enzyme load, 20%; reaction temperature, 55 degreesC; water content, 1%; and reaction time, 9 h. The maximum incorporation of nervonic acid into phosphatidylcholine was 48 mol%, with PC recovery at 61.6 mol%. The positional distribution of structured phosphatidylcholine shows that nervonic acid was found in the sn-1 position due to enzyme specificity and in the sn-2 position, possibly due to acyl migration.
ESTHER : Ang_2024_Molecules_29_
PubMedSearch : Ang_2024_Molecules_29_
PubMedID: 38611818

Title : Phytochemical analysis, antioxidant, antimicrobial, and anti-enzymatic properties of Alpinia coriandriodora (sweet ginger) rhizome - Wu_2023_Front.Plant.Sci_14_1284931
Author(s) : Wu X , Wei F , Ding F , Yang N , Niu J , Ran Y , Tian M
Ref : Front Plant Sci , 14 :1284931 , 2023
Abstract : Alpinia coriandriodora, also known as sweet ginger, is a medicinal and edible plant. A. coriandriodora rhizome is popularly utilized in traditional Chinese medicine and as flavouring spices, but there are few reports on its constituents and bioactivities. This study analyzed the phytochemical components of A. coriandriodora rhizome by GC-MS and UHPLC-Q-Orbitrap-MS and evaluated its antioxidant, antimicrobial, and anti-enzymatic properties. According to the GC-FID/MS data, its rhizome essential oil (EO) consisted mainly of (E)-2-decenal (53.8%), (E)-2-decenyl acetate (24.4%), (Z)-3-dodecenyl acetate (3.5%), and (E)-2-octenal (3.5%). Its water extract (WE) and 70% ethanol extract (EE) showed high total phenolic content (TPC, 52.99-60.49 mg GAEs/g extract) and total flavonoid content (TFC, 260.69-286.42 mg REs/g extract). In addition, the phytochemicals of WE and EE were further characterized using UHPLC-Q-Orbitrap-MS, and a total of sixty-three compounds were identified, including fourteen phenolic components and twenty-three flavonoid compounds. In the antioxidant assay, WE and EE revealed a potent scavenging effect on DPPH (IC(50): 6.59 +/- 0.88 mg/mL and 17.70 +/- 1.15 mg/mL, respectively), surpassing the BHT (IC(50): 21.83 +/- 0.89 mg/mL). For the antimicrobial activities, EO displayed excellent antibacterial capabilities against Proteus vulgaris, Enterococcus faecalis, Bacillus subtilis, Escherichia coli, and Staphylococcus aureus with DIZ (12.60-22.17 mm), MIC (0.78-1.56 mg/mL), and MBC (3.13 mg/mL) and significantly inhibited Aspergillus flavus growth (MIC = 0.313 mg/mL, MFC = 0.625 mg/mL, respectively). In addition to weak tyrosinase and cholinesterase inhibition, EE and WE had a prominent inhibitory effect against alpha-glucosidase (IC(50): 0.013 +/- 0.001 mg/mL and 0.017 +/- 0.002 mg/mL), which was significantly higher than acarbose (IC(50): 0.22 +/- 0.01 mg/mL). Hence, the rhizome of A. coriandriodora has excellent potential for utilization in the pharmaceutical and food fields as a source of bioactive substances.
ESTHER : Wu_2023_Front.Plant.Sci_14_1284931
PubMedSearch : Wu_2023_Front.Plant.Sci_14_1284931
PubMedID: 37936928

Title : A dual-emission ratiometric fluorescence strategy with enzyme-based inhibition for organophosphorus pesticides determination - Xu_2023_Mikrochim.Acta_190_337
Author(s) : Xu F , Li X , Chen C , Liang Z , Xu G , Wei F , Yang J , Hu Q , Cen Y
Ref : Mikrochim Acta , 190 :337 , 2023
Abstract : A fast, eco-friendly and accurate ratiometric fluorescent strategy is presented for the determination of organophosphorus pesticides (OPs) using intrinsic dual-emission silica nanoparticles modified with Rhodamine 6G (SiNPs-Rho6G). SiNPs-Rho6G had intrinsic dual-emission at 410 and 550 nm. The substrate acetylcholine was catalyzed by acetylcholinesterase (AChE) to produce thiocholine (TCh). TCh triggered the specific reaction of Ellman's reagent 5, 5-dithiobis (2-nitrobenzoic acid) to obtain 5-thio-2-nitrobenzoic acid, which caused the decrease in fluorescence intensity of SiNPs-Rho6G at 410 nm by the inner filter effect, while the fluorescence intensity of SiNPs-Rho6G at 550 nm was not significantly changed. OPs caused the recovery of the fluorescence at 410 nm by inhibiting the activity of AChE. Thus, the quantitative detection of OPs could be achieved through utilizing the catalytic characteristic of AChE. The linear curve from 0.010 to 0.250 microg mL(-1) with a detection limit of 7 ng mL(-1) was obtained for the determination of chlorpyrifos (Cpf). The ratiometric probe was used to detect the spiked Cpf in environmental and food samples with good recoveries. Therefore, combined with the dual emission characteristics of SiNPs-Rho6G and the specificity of the enzyme, the ratio fluorescence sensing platform has potential application prospects in OPs determinations.
ESTHER : Xu_2023_Mikrochim.Acta_190_337
PubMedSearch : Xu_2023_Mikrochim.Acta_190_337
PubMedID: 37516685

Title : Narciclasine inhibits phospholipase A2 and regulates phospholipid metabolism to ameliorate psoriasis-like dermatitis - Kong_2022_Front.Immunol_13_1094375
Author(s) : Kong Y , Jiang J , Huang Y , Liu X , Jin Z , Li L , Wei F , Yin J , Zhang Y , Tong Q , Chen H
Ref : Front Immunol , 13 :1094375 , 2022
Abstract : INTRODUCTION: Psoriasis is a common inflammatory skin disease recognized by the World Health Organization as "an incurable chronic, noninfectious, painful, disfiguring and disabling disease." The fact that metabolic syndrome (MetS) is the most common and important comorbidities of psoriasis suggests an important role of lipid metabolism in the pathogenesis of psoriasis. Narciclasine (Ncs) is an alkaloid isolated from the Amaryllidaceae plants. Its biological activities include antitumor, antibacterial, antiinflammatory, anti-angiogenic and promoting energy expenditure to improve dietinduced obesity. Here, we report that Ncs may be a potential candidate for psoriasis, acting at both the organismal and cellular levels. METHODS: The therapeutic effect of Ncs was assessed in IMQ-induced psoriasis-like mouse model. Then, through in vitro experiments, we explored the inhibitory effect of Ncs on HaCaT cell proliferation and Th17 cell polarization; Transcriptomics and lipidomics were used to analyze the major targets of Ncs; Single-cell sequencing data was used to identify the target cells of Ncs action. RESULTS: Ncs can inhibit keratinocyte proliferation and reduce the recruitment of immune cells in the skin by inhibiting psoriasis-associated inflammatory mediators. In addition, it showed a direct repression effect on Th17 cell polarization. Transcriptomic and lipidomic data further revealed that Ncs extensively regulated lipid metabolismrelated genes, especially the Phospholipase A2 (PLA2) family, and increased antiinflammatory lipid molecules. Combined with single-cell data analysis, we confirmed that keratinocytes are the main cells in which Ncs functions. DISCUSSION: Taken together, our findings indicate that Ncs alleviates psoriasiform skin inflammation in mice, which is associated with inhibition of PLA2 in keratinocytes and improved phospholipid metabolism. Ncs has the potential for further development as a novel anti-psoriasis drug.
ESTHER : Kong_2022_Front.Immunol_13_1094375
PubMedSearch : Kong_2022_Front.Immunol_13_1094375
PubMedID: 36700214

Title : Phytochemical Analysis, Antioxidant, Antibacterial, Cytotoxic, and Enzyme Inhibitory Activities of Hedychium flavum Rhizome - Tian_2020_Front.Pharmacol_11_572659
Author(s) : Tian M , Wu X , Lu T , Zhao X , Wei F , Deng G , Zhou Y
Ref : Front Pharmacol , 11 :572659 , 2020
Abstract : Hedychium flavum Roxb., a medicinal, edible, and ornamental plant, is widely cultivated throughout China, India, and Southeast Asia. The rhizome from this plant has been used for food flavoring and in traditional Chinese medicine to treat diverse diseases, but the detailed constituents and bioactivities are still limited known. Therefore, phytochemical analysis by GC-MS and UHPLC-Q-Orbitrap-MS, and antioxidant, antibacterial, cytotoxic, and enzyme inhibitory activities tests have been conducted in the current study. Based on the GC-MS results, the essential oil (EO) of rhizome was mainly composed of coronarin E (20.3%), beta-pinene (16.8%), E-nerolidol (11.8%), and linalool (8.5%). Among them, coronarin E was reported in H. flavum EO firstly. Furthermore, the spectrophotometric indicated rhizome had high total phenolic content (TPC, 50.08-57.42 mg GAEs/g extract) and total flavonoid content (TFC, 12.45-21.83 mg REs/g extract), no matter in water extract (WE) or in 70% ethanol extract (EE). UHPLC-Q-Orbitrap-MS was applied to further characterize composition, and 86 compounds were putatively identified from WE and EE, including 13 phenolic components. For the bioactivities, both WE and EE showed remarkable antioxidant activity by DPPH and ABTS tests, being superior to the positive control (butylated hydroxytoluene, BTH). EO revealed significant antibacterial activity against Staphylococcus aureus, Bacillus subtilis, Pseudomonas aeruginosa, and Proteus vulgaris with DIZ (10.34-24.43 mm), MIC (78.13-312.50 mug/mL), and MBC (156.25-625.00 mug/mL). Moreover, EO exhibited a considerable selectivity to human tumor cell K562 (IC(50) = 27.16 mug/mL), and its toxicity was more than 3.5-fold different from that of non-cancerous MRC-5 cell (IC(50) = 95.96 mug/mL) and L929 cell (IC(50) = 129.91 mug/mL). A series of apoptosis analysis demonstrated that EO induced apoptosis against K562 cells in a dose-dependent manner. In enzyme inhibitory effect assays, WE and EE showed strong alpha-glucosidase inhibition activity, being superior to the positive control (acarbose). Besides, the EO, WE, and EE didn't show a promising inhibition on tyrosinase (19.30-32.51 mg KAEs/g sample) and exhibited a weak inhibitory effect on cholinesterase. Based on the current results, H. flavum could be considered as a source of bioactive compounds and has high exploitation potential in the cosmetics, food, and pharmaceutical industries.
ESTHER : Tian_2020_Front.Pharmacol_11_572659
PubMedSearch : Tian_2020_Front.Pharmacol_11_572659
PubMedID: 33041813

Title : Chemical Composition, Antibacterial, Anti-Inflammatory, and Enzyme Inhibitory Activities of Essential Oil from Rhynchanthus beesianus Rhizome - Zhao_2020_Molecules_26_
Author(s) : Zhao X , Chen Q , Lu T , Wei F , Yang Y , Xie D , Wang H , Tian M
Ref : Molecules , 26 : , 2020
Abstract : Rhynchanthus beesianus W. W. Smith, an edible, medicinal, and ornamental plant, is mainly cultivated in China and Myanmar. The essential oil (EO) from R. beesianus rhizome has been used as an aromatic stomachic in China. The chemical composition and biological activities of EO from R. beesianus rhizome were reported for the first time. Based on gas chromatography with flame ionization or mass selective detection (GC-FID/MS) results, the major constituents of EO were 1,8-cineole (47.6%), borneol (15.0%), methyleugenol (11.2%), and bornyl formate (7.6%). For bioactivities, EO showed a significant antibacterial activity against Staphylococcus aureus, Enterococcus faecalis, Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, and Proteus vulgaris with the diameter of the inhibition zone (DIZ) (8.66-10.56 mm), minimal inhibitory concentration (MIC) (3.13-6.25 mg/mL), and minimal bactericidal concentration (MBC) (6.25-12.5 mg/mL). Moreover, EO (128 microg/mL) significantly inhibited the production of proinflammatory mediators nitric oxide (NO) (92.73 +/- 1.50%) and cytokines tumor necrosis factor-alpha (TNF-alpha) (20.29 +/- 0.17%) and interleukin-6 (IL-6) (61.08 +/- 0.13%) in lipopolysaccharide (LPS)-induced RAW264.7 macrophages without any cytotoxic effect. Moreover, EO exhibited significant acetylcholinesterase (AChE) inhibitory activity (the concentration of the sample that affords a 50% inhibition in the assay (IC(50)) = 1.03 +/- 0.18 mg/mL) and moderate alpha-glucosidase inhibition effect (IC(50) = 11.60 +/- 0.25 mg/mL). Thus, the EO could be regarded as a bioactive natural product and has a high exploitation potential in the cosmetics and pharmaceutical industries.
ESTHER : Zhao_2020_Molecules_26_
PubMedSearch : Zhao_2020_Molecules_26_
PubMedID: 33396533

Title : A ratiometric fluorescence probe based on carbon dots for discriminative and highly sensitive detection of acetylcholinesterase and butyrylcholinesterase in human whole blood - Xu_2019_Biosens.Bioelectron_131_232
Author(s) : Xu X , Cen Y , Xu G , Wei F , Shi M , Hu Q
Ref : Biosensors & Bioelectronics , 131 :232 , 2019
Abstract : A ratiometric fluorescence probe based on carbon dots (CDs) was developed for discriminative and highly sensitive detection of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) activity in human whole blood. When o-phenylenediamine (OPD) was oxidized by Cu(2+), the product 2,3-diaminophenazine (oxOPD) could effectively quench the fluorescence of CDs at 460nm due to the inner filter effect and gave rise to a new emission peak at 570nm. The AChE or BChE catalyzed hydrolysis reaction of acetylthiocholine or butyrylthiocholine to generate thiocholine, whose sulfhydryl group strongly captured Cu(2+) to inhibit the oxidization of OPD, thus effectively preserving the natural fluorescence emission of CDs. The resulting fluorescence intensity ratio served as the signal output of the probe for cholinesterases (ChEs) activity sensing. The activities of AChE and BChE were determined to range from 0.2 to 14.0 U L(-1) and from 0.1 to 5.0 U L(-1), with detection limits of 0.1 U L(-1) and 0.04 U L(-1), respectively. Additionally, the IC50 of tacrine and ethopropazine for the inhibition of AChE and BChE were estimated to be 29.8nM and 132.6nM, respectively. Moreover, the probe was successfully applied to the discriminative determination of AChE and BChE in human whole blood without any pretreatment. These results suggested that the proposed strategy provided a discriminative, sensitive and robust analytical platform for ChEs clinical diagnostics and drug screening.
ESTHER : Xu_2019_Biosens.Bioelectron_131_232
PubMedSearch : Xu_2019_Biosens.Bioelectron_131_232
PubMedID: 30849722

Title : Ultrasonic pretreatment in lipase-catalyzed synthesis of structured lipids with high 1,3-dioleoyl-2-palmitoylglycerol content - Liu_2015_Ultrason.Sonochem_23_100
Author(s) : Liu SL , Dong XY , Wei F , Wang X , Lv X , Zhong J , Wu L , Quek SY , Chen H
Ref : Ultrason Sonochem , 23 :100 , 2015
Abstract : Production of structured lipid 1,3-dioleoyl-2-palmitoylglycerol (OPO), from tripalmitin (PPP) and oleic acid (OA) using lipases and ultrasonic pretreatment was conducted. Factors influencing both the ultrasonic conditions and enzymatic reaction were investigated. Optimum conditions could be attained with 6 min pretreatment time, 50% ultrasonic power, 3 s/9 s (work/pause) cycle of ultrasonic pulse, 1:8 PPP/OA molar ratio, 12% enzyme dosage and 50 degreeC temperature of. At the optimum conditions, the OPO yield of 51.8% could be achieved in 4h. Studies showed that the OPO content increased to 35.9% in 1h with ultrasonic pretreatment, in comparison to 4h without ultrasonic pretreatment. Reuse of Lipozyme RM IM for 10 cycles under ultrasonic irradiation did not cause essential damage to its lipase activity. Reaction kinetic model fitted well with the proposed Ping-Pong mechanism. The apparent kinetic constant (Vm'/K) of ultrasound pretreatment reaction was 2.52 times higher than the conventional mechanical stirring, indicating that ultrasound pretreatment enhanced the substrates affinity to the enzyme. This study confirmed that ultrasonic pretreatment was more efficient in OPO production than conventional mechanical agitation.
ESTHER : Liu_2015_Ultrason.Sonochem_23_100
PubMedSearch : Liu_2015_Ultrason.Sonochem_23_100
PubMedID: 25453210

Title : The sequence and de novo assembly of the giant panda genome - Li_2010_Nature_463_311
Author(s) : Li R , Fan W , Tian G , Zhu H , He L , Cai J , Huang Q , Cai Q , Li B , Bai Y , Zhang Z , Zhang Y , Wang W , Li J , Wei F , Li H , Jian M , Nielsen R , Li D , Gu W , Yang Z , Xuan Z , Ryder OA , Leung FC , Zhou Y , Cao J , Sun X , Fu Y , Fang X , Guo X , Wang B , Hou R , Shen F , Mu B , Ni P , Lin R , Qian W , Wang G , Yu C , Nie W , Wang J , Wu Z , Liang H , Min J , Wu Q , Cheng S , Ruan J , Wang M , Shi Z , Wen M , Liu B , Ren X , Zheng H , Dong D , Cook K , Shan G , Zhang H , Kosiol C , Xie X , Lu Z , Li Y , Steiner CC , Lam TT , Lin S , Zhang Q , Li G , Tian J , Gong T , Liu H , Zhang D , Fang L , Ye C , Zhang J , Hu W , Xu A , Ren Y , Zhang G , Bruford MW , Li Q , Ma L , Guo Y , An N , Hu Y , Zheng Y , Shi Y , Li Z , Liu Q , Chen Y , Zhao J , Qu N , Zhao S , Tian F , Wang X , Wang H , Xu L , Liu X , Vinar T , Wang Y , Lam TW , Yiu SM , Liu S , Huang Y , Yang G , Jiang Z , Qin N , Li L , Bolund L , Kristiansen K , Wong GK , Olson M , Zhang X , Li S , Yang H
Ref : Nature , 463 :311 , 2010
Abstract : Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.
ESTHER : Li_2010_Nature_463_311
PubMedSearch : Li_2010_Nature_463_311
PubMedID: 20010809
Gene_locus related to this paper: ailme-ABH15 , ailme-ACHE , ailme-BCHE , ailme-d2gtv3 , ailme-d2gty9 , ailme-d2gu87 , ailme-d2gu97 , ailme-d2gve7 , ailme-d2gwu1 , ailme-d2gx08 , ailme-d2gyt0 , ailme-d2gz36 , ailme-d2gz37 , ailme-d2gz38 , ailme-d2gz39 , ailme-d2gz40 , ailme-d2h5r9 , ailme-d2h7b7 , ailme-d2h9c9 , ailme-d2h794 , ailme-d2hau7 , ailme-d2hau8 , ailme-d2hcd9 , ailme-d2hdi6 , ailme-d2heu6 , ailme-d2hga4 , ailme-d2hqw5 , ailme-d2hs98 , ailme-d2hsx4 , ailme-d2hti6 , ailme-d2htv3 , ailme-d2htz6 , ailme-d2huc7 , ailme-d2hwj8 , ailme-d2hwy7 , ailme-d2hxm1 , ailme-d2hyc8 , ailme-d2hyv2 , ailme-d2hz11 , ailme-d2hza3 , ailme-d2hzr4 , ailme-d2i1l4 , ailme-d2i2g8 , ailme-g1l7m3 , ailme-g1lu36 , ailme-g1m769 , ailme-g1mc29 , ailme-g1mdj8 , ailme-g1mdr5 , ailme-g1mfp4 , ailme-g1mfx5 , ailme-g1lj41 , ailme-g1lm28 , ailme-g1l3u1 , ailme-g1l7l1 , ailme-g1m5i3 , ailme-g1l2f6 , ailme-g1lji5 , ailme-g1lqk3 , ailme-g1l8s9 , ailme-d2h717 , ailme-d2h718 , ailme-d2h719 , ailme-d2h720 , ailme-g1m5v0 , ailme-g1m5y7 , ailme-g1lkt7 , ailme-g1l2a1 , ailme-g1lsc8 , ailme-g1lrp4 , ailme-d2gv02 , ailme-g1mik5 , ailme-g1ljr1 , ailme-g1lxw7 , ailme-d2h8b5 , ailme-d2h2r2 , ailme-d2h9w7 , ailme-g1meh3 , ailme-g1m719

Title : The B73 maize genome: complexity, diversity, and dynamics - Schnable_2009_Science_326_1112
Author(s) : Schnable PS , Ware D , Fulton RS , Stein JC , Wei F , Pasternak S , Liang C , Zhang J , Fulton L , Graves TA , Minx P , Reily AD , Courtney L , Kruchowski SS , Tomlinson C , Strong C , Delehaunty K , Fronick C , Courtney B , Rock SM , Belter E , Du F , Kim K , Abbott RM , Cotton M , Levy A , Marchetto P , Ochoa K , Jackson SM , Gillam B , Chen W , Yan L , Higginbotham J , Cardenas M , Waligorski J , Applebaum E , Phelps L , Falcone J , Kanchi K , Thane T , Scimone A , Thane N , Henke J , Wang T , Ruppert J , Shah N , Rotter K , Hodges J , Ingenthron E , Cordes M , Kohlberg S , Sgro J , Delgado B , Mead K , Chinwalla A , Leonard S , Crouse K , Collura K , Kudrna D , Currie J , He R , Angelova A , Rajasekar S , Mueller T , Lomeli R , Scara G , Ko A , Delaney K , Wissotski M , Lopez G , Campos D , Braidotti M , Ashley E , Golser W , Kim H , Lee S , Lin J , Dujmic Z , Kim W , Talag J , Zuccolo A , Fan C , Sebastian A , Kramer M , Spiegel L , Nascimento L , Zutavern T , Miller B , Ambroise C , Muller S , Spooner W , Narechania A , Ren L , Wei S , Kumari S , Faga B , Levy MJ , McMahan L , Van Buren P , Vaughn MW , Ying K , Yeh CT , Emrich SJ , Jia Y , Kalyanaraman A , Hsia AP , Barbazuk WB , Baucom RS , Brutnell TP , Carpita NC , Chaparro C , Chia JM , Deragon JM , Estill JC , Fu Y , Jeddeloh JA , Han Y , Lee H , Li P , Lisch DR , Liu S , Liu Z , Nagel DH , McCann MC , SanMiguel P , Myers AM , Nettleton D , Nguyen J , Penning BW , Ponnala L , Schneider KL , Schwartz DC , Sharma A , Soderlund C , Springer NM , Sun Q , Wang H , Waterman M , Westerman R , Wolfgruber TK , Yang L , Yu Y , Zhang L , Zhou S , Zhu Q , Bennetzen JL , Dawe RK , Jiang J , Jiang N , Presting GG , Wessler SR , Aluru S , Martienssen RA , Clifton SW , McCombie WR , Wing RA , Wilson RK
Ref : Science , 326 :1112 , 2009
Abstract : We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.
ESTHER : Schnable_2009_Science_326_1112
PubMedSearch : Schnable_2009_Science_326_1112
PubMedID: 19965430
Gene_locus related to this paper: maize-b4ffc7 , maize-b6u7e1 , maize-c0pcy5 , maize-c0pgf7 , maize-c0pgw1 , maize-c0pfl3 , maize-b4fpr7 , maize-k7vy73 , maize-a0a096swr3 , maize-k7v3i9 , maize-b6u9v9 , maize-a0a3l6e780 , maize-b4fv80 , maize-a0a1d6nse2 , maize-c4j9a1 , maize-k7uba1

Title : Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species - Buell_2005_Genome.Res_15_1284
Author(s) : Buell CR , Yuan Q , Ouyang S , Liu J , Zhu W , Wang A , Maiti R , Haas B , Wortman J , Pertea M , Jones KM , Kim M , Overton L , Tsitrin T , Fadrosh D , Bera J , Weaver B , Jin S , Johri S , Reardon M , Webb K , Hill J , Moffat K , Tallon L , Van Aken S , Lewis M , Utterback T , Feldblyum T , Zismann V , Iobst S , Hsiao J , de Vazeille AR , Salzberg SL , White O , Fraser C , Yu Y , Kim H , Rambo T , Currie J , Collura K , Kernodle-Thompson S , Wei F , Kudrna K , Ammiraju JS , Luo M , Goicoechea JL , Wing RA , Henry D , Oates R , Palmer M , Pries G , Saski C , Simmons J , Soderlund C , Nelson W , de la Bastide M , Spiegel L , Nascimento L , Huang E , Preston R , Zutavern T , Palmer LE , O'Shaughnessy A , Dike S , McCombie WR , Minx P , Cordum H , Wilson R , Jin W , Lee HR , Jiang J , Jackson S
Ref : Genome Res , 15 :1284 , 2005
Abstract : Rice (Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. To begin to completely understand this chromosome, we sequenced, finished, and annotated 36.1 Mb ( approximately 97%) from O. sativa subsp. japonica cv Nipponbare. Annotation features of the chromosome include 5915 genes, of which 913 are related to transposable elements. A putative function could be assigned to 3064 genes, with another 757 genes annotated as expressed, leaving 2094 that encode hypothetical proteins. Similarity searches against the proteome of Arabidopsis thaliana revealed putative homologs for 67% of the chromosome 3 proteins. Further searches of a nonredundant amino acid database, the Pfam domain database, plant Expressed Sequence Tags, and genomic assemblies from sorghum and maize revealed only 853 nontransposable element related proteins from chromosome 3 that lacked similarity to other known sequences. Interestingly, 426 of these have a paralog within the rice genome. A comparative physical map of the wild progenitor species, Oryza nivara, with japonica chromosome 3 revealed a high degree of sequence identity and synteny between these two species, which diverged approximately 10,000 years ago. Although no major rearrangements were detected, the deduced size of the O. nivara chromosome 3 was 21% smaller than that of japonica. Synteny between rice and other cereals using an integrated maize physical map and wheat genetic map was strikingly high, further supporting the use of rice and, in particular, chromosome 3, as a model for comparative studies among the cereals.
ESTHER : Buell_2005_Genome.Res_15_1284
PubMedSearch : Buell_2005_Genome.Res_15_1284
PubMedID: 16109971
Gene_locus related to this paper: orysa-Q852M6 , orysa-Q8S5X5 , orysa-Q84QZ6 , orysa-Q84QY7 , orysa-Q851E3 , orysa-q6ave2 , orysj-cgep , orysj-q0dud7 , orysj-q10j20 , orysj-q10ss2