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    26 June 2021, Volume 37 Issue 6
    Research Advances in Plant Genome Assembly Open Access
    TANG Die, ZHOU Qian
    2021, 37(6):  1-12.  doi:10.13560/j.cnki.biotech.bull.1985.2021-0450
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    The construction of reference genome containing genome-wide sequence is a prerequisite to genomic exploiting and utilizing of a species. Majority of angiosperms have undergone genome-wide duplication or polyploidization and subsequent chromosome rearrangement and loss. Many plants have also experienced large-scale expansion of repetitive sequences,resulting in a dramatic expansion of the genome size. These evolution events shape plant genomes with specific characteristics and extensive biodiversity,to a certain extent,has also led to many problems in plant genome assembly. Here,we classified plant genomes to simple,highly heterozygous,highly repetitive,polyploidy and pan-genome,summarized their corresponding assembly strategies and applications. Moreover,we prospecte the application trend of new sequencing technologies in resolving plant genomes.

    Cloning and Expression Analysis of GjPAL Genes in Gerbera jamesonni Open Access
    HAO Xiang-yang, LIU Fan, WU Huan, WANG Bin, SUN Xue-li, XIANG Lei-lei, WANG Tian-chi, LAI Zhong-xiong, CHENG Chun-zhen
    2021, 37(6):  13-23.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1343
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    To clarify the physicochemical properties of the proteins encoded by the gerbera PAL genes,and to explore their expression pattern, four plenylalanine ammonia lyase genes(named as GjPAL1-GjPAL4)were successfully cloned from Gerbera jamesonni cv ‘Linglong’ using RACE and RT-PCR techniques. Then,a series of bioinformatics software were used to study their sequence structures and characteristics of their encoded proteins. qPCR was used to show their expression patterns in different tissues and organs,and under different stress treatments. The results from sequence analysis showed that the coding sequence(CDS)length of 4 GjPALs ranged from 2 115 to 2 136 bp,which encoded protein containing 704-711 amino acids,respectively. All the encoded proteins of the 4 GjPALs were found to be stable acidic hydrophilic proteins without signal peptide. qRT-PCR results demonstrated that GjPAL1 expressed the highest in leaf,while GjPAL2-GjPAL4 expressed the highest in root. Under low temperature treatment,the expressions of the 4 GjPALs were all significantly inhibited. GjPAL1 and GjPAL2 were significantly inhibited by SA,NaCl and PEG treatments,GjPAL3 and GjPAL4 showed ‘rise-fall’ expression patterns under SA treatment,while GjPAL3 expression was found to be significantly induced by NaCl and PEG treatments. Under Phytophthora cryptogea inoculation treatment,GjPAL1 and GjPAL4 were significantly induced,GjPAL2 was significantly suppressed,and GjPAL3 showed a ‘fall-rise’ expression pattern. Results indicated that GjPALs widely participated in the gerbera stress responses,but their response patterns to different stresses varied greatly.

    Effects of Planting Density,Amount of Nitrogen Application and Left Leaf Number on the Highlighting of Flavor Style in Qushou 1 Open Access
    ZHANG Qian, XUE Yu, HE Ling-xiao, WU Jiang, CHENG Yu-yuan, YANG Tie-zhao, DING Yong-le, XU Shi-xiao, XUE Gang
    2021, 37(6):  24-35.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1245
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    The Sibyl like compounds,their degradation products and petroleum ether extracts are important aroma compounds in tobacco. In this study,the effects of planting density,amount of nitrogen application and number of left leaves on the Sibyl like compounds and petroleum ether extracts of tobacco leaves were investigated,for providing effective measures to further highlight the strong flavor style of tobacco leaves. Taking flue-cured tobacco variety Qushou 1 as test material,the above three factors were set at three different levels according to L9(3 4)orthogonal design. The morphology and density of glandular hair in different treatments were observed,and the secretion of glandular hair in different treatments was measured. The expression levels of gene CYC-1,CYP71D16,etc. related to the metabolism of cembratriene-diols were compared by using fluorescence quantitative PCR,the contents of petroleum ether extract and solanone in flue-cured tobacco leaves with different treatments were compared,and the sensory quality was evaluated. Planting density was the key factor affecting the total density of glandular hairs,the content of alkanes on leaf surface and petroleum ether extract of flue-cured tobacco. The number of left leaves had the greatest influence on the content of solanone. The amount of nitrogen application was the key factor affecting the total amount of cembratriene-diols,total amount of leaf exudates,relative expressions of CYC-1 and CYP71D16,and sensory quality evaluation. Via appropriate cultivation measures the up-regulation of genes related to the metabolism of cembratriene-diols can be promoted,the secretion of flue-cured tobacco leaves improved,and the contents of petroleum ether extract and solanone increased,thus the sensory quality improved,further and the flavor style of tobacco leaves highlighted.

    Diversity of Arbuscular Mycorrhizal Fungi Inhabiting the Roots of Lycium barbarum in Different Varieties and Cultivation Regions Open Access
    LV Yan, LIU Jian-li, LI Jing-yu, HOU Lin-lin, SUN Min, GOU Qi
    2021, 37(6):  36-48.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1331
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    Arbuscular mycorrhizal fungi(AMF)plays important role in nutrient absorption and ecological function of plants. Lycium barbarum in Ningxia is an indigenous tree of significant ecological and economic importance in the northwest region of China,and AMF of its root occupies unique niche and thus functions specially. Based on the amplicon high throughput sequencing,we investigated the diversity of AMF in the root systems of Ningxia L. barbarum from different varieties and cultivation regions,aiming to lay a foundation for developing AMF agent of Ningxia L. barbarum. Root and fresh fruits samples were collected from 4 varieties “Ningqi 7”,“Ningqi 9”,“Mengqi 1”,“Mengqi 2” and main variety “Ningqi 7” in 4 cultivation regions(Zhongning county and Haiyuan county of Ningxia Hui Autonomous Region,Jingyuan county of Gansu province,Wulate county of Inner Mongolia Autonomous Region). PCR amplification was conducted using AMF specific primers,then Illumina Miseq sequencing was performed,and the diversity of AMF was compared and analyzed. Meanwhile the contents of polysaccharides,total flavonoids,betaine and other active components in the fresh fruits were determined,and correlation analysis of the AMF related to the active component content was conducted. Total of 49 AMF OTUs were detected,belonging to 3 orders,3 families and 3 genera,with Glomus as the most dominant genus. Glomus sp.VTX00113 is the common species in 4 varieties and 4 regions,which also was the dominant species of “Ningqi 7”,“Mengqi 1”,“Mengqi 2” and Haiyuan and Gansu region. However,the dominant species in “Ningqi 9” was Glomus sp.VTX00156. The dominant species from the Inner Mongolia and Zhongning were the not-identified-yet unclassified_OTU3 and unclassified_OTU39,respectively. There were significant differences in α-diversity among different varieties,that of “Ningqi 7” was the highest,and that of “Mengqi 2” was the lowest. On the contrary,there was no significant difference among cultivation regions. The proportions of Glomus sp.VTX00113 across the 4 regions was of significant difference(P<0.001);however,no species was in significant differences among 4 varieties. There was no significant difference in terms of the β-diversity for AMF community across the 4 varieties(P=0.123),but significant difference among the 4 regions(P=0.001). There was no correlation between fruit polysaccharide content and AMF. Glomus sp. VTX00113 was significantly positively correlated with betaine,and unclassified_OTU14 was only negatively correlated with betaine content in different samples of varieties. Glomus.sp.VTX00393 was significantly positively correlated with total flavonoids in different varieties. Glomus.sp.VTX00247 was also significantly positively correlated with total flavonoids only in different regions. L. barbarum varieties affect α-diversity and dominant species of root AMF communities,but not β-diversity. Cultivation region affects β-diversity and dominant species,but not α-diversity. AMF is correlated with betaine and total flavonoids content,but not with the polysaccharide content.

    Influence of Nitrogen Fertilizer Reduction on the Structure of Bacterial Community in Tea Garden Soil Open Access
    XIANG Fen, LI Wei, LIU Hong-yan, YIN Xia, ZENG Ze-xuan, ZHOU Ling-yun
    2021, 37(6):  49-57.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1287
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    This work is to study the effect of different nitrogen reduction modes on the bacterial community structure in the underground soil of tea plant. Four nitrogen levels were applied in the soil:16 kg/667 m2pure nitrogen(reducing nitrogen by 55.6%,treatment A),26 kg/667 m2 pure nitrogen(reducing nitrogen by 27.8%,treatment B),36 kg/667 m2 pure nitrogen(conventional fertilization,treatment C),and no nitrogen application(CK). The 36 samples of rhizosphere and non- rhizosphere soil of 0-20 cm and non- rhizosphere soil of 20-40 cm were sequenced by 16S rRNA,and the community structures of soil bacteria under different nitrogen reduction treatments were analyzed at IonS5TMXL high-throughput sequencing platform. The results showed that the OTUs of the 0-20 cm rhizosphere and non rhizosphere soil and 20-40 cm non rhizosphere soil were 505,854 and 835 under the A,B and C treatment,respectively. The specific OTUs gradually decreased with the increase of nitrogen application. The bacterial abundance of the soil was higher in the rhizosphere soil and non- rhizosphere soil of 0-20 cm under nitrogen reduction treatment B,with the highest bacterial diversity. The results of soil carbon flux also confirmed that there were more microorganism in soil under nitrogen reduction treatment B. The dominant bacteria in the underground part of the fertilized tea garden at the phylum level were basically nitrogen metabolism related ones,among which there were three dominant groups,namely Proteobacteria,Actinobacteria and Chloroflexi. At the genus level,the dominant bacteria in the rhizosphere soil and non rhizosphere soil were totally different. The diversity of bacterial community in the tea garden soil was more and the abundance was higher under proper nitrogen reduction treatment,and it was mainly concentrated in the rhizosphere and surrounding soil of nutrient absorption and utilization,which is conducive to the efficient utilization of nutrients in tea garden.

    Inhibitory Effect of Resveratrol on Walnut Bacterial Black Spot Pathogen Open Access
    LI Feng, CHEN Wen-wen, DENG Jiang-li, MAO Qing-li, QUAN Wen-li, MAO Ya-hui
    2021, 37(6):  58-65.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1267
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    It aims to provide theoretical basis for the development of natural bactericide for walnut bacterial black spot,and to lay a foundation for the application of resveratrol in the prevention and control of agricultural and forestry crop diseases. The minimum inhibitory concentration(MIC)and minimum bactericidal concentration(MBC)of resveratrol against Xanthomonas arboricola pv. juglandis(Xaj)were determined. The following experiments were carried out under the sub-inhibitory concentration of resveratrol:1)The formation of Xaj biofilm was detected by crystal violet staining. 2)The production of exopolysaccharide(EPS)was determined. 3)The secretion of extracellular enzyme was analyzed on the corresponding solid medium by biochemical method. 4)The motility of Xaj was detected on swarming medium. The results revealed that the MIC of resveratrol against Xaj was 20 μg/mL,and MBC was 45 μg/mL. The formation of Xaj biofilm was effectively inhibited by resveratrol at a sub-inhibitory concentration of 15 μg/mL. Under this concentration,the production of EPS was also significantly inhibited. Resveratrol effectively inhibited the secretion of Xaj protease,promoted the secretion of amylase,but had no effect on the secretion of cellulase. There was no effect on motility(swarming). Resveratrol has an inhibitory effect on walnut bacterial black spot pathogen,affecting the virulence factors of this bacterium,and is expected to develop a suitable plant-derived fungicide for the prevention and treatment of walnut black spot disease.

    Screening and Identification of an Antagonist Against the Pathogen of Kiwifruit Canker and Its Antifungal Activity to the Phytopathogenic Fungus Open Access
    ZHU Hai-yun, MA Yu, KE Yang, LI Bo
    2021, 37(6):  66-72.  doi:10.13560/j.cnki.biotech.bull.1985.2020-0473
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    The objective is to screen and identify the endophytic bacteria from wild Ginkgo biloba against the pathogen of kiwifruit canker,and to determine the bacteriostatic spectrum of common plant fungal diseases. Three-step method was used to isolate the endophytic bacteria from G. blioba. And then the Pseudomonas syringae pv.Actinidiae(Psa)was used as indicator bacterium for screening the antagonistic bacteria. Combination of morphological,physiological and biochemical characteristics and 16S rRNA sequence analysis was used to identify the antagonistic bacteria. Finally,the pot experiment was carried out to study its control efficacy against kiwifruit canker,and the confrontation method was used to evaluate the antifungal activity of the strain. Total 7 endophytic bacterial strains with antagonistic activities to Psa were obtained. The strain MA23 demonstrated the greatest antagonistic activity toward Psa and was identified as Bacillus cereus. The control efficacy of MA23 fermentation broth supernatant against kiwifruit canker was 93.6%. Meanwhile,MA23 had great capability of antagonism to some plant pathogenic fungi. In conclusion,endophytic bacterium B. cereus MA23 isolated from wild G. biloba not only has good antagonistic activity against the pathogen of kiwifruit canker,but also has significant inhibitory effect on a variety of plant pathogenic fungi.

    Transcriptome Different Analysis of Tremella aurantialba at Mycelium and Fruiting Body Stages Open Access
    CHEN Zheng-qi, YU Jin-feng, FENG Yun-li, MA Ming, YUE Wan-song, GUO Xiang
    2021, 37(6):  73-84.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1038
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    To better understand the gene expression changes of mycelium and fruiting body stages in Tremella aurantialba,high-throughout sequencing were adopted to investigate differentially expressed genes by using RNA sequencing approach. Analysis revealed that 10 992 genes presented differences in gene expression,9 988 genes were up-regulated and 1 004 genes were down-regulated during the fruiting body stage. The Gene Ontology classification showed that the differentially expressed genes were mostly enriched in catalytic activity,binding,cellular process,metabolic process,cell and cell parts. KEGG pathway analysis revealed that the differential expressed genes were involved in three metabolic pathways of amino acid metabolism,carbohydrate metabolism and lipid metabolism. Most genes related to the three metabolic pathways were up-regulated,suggesting that a series of metabolic reactions and other co-regulation were needed during the development of T. aurantialba fruiting body,and these genes may play an important role in the development of T. aurantialba fruiting body. In this study,a lot of gene data were obtained by analyzing transcriptional expressions in T. aurantialba at mycelium and fruiting body stages,and may provide important basis in further revealing the developmental mechanisms and functional genes of T. aurantialba.

    Screening and Genome Sequencing of Cellulytic Bacterium Raoultella ornithinolytica LL1 Open Access
    TANG Hao, SUN Can, LI Yuan-qiu, LUO Chao-bing
    2021, 37(6):  85-96.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1174
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    As a resource-rich natural polymer,cellulose can be degraded into soluble sugar by microorganism. Therefore,screening of efficient cellulose-degrading microorganism has attracted much attention. In the present study,CMC selective medium was used to screen a cellulose-degrading bacterium Raoultella ornithinolytica LL1.The genome sequence of R. ornithinolytica LL1 was conducted by Pacbio Sequl V3 and Illumina Novaseq platform. Furthermore,the cellulase activities of the strain were determined by DNS method. The results showed that the genome size of R. ornithinolytica LL1 was 5 584 354 bp and contained 5 512 genes,of which 5 511,4 419,4 584,4 745,3 610,3 336 and 128 genes were annotated in NR,Swiss-Prot,Pfam,COG,GO,KEGG and CAZyme databases. The genes related to lignocellulose degrading in the genome were also annotated. R. ornithinolytica LL1 presented high cellulase activities,among which β-glucosidase showed the highest activity,followed by endoglucanase and exoglucanase. In this study,the cellulose-degrading ability of R. ornithinolytica LL1 was revealed by genome sequencing and the determination of cellulase activity,which laid a foundation for further cellulose degradation and bioconversion.

    Expression of Glucose Oxidase Gene from Aspergillus niger in Pichia pastoris and Optimization of Enzyme Production Conditions Open Access
    LIAO Zhao-min, CAI Jun, LIN Jian-guo, DU Xin, WANG Chang-gao
    2021, 37(6):  97-107.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1353
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    Glucose oxidase gene(GOD)was cloned from Aspergillus niger and highly expressed in Pichia pastoris GS115. The GOD gene was amplified by designing degenerate primers,and the gene was connected to the plasmid pPICZαA and expressed in P. pastoris. The optimized induction conditions for enzyme production were optimized according to the shaking flask level. The fermentation scale-up experiment was carried out in a 30 L bioreactor. The His4 was co-expressed and the methanol feed strategy of DO-STAT was used for high-density fermentation. The results showed that the GOD enzyme activity in the supernatant of the fermentation broth reached 32.25 U/mL after the recombinant P. pastoris GS115/pPICZ-GOD was induced by 0.5% methanol at the shake flask level for 96 h. The optimal fermentation conditions were obtained as follows:under the condition of 30℃,pH 6.0 and 250 r/min,the activity of GOD enzyme induced by 1.0% methanol for 96 h reached 50.1 U/mL,which was 55.3% higher than that of the initial fermentation. Through the scale-up experiment in a 30 L bioreactor,the GOD enzyme activity reached 307.52 U/mL,which increased by 5.1 times. Co-expression of the His4 increased the wet cell weight by 72.5% and the GOD enzyme activity reached 461 U/mL,which was an increase of 50.2% compared to the original recombinant yeast. SDS-PAGE analysis showed that the molecular weight of GOD was about 90 kD. Recombinant GOD can be highly expressed in P. pastoris with high purity and few miscellaneous proteins,which is beneficial to purification.

    Distribution and Function of Kazachstania Yeast in the Fermentation of Strong Flavor Baijiu Open Access
    YOU Ling, ZHOU Rong-qing, TAN Yi, WANG Tao, QIAO Zong-wei, ZHAO Dong
    2021, 37(6):  108-116.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1159
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    This work aims to investigate the growth characteristics and function of Kazachstania yeast in fermentation of strong flavor Baijiu. The 52 OTUs belonging to Kazachstania turicensis and 7 OTUs belonging to Kazachstania humilis were detected by high-throughput sequencing in the fermentation process of strong flavor Baijiu “Wuliangye”,and 63 K. turicensis strains and 30 K. humilis strains were isolated and identified for the study of their characteristics in solid state fermentation. It was revealed that K. turicensis and K. humilis were mainly active in the main fermentation period of 0-24 d and K. turicensis was the major dominant yeast in the main fermentation stage of strong flavor Baijiu “Wuliangye. K. turicensis produced more organic acid than K. humilis;while the difference in ethanol production and sugar utilization between K. turicensis and K. humilis was at the strain level. The average ethanol yield by K. turicensis strains was 4.94 mL/100 g and that by K. humilis strains was 5.67 mL/100 g,1 strain of K. humilis produced 11.11 mL/100 g. K. turicensis and K. humilis mainly produced the favor substances of isoamyl alcohol,isoamyl acetate,furfuryl alcohol,β-phenylethanol,and higher fatty acid ethyl ester in the fermentation of grains. The yield of isoamyl alcohol,furfuryl alcohol and β-phenylethanol by K. humilis strains was significantly higher than that by K. turiciensis strains,while the yield of acetic acid and ethyl ester of higher fatty acids above C10 were significantly lower than that by K. turiensis. The results indicated that Kazachstania yeast could be regarded as one of the landmark species of micro environment in the fermentation of strong flavor Baijiu,and have important impacts on the flavor of strong flavor Baijiu.

    Physiological and Biochemical Characteristics of Inquilinus sp. P6-4 Strain and Its Degradation Characteristics for Naphthalene Open Access
    WANG Ying, CHEN Yong-jing, SUN Qing-ye, YANG Meng-yao, WU Dun
    2021, 37(6):  117-126.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1392
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    The P6-4 strain screened from tailings was taken as the research object,its taxonomic status was determined based on 16S rDNA sequencing,and its physiological and biochemical characteristics and degradation characteristics for naphthalene were studied. Concurrently,the optimal degradation conditions and degradation pathways of the strain for naphthalene were analyzed. The results showed that P6-4 strain was a gram-negative aerobic bacterium of the genus Inquilinus,grew on R2A medium with a salinity of 1%-3% and citrate medium,and produced catalase,IAA and iron carriers. It had the function of dissolving phosphorus and fixing nitrogen. It did not produce amylase and acetyl methyl methanol while decomposing glucose. The strain grew the best under the conditions of initial naphthalene mass concentration of 400 mg/L,30℃,pH 9.0,and 150 r/min. After 7 d of culture under the optimal degradation conditions,using n-hexane as the extractant,the degradation rate measured by UV-V is spectrophotometry was 93.22%. The study of molecular biology revealed that the strain contained PAH(PAH-ring hydroxylating dioxygenase gene),HBHA(trans-o-hydroxybenzylidenepyruvate hydratase-aldolase gene),nahU(salicylate hydroxylase gene),S5H(salicylate 5-hydroxylase gene),CATA(catechol 1,2-dioxygenase gene),C230(catechol 2,3-dioxygenase gene),and GDO(gentisate 1,2-dioxygenase gene),and it was speculated that the P6-4 strain degraded naphthalene in two pathways:salicylic acid and and gentianic acid.

    Screening,Identification and Characteristics of Petroleum Degrading Bacteria from the Contaminated Soil of Yanchi Aera Open Access
    SHEN Cong, LIU Shuang, WANG Chun-xia, YAN Xue-mei, DAI Jin-xia
    2021, 37(6):  127-135.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1273
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    Highly efficient petroleum degrading bacteria were isolated and screened from the crude oil contaminated soil in Yanchi,Ningxia. The degradation characteristics of the strains and their remediation effect on the contaminated soil were studied,aiming to provide efficient microbial resource and theoretical basis for microbial remediation of oil contaminated soil in this area. The petroleum degrading bacteria were screened by the methods of enrichment culture and isolation and purification. The strains were identified based on physiological and biochemical characteristics and the 16S rRNA gene sequence analysis. According to the ability of producing surfactant and the degradation rate of crude oil,two efficient strains were selected to prepare single microbial agent and compound microbial agent,and their remediation effects on petroleum contaminated soil was studied. The results showed that 25 strains of petroleum degrading bacteria were isolated from petroleum contaminated soil,and most of them were gram positive. The strains belonged to 12 genera,including 6 strains each of Streptomyces and Pseudomonas as dominant genus,3 strains of Rhodococcus and 2 strains of Bacillus,and 1 strain each of the other 8 genera,with rich diversity. The strains showed different surfactant producing abilities and crude oil degradation rates. Among them,Rhodococcus strains S25 and S18 presented the highest degradation rates,50.0% and 47.2%,respectively;followed by Cytobacillus S19 and Streptomyces S10 with 44.4% degradation rate. The degradation rate of petroleum by Pseudomonas S23 was the lowest,only 25.0%. Soil remediation experiments demonstrated that the degradation rate of petroleum was 62.7% and 75.4% with the single bacterial agent prepared by S18 and S25 incubated in the contaminated soil for 90 d. The degradation effect of the composite bacterial agent prepared by the two strains was significantly better than that of the single bacterial agent,and the degradation rate reached 84.7%,indicating that there was a synergistic promotion effect between them,and they have the potential to be developed as soil remediation agents.

    Biological Characterization and Genome Analysis of a Lytic Phage Infecting Salmonella Open Access
    HUANG Jing-xiao, SHANG Jun-kang, CHEN Hui-min, SHEN Jia-min, LI Yuan-yuan, YU Yu-li, NI Jin-dong, LIN Bo-kun
    2021, 37(6):  136-146.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1385
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    With the situation of antibiotic resistance becoming more and more serious,it is increasingly difficult to prevent and cure pathogenic bacteria,thus research and development of new antibacterial agents is urgent. The use of bacteriophages to control pathogenic bacteria has received huge attentions. In order to obtain bacteriophages with potential applications in the biological control of Salmonella,a virulent phage PSM6 was isolated from river water by double-layer agar plate method,and transparent and uniform plaques with diameters of about 1.5-2 mm were formed on the lawn of Salmonella enteritidis. Phage PSM6 showed lytic activities on Salmonella of multiple serotypes,some Escherichia. coli strains and Shigella sonnei,indicating a broad-spectrum lytic activity. Phage PSM6 showed the maximal lytic activity to Salmonella with a MOI of 0.01. It demonstrated strong reproductive activity,of which the incubation period was about 20 min and the outbreak amount was about 56 PFU/cell. Phage PSM6 presented a good stability in 40-60℃ and kept a stable titer at pH5-10. The genome nucleic acid was double-stranded DNA. The genome was of 90 730 bp with a G+C content of 39.6%,133 ORFs and the holin-lysin lysis system,did not contain known virulence-associated and antibiotic resistance genes. Phage PSM6 should belong to Myoviridae according to the results of transmission electron microscopy and genome sequencing.

    Screening and Identification of Algal Polysaccharide-degrading Bacteria in the Intestinal Contents of Sea Cucumber Open Access
    BAI Xin-feng, JIA Ai-rong, LIU Xue, ZHANG Mian-song, CUI Ting-ting, LIU De-ting, LIU Chang-heng
    2021, 37(6):  147-153.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1113
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    In order to promote the application of algae in sea cucumber culture,algae polysaccharide-degrading bacteria were screened. In this study,algal powder was used to enrich the algal polysaccharide-degrading bacteria in the intestinal tract of sea cucumbers. Alginate and carrageenan were used as the sole carbon source to screen alginate- and carrageenan-degrading bacteria,respectively. The alginate- and carrageenan-biodegrading activities of the strain were determined by DNS method,and the strains were identified by 16S rDNA sequencing combined with physiological and biochemical index detection. Concurrently,the growth characteristics of the strains,the abilities of bacteria to degrade other main components of sea cucumber feed and the biosafety were detected. The results showed that two strains of algae polysaccharide-degrading bacteria with high activity were screened. Both strains belonged to Bacillus,which grew rapidly and had strong adaptability to acid,alkali and salt concentration,and had no significant effect on the health of sea cucumbers. The alginate-degrading bacterium HZ-1,which was the most similar with Bacillus altitudinis,had an alginate-degrading activity of 43.2 U/mL,and it also presented amylase,cellulase and protease activities. Carrageenan-degrading bacterium KL-6,which was the most similar with Bacillus megaterium,had a carrageenan-degrading activity of 1.45 U/mL,and it also had amylase and protease activity. Two strains of Bacillus with algae polysaccharide-degrading ability are screened. The two strains demonstrate fast growth speed and high enzyme activity,and can be used as breeding probiotics or used in the fermentation process of algae feed.

    Effects of the Polymorphism of the Seed Sequence in Porcine miR-378 on Its Function and Carcass Traits Open Access
    ZHANG Ting-huan, ZHANG Li-juan, CHEN Si-qing, GUO Zong-yi
    2021, 37(6):  154-162.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1165
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    The aim of this study is to explore the effects of miR-378 on its structure,function,and porcine carcass traits for the polymorphism of its seed sequence. The single nucleotide polymorphism(SNP)of Rongchang pig and Asian wild boar was used to analyze population genetic selection,to predict the changes of its structure by the polymorphism of miR-378 seed sequence,and to count the allele frequencies of miR-378 in different pig breeds. microRNA mimics were used to verify the function of miR-378 and related gene expressions in adipocytes for the polymorphism of its seed sequence. The association between the slaughter data of pig and the allele frequency of miR-378 were analyzed. The results showed that there was a strong selection signal at the miR-378 locus of Rongchang pig,and A> G mutation was found in the 5th position of miR-378-3p seed sequence. The allele frequency of this locus differed in different pig breeds,and the frequency of A allele in the pig breeds with the stronger artificial selection was higher. This mutation inhibited the function of miR-378 promoting lipid production in adipocytes,and eliminated the regulation of miR-378 on the adipocyte differentiation-related genes(PGC-1α and PGC-1 β)and the adipolysis-related genes(HSL,ATGL and CGI-58). Moreover,the genotype of this locus was significantly correlated with porcine carcass traits. Compared with the GG genotype,the thickness of backfat in AA and AG genotypes was significantly lower,and the eye-muscle area of AA genotype was significantly higher. The polymorphism of miR-378 seed sequence identified in this study could be used as a molecular marker for assisted selection of pig growth and carcass traits in pig breeding practice.

    Study on the Function of Glycolysis in Inducing Chicken PGCLC in vitro Formation Open Access
    ZHANG Chen, ZUO Qi-sheng, ZOU Yi-chen, ZHAO Juan-juan, ZHANG Ya-ni, LI Bi-chun
    2021, 37(6):  163-170.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1323
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    Studies have shown that glycolysis is mainly involved in cell reprogramming and maintaining cell totipotency,but its role in germ cell differentiation is still poorly understood. This study aims to explore the function of glycolysis system in the formation of Primordial Germ Cell(PGC)based on the in vitro model of inducing PGC differentiation in chicken Embryonic Stem Cell(ESC)induced by Bone Morphogenetic Protein 4(BMP4),and to lay a theoretical foundation for analyzing the molecular mechanism of PGC formation in chickens from the metabolic level. The expression variations of glycolysis related genes of Pgk1(phosphoglycerate kinase 1),Hk1(hexokinase 1),Pkm2(pyruvate kinase M2),Ldha(lactate dehydrogenase A),Glut1(glucose transporter type 1),Pfkp(phosphofructokinase,platelet,)and Aldoc(aldolase,fructose-bisphosphate C)were detected by qRT-PCR during BMP4 induction with glycolysis inhibitor VK3 and activator DASA58. Cell morphology was observed under different treatments. Flow cytometry was used to analyze the percentage of DDX4 positive cells(PGC like cells,PGCLC)on the day 6 after induction. qRT-PCR results showed that during the differentiation of chicken ESC into PGC-like induced by BMP4,the glycolysis related genes were significantly down regulated,and the glycolysis pathway was inhibited;while the glycolysis pathway was significantly inhibited after adding VK3,and was significantly activated after adding DASA58. Morphological observation of cells showed that the number of embryoid bodies increased significantly after adding VK3 compared with the normal induction process,but decreased significantly after adding DASA58. Analysis by flow cytometry showed that the proportion of DDX4 positive cells increased after VK3 addition,and decreased after adding DASA58. In sum,the results indicate that inhibition of glycolysis may promote the formation of chicken PGC-like in vitro,that is,glycolysis is suppressed in the process of chicken PGCs formation.

    Effects of Dietary Protein Deficiency Followed by Realimentation on the Antioxidation of Lamb Based on Transcriptomics Analysis Open Access
    KANG Ling-yun, CHEN Jian-sheng, GAN Han-ling, HAN Lu-lu, FENG Hai-xia, DIAO Qi-yu, XING Kai, CUI Kai
    2021, 37(6):  171-180.  doi:10.13560/j.cnki.biotech.bull.1985.2021-0224
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    This study is aimed to investigate the effects of dietary protein deficiency followed by realimentation on the antioxidation of lamb based on RNA-seq analysis at transcriptome level. Thirteen-two Hu twin lambs weaned on 15 d were selected and randomly divided into two groups. The control group was fed milk replacer(CP 25%)and starter(CP 21%)of normal protein level(NPL),and the other group fed milk replacer(19%)and starter(15%)of low protein level(LPL). Milk replacer was fed from weaning to d 60,and starter was freely taken. LPL group of 60-90 d freely took the starter of normal protein level(CP 21%). Two 60 and 90 d lambs in each group were selected and slaughtered for tissue collection. RNA-seq technology was used to identify the difference expression genes(DEGs)in liver tissue under dietary protein deficiency followed by realimentation,to screen pathways closely related to antioxidant function through bioinformatics analysis,and to verify the expressions of genes of antioxidant enzymes using qRT-PCR method. Low level protein diet led to 302 differentially expressed genes(DEGs)in the sheep liver and 23 down regulated genes involved in antioxidant process. GO analysis showed that DEGs were mainly involved in oxidoreductase activity(GO:0016491),glutathione transferase activity(GO:0004364)and oxidation-reduction process(GO:0055114). KEGG analysis discovered that antioxidant related genes were enriched in metabolism of xenobiotics by cytochrome P450 and glutathione metabolism. The expression of genes involved in cytokine-cytokine receptor interaction was significantly up-regulated. Compared with NPL group,the expressions of genes related to antioxidation showed no significant difference after protein realimentation for 30 d. In conclusion,protein deficiency led to the changes of liver gene expression,decreased the expressions of genes related to antioxidation. The DEGs affect the antioxidation and immune function of liver via pathways of xenobiotics metabolism,glutathione metabolism,and cytokine-cytokine receptor.

    Advances in Plant Vacuolar Processing Enzymes Open Access
    SU Yu, LI Zong-yun, HAN Yong-hua
    2021, 37(6):  181-191.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1131
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    Plant vacuolar processing enzyme(VPE)is an aspartic acid specific cysteine protease. VPE belongs to the peptidase C13 family and has substrate specificity for the carboxyl peptide chain of aspartic acid and asparagine residues. VPE is similar to caspase-1 protein from animal in both structure and function. VPE is a protease responsible for maturation and activation of vacuolar proteins in plants. It plays a multifunctional role in different plant organs and different stages of plant development and death,and mediates programmed cell death(PCD)by triggering vacuole rupture and initiating the proteolytic cascade. VPE also has peptide linking activity,which is responsible for the production of cyclic peptides in certain plants. There are four types of VPE in angiosperms during the evolution process:alpha-type VPE,beta-type VPE,gamma-type VPE,and delta-type VPE. This article summarizes the evolution,classification,maturation,activation processes and the functions of VPE in plant,as well as the latest progress and future research areas in this field,aiming to more comprehensively understand the role of VPE in plants.

    Research Progress on the Regulation of NO3- Uptake and Transport in Plant Open Access
    LIU Hai-guang, LUO Zhen, DONG He-zhong
    2021, 37(6):  192-201.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1347
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    Nitrogen is the most demanded macro-nutrient during growth of plants,plays an important role in the growth and development as well as morphogenesis of plants. Excessive application of nitrogen fertilizer leads to a decline in plant nitrogen use efficiency(NUE),which not only causes waste of nitrogen fertilizer,but also leads to soil diffused pollution,thus brings severe challenges to the development of green agriculture and has attracted widespread global attention. NO3- is the main inorganic nitrogen sources used by plants,and studying the uptake and transport mechanism of NO3- is of practical significance for improving NUE. In this paper,we reviewed the physiological processes and molecular mechanisms about how NO3- is of uptake from soil via plant roots and further transported from the roots to the shoot and distributed among the organs. We summarized and put forward the techniques and measures to regulate plant nitrogen uptake and transport,and prospected future research and application,aiming to provide basis and guidance for rational application of nitrogen fertilizer and improvement of NUE.

    On the Function of Plant Cysteine Protease in Plant Growth and Development Open Access
    MO Li-jie, LIU Xia-tong, LI Hui, LU Hai
    2021, 37(6):  202-212.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1220
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    Cysteine proteases are an important class of proteolytic enzymes and play an important role in regulating plant growth and development. Based on the expression patterns of different cysteine proteases in different tissues and organs,this article reviews the functional research and progress of cysteine proteases involved in seed germination,root development,leaf senescence,programmed cell death of tracheary elements in stems and of tapetum in anthers,aiming to provide references for further studying the function of cysteine protease.

    Advances in HKT1 Study on the Mechanism of Salt Tolerance in Plants Open Access
    ZHANG Yong-lan, XIE Li-nan
    2021, 37(6):  213-224.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1379
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    Soil salinization is an important factor affecting the reduction of crop yield. Under salt stress,plants have evolved a series of strategies to deal with salt. In these strategies,ion transporters play a pivotal role in plant response to salt stress. HKT1 transporters are a kind of ion transporters with the function of transporting Na+,which are mainly located near vascular bundles and widely found in monocotyledons and dicotyledons. In plants,they participate in the long-distance transport of Na+,regulate the concentration of Na+,and help to maintain ion balance. In this paper,the functions and corresponding regulatory processes of HKT1 proteins in different plants are discussed,and the different action models of HKT1 participating in Na+ long-distance transportation are summarized. By making a synthesis of the research on HKT1 in recent years and rational use of molecular breeding,it lays a theoretical foundation for increasing the salt stress tolerance of crops and improving the quality and yield of crops.

    Low Temperature Stress Response Mediated by Protein Ubiquitination in Plant Open Access
    WU Feng-zhang, WANG He-xin
    2021, 37(6):  225-235.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1389
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    Low-temperature stress restricts plant growth,development,and geographical distribution. A large transcriptome reprogramming occurs as a response to low-temperature stress in diverse species,and a number of proteins have been identified as important factors in this adaptive response. Ubiquitination is a post-translational modification that regulates abundance,activities,subcellular compartmentalization and transport,and involved in the low-temperature stress response. The E3 is a major component of the ubiquitin-proteasome system that recognizes the target protein and transfer of ubiquitin from the E2 to the target protein. Owing to its substrate recognition specificity,the E3 regulates various signaling pathways involved in the low-temperature stress response in plants. Therefore,components involved in the ubiquitin-proteasome system are summarized in the present study,and the role of E3 in the low-temperature stress response is described in detail.

    Progress in Research of Rice Trichome Related Genes Open Access
    FENG Lian-jie, AN Wen-jing, LIU Di, LIU Ya-fei, WANG Kai-jie, LIANG Wei-hong
    2021, 37(6):  236-243.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1231
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    As the common structures on the surface of most terrestrial plants,trichome not only enhance the ability of plants to resist adverse environmental factors such as drought,UV rays,pests and diseases,but also its development and formation process is an important model for the study of plant cell fate differentiation. Therefore,the research on development and regulation mechanism of trichome is of great significance. At present,some key genes for the development of the trichome in model plant Arabidopsis have been cloned,and the regulation mechanism of trichome development has been gradually uncovered. However,the research on the development mechanism of rice trichome is largely unclear. In recent years,some rice trichome-related genes have been identified or cloned one after another,and the research on their functions is also deepening. This review states the research history and progress of rice trichome-related genes,summarizes the regulation pathways of rice trichome development,and looks forward to the value and application prospects of rice trichome-related genes in molecular design breeding of rice trichome.

    Advances in the Application of Immobilized Fungal Laccase for the Bioremediation of Environmental Organic Contamination Open Access
    CHEN Ming-yu, NI Xuan, SI You-bin, SUN Kai
    2021, 37(6):  244-258.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1205
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    The total discharged amount of organic wastewater in China is huge,and its release into the ecological environments causes a serious threat to the health of wild animals and humans. Bioremediation technology attracts much concerns because it is green,economic and efficient. Laccase catalyzes the oxidative coupling and decomposition of varied organic pollutants in water and this reaction has several advantages such as simple operation,controllable condition,high catalytic efficiency,broad substrate spectrum,and environmental friendliness. Free laccase is unstable and difficult to be recycled,while immobilization technology can improve the catalytic efficiency,operational stability,and reusability of enzyme. Thus,it is expected to have the large-scale applications of laccase in the environmental bioremediation. This paper reviews the molecular structure,substrate spectrum,and catalytic properties of fungal laccase,clarifies the advantages and disadvantages of four conventional immobilization approaches of laccase such as adsorption,entrapment,covalent bonding,and cross-linking. Further this paper emphatically summarizes the radical coupling and oxidative decomposition mechanisms of immobilized laccase-mediated estrogens,antibiotics,polycyclic aromatic hydrocarbons,personal care products,synthetic dye,and sulfa drugs. Immobilized laccase catalyzes the oxidation of organic contaminants to radical and/or quinone intermediates only using molecular oxygen as an electron acceptor. These reactive intermediates not only can covalently couple to form oligomers and polymers,but yield decomposition products by radical-initiated attack each other,thereby reducing the bioavailability and biotoxicity of the parent compounds. Immobilized laccase shows a huge potential in the purification of organic wastewater,elimination of environmental pollution,and maintenance of ecological health. However,it is necessary to further screen the inexpensive immobilized carriers and improve the recycling rate of immobilized laccase.

    The Strategy for Enhancing Foreign Proteins Expression by Signal Peptide in Bacillus subtilis Open Access
    MIAO Hua-biao, CAO Yan, YANG Meng-han, HUANG Zun-xi
    2021, 37(6):  259-271.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1255
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    As an important prokaryotic expression host strain,Bacillus subtilis has always been regarded as preferred model strain for foreign protein expression,featuring strong protein secretion,clear genetic background,no codon preference,rapid growth and non-pathogenicity. Signal peptide is a short peptide chain located in the N-terminal of the precursor protein,with the function of guiding and regulating the folding of the precursor protein. Meanwhile,it plays a very important role in the process of protein transfer and secretion. At present,there is no regularity to find the efficient secretion of different foreign proteins by using the signal peptide of B. subtilis. For this reason,the structural characteristics,classification,transport pathway and application of signal peptides from B. subtilis are reviewed here,aiming to provide certain reference for further screening the optimal signal peptides of foreign proteins in B. subtilis expression system.

    Research Progress of MicroRNA Involvement in the Stress Responses of Aquatic Animals to Envirnmental Pollutants Open Access
    WANG Meng-ting, CAO Jie-yu, WANG Zhong-xin, WANG Ya-yu, YANG Da-zuo, ZHOU Yi-bing, ZHAO Huan
    2021, 37(6):  272-278.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1224
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    MicroRNAs(miRNA)are small non-coding RNA encoded by endogenous genes. They play important role in various life activities including cell apoptosis,development and growth,metabolism and so on. Recent studies revealed that the changing of miRNA expressions,when organisms are exposing to environmental pollutants such as heavy metal,organic pollutants and so on,may affect the expressions of target genes,further regulate the toxic effect of organism to exogenous pollutants. This review summarizes the research progress of miRNA involved in aquatic animals under different environmental pollutants exposure as well as its mechanisms,discusses and prospects the future research direction of miRNA,aiming to provide some references for studying the stress tolerance of aquatic animals.

    Optimization of CRISPR/Cas12a System and Development of It-mediated Adenine Base Editor in Rice Open Access
    WANG Jing-wen, YAN Fang, LIU Lang, ZHOU Xue-ping, WANG Dao-wen, ZHOU Huan-bin
    2021, 37(6):  279-285.  doi:10.13560/j.cnki.biotech.bull.1985.2021-0231
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    In order to develop an efficient CRISPR/Cas12a-mediated gene editing system in rice,different Cas12a homologous proteins and crRNA configurations and lengths were tested to explore the factors affecting the editing activity of Cas12a. We found that LbCas12a had a high editing efficiency with crRNA 23 nt compared with AsCas12a,and the U4AU4 sequence at the 3' end of crRNA didn’t enhanced its editing activity. Meanwhile,we fused the Escherichia coli adenine deaminase variant TadA8e to develop the CRISPR/LbCas12a-mediated adenine base editing system pUbi∶rBE58,which successfully induced the conversion A to G at the target loci in rice endogenous gene OsCPK15,with an efficiency of 33.33%. Our results demonstrate that using CRISPR/Cas12a-mediated may genetically edit the genes of rice,and this enriches rice gene editing tools and broadens gene editing toolkits.

    Genomic DNA Rapid Preparation and PCR Detection Methods for Genetically Modified Papaya Open Access
    PAN Zhi-wen, CHEN Wei-ting, GAO Jie-er, ZHOU Feng, YAO Juan, WANG Sheng-bin, JIANG Da-gang
    2021, 37(6):  286-294.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1587
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    The preparation of genomic DNA template is the key step in the detection of genetically modified papaya. In order to improve detection efficiency,it is very important to establish rapid genomic DNA preparation and PCR detection methods for papaya samples. In this study,a rapid preparation method of papaya genomic DNA was developed,including sample preparation,homogenisation with preparation buffer and supernatant dilution. After the rapid preparation of genomic DNA solutions from different papaya samples,the obtained genomic DNA solutions were verified by PCR method. The results of qualitative PCR showed that the amplified bands were clear when the genomic DNA solutions of the leaves and fruits were diluted for 5 times. The PCR amplification results of leaf genomic DNA were better than that of the fruits when the DNA solution were diluted for 25 times. The PCR amplification efficiencies of leaf genomic DNA were reasonable in the real-time fluorescence PCR reaction. Sensitivity testing results indicated the specific fragments of endogenous reference and exogenous genes were amplified as expected by both qualitative and real-time fluorescence PCR methods when the contents in the leaves and fruits samples was 0.1%. The rapid preparation and PCR detection methods of papaya genomic DNA established here is efficient and stable.

    Method Application of Leading Fluorescent Tracers into the Vascular Tissues of Ziziphus jujuba Mill cv. Lingwuchangzao Fruits Open Access
    ZHANG Ying-cai, HUANG Yue, HAI Yuan, ZHANG Yuan, HU Ya-jie, ZHAO Meng-yi
    2021, 37(6):  295-304.  doi:10.13560/j.cnki.biotech.bull.1985.2020-1502
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    The fruits of Ziziphus jujuba Mill cv. Lingwuchangzao in different developmental stages were used as experimental materials,the microstructure and change laws of vascular bundles in the fruits of different developmental stages can be clarified using paraffin section method. Based on these results and applying methods of leading fluorescent tracers into vascular tissues of Z. jujuba Mill cv. Lingwuchangzao fruits,the techniques of fluorescent dye tracer in living cell were used to explore the research methods of the unloading path of photosynthates in vascular bundles phloem in the Z. jujuba Mill cv. Lingwuchangzao fruit timely. The results showed that:1)The vascular bundles(especially the vascular bundles nearby endocarp)in the fruit was concentrated and abundant in the early bulking period,the vascular bundles were single or two back-to-back gathered together to be developing. In the rapid enlargement period fruit,the parenchyma cells in the mesocarp developed rapidly and arranged loosely,they gradually increased from the outer to the inner volume,some even arranged into a reticular structure,surrounded by a larger cavity,the number of vascular bundles decreased in the same visual field,and the vascular bundles were mostly two back-to-back,three or four gathered together to be developing. The cell cavities were further enlarged and the number increased in the pericarp in the coloring period,compared with the previous two stages,the number of vascular bundles was fewer in the same visual field,and formed multi-branch structures by multiple vascular bundles. Compared with the coloring period,the cavity space formed by parenchyma cells continued to increase,and the number of vascular bundles did not change significantly,multi-branch structures of multiple vascular bundles were slightly different in the maturation period fruit. 2)By using the techniques of fluorescent dye tracer in living cell,the fluorescent tracer carboxyfluorescein diacetate and plasma membrane penetrating reagent digitonin were led into the phloem of vascular bundles,and the fluorescent tracer Texas-Red were led into the vascular bundles xylem of Z. jujuba Mill cv. Lingwuchangzao fruit in different developmental stages,the fluorescence characteristics were observed by CLSM,the research methods of the phloem unloading path of photosynthates in Z. jujuba Mill cv. Lingwuchangzao fruit were gained,which provides scientific bases for photosynthates accumulation and quality regulation for Z. jujuba Mill cv. Lingwuchangzao fruit.