Characteristics of the chloroplast genome of Dracaena marginata and phylogenetic analysis / 生物工程学报

Dracaena marginata is a widely cultivated horticultural plant in the world, which has high ornamental and medicinal value. In this study, the whole genome of leaves from D. marginata was sequenced by Illumina HiSeq 4000 platform. The chloroplast genome were assembled for functional annotation, sequence characteristics and phylogenetic analysis. The results showed that the chloroplast genome of D. marginata composed of four regions with a size of 154 926 bp, which was the smallest chloroplast genome reported for Dracaena species to date. A total of 132 genes were identified, including 86 coding genes, 38 tRNA genes and 8 rRNA genes. Codon bias analysis found that the codon usage bias was weak and there was a bias for using A/U base endings. 46 simple sequence repeat and 54 repeats loci were detected in the chloroplast genome, with the maximum detection rate in the large single copy region and inverted repeat region, respectively. The inverted repeats boundaries of D. marginata and Dracaena were highly conserved, whereas gene location differences occurred. Phylogenetic analysis revealed that D. serrulata and D. cinnabari form a monophyletic clade, which was the closest relationship and conformed to the morphological classification characteristics. The analysis of the chloroplast genome of D. marginata provides important data basis for species identification, genetic diversity and chloroplast genome engineering of Dracaena.

Identification and expression analysis of MADS-box gene family in Docynia delavayi (Franch.) Schneid / 生物工程学报

MADS-box gene family is a significant transcription factor family that plays a crucial role in regulating plant growth, development, signal transduction, and other processes. In order to study the characteristics of MADS-box gene family in Docynia delavayi (Franch.) Schneid. and its expression during different stages of seed germination, this study used seedlings at different stages of germination as materials and screened MADS-box transcription factors from the transcriptome database of D. delavayi using bioinformatics methods based on transcriptome sequencing. The physical and chemical properties, protein conservative motifs, phylogenetic evolution, and expression patterns of the MADS-box transcription factors were analyzed. Quantitative real-time PCR (qRT-PCR) was used to verify the expression of MADS-box gene family members during different stages of seed germination in D. delavayi. The results showed that 81 genes of MADS-box gene family were identified from the transcriptome data of D. delavayi, with the molecular weight distribution ranged of 6 211.34-173 512.77 Da and the theoretical isoelectric point ranged from 5.21 to 10.97. Phylogenetic analysis showed that the 81 genes could be divided into 15 subgroups, among which DdMADS27, DdMADS42, DdMADS45, DdMADS46, DdMADS53, DdMADS61, DdMADS76, DdMADS77 and DdMADS79 might be involved in the regulation of ovule development in D. delavayi. The combination of the transcriptome data and the qRT-PCR analysis results of D. delavayi seeds indicated that DdMADS25 and DdMADS42 might be involved in the regulation of seed development, and that DdMADS37 and DdMADS38 might have negative regulation effects on seed dormancy. Previous studies have reported that the MIKC* subgroup is mainly involved in regulating flower organ development. For the first time, we found that the transcription factors of the MIKC* subgroup exhibited a high expression level at the early stage of seed germination, so we speculated that the MIKC* subgroup played a regulatory role in the process of seed germination. To verify the accuracy of this speculation, we selected DdMADS60 and DdMADS75 from the MIKC* subgroup for qRT-PCR experiments, and the experimental results were consistent with the expression trend of transcriptome sequencing. This study provides a reference for further research on the biological function of D. delavayi MADS-box gene family from the perspective of molecular evolution.

Genome-wide identification of SUN gene family in Fragaria vesca and stresses-response analysis / 生物工程学报

SUN gene is a group of key genes regulating plant growth and development. Here, SUN gene families of strawberry were identified from the genome of the diploid Fragaria vesca, and their physicochemical properties, genes structure, evolution and genes expression were also analyzed. Our results showed that there were thirty-one FvSUN genes in F. vesca and the FvSUNs encoded proteins were classified into seven groups, and the members in the same group showed high similarity in gene structures and conservative motifs. The electronic subcellular localization of FvSUNs was mainly in the nucleus. Collinearity analysis showed that the members of FvSUN gene family were mainly expanded by segmental duplication in F. vesca, and Arabidopsis and F. vesca shared twenty-three pairs of orthologous SUN genes. According to the expression pattern in different tissues shown by the transcriptome data of F. vesca, the FvSUNs gene can be divided into three types: (1) expressed in nearly all tissues, (2) hardly expressed in any tissues, and (3) expressed in special tissues. The gene expression pattern of FvSUNs was further verified by quantitative real-time polymerase chain reaction (qRT-PCR). Additionally, the seedlings of F. vesca were treated by different abiotic stresses, and the expression level of 31 FvSUNs genes were assayed by qRT-PCR. The expression of most of the tested genes was induced by cold, high salt or drought stress. Our studies may facilitate revealing the biological function and molecular mechanism of SUN genes in strawberry.

Screening of reference genes for quantitative real-time PCR in Artemisia argyi / 中国中药杂志

Artemisia Argyi Folium, a traditional Chinese medicine of important medicinal and economic value, sees increasing demand in medicinal and moxibustion product market. Screening stable and reliable reference genes for quantitative real-time PCR(qRT-PCR) is a prerequisite for the analysis of gene expression in Artemisia argyi. In this study, eight commonly used reference genes, Actin, 18s, EF-1α, GAPDH, SAND, PAL, TUA, and TUB, from the transcriptome of A. argyi, were selected as candidate genes. The expression of each gene in different tissues(roots, stems, and leaves) of A. argyi and in leaves of A. argyi after treatment with methyl jasmonate(MeJA) for different time(0, 4, 8, 12 h) was detected by qRT-PCR. Then, geNorm, NormFinder, BestKeeper, ΔCT, and RefFinder were employed to evaluate their expression stability. The results demonstrated that Actin was the most stable reference gene in different tissues and in leaves treated with MeJA, and coming in the second was SAND. Furthermore, the expression of DXS and MCT which are involved in terpenoid backbone biosynthesis was detected in different tissues and after MeJA treatment. The results showed that the expression patterns of DXS and MCT in different tissues and under MeJA treatment calculated with Actin and SAND as internal reference genes were consistent, which validated the screening results. In conclusion, Actin is the most suitable reference gene for the analysis of gene expression in different tissues of A. argyi and after MeJA treatment. This study provides valuable information for gene expression analysis in A. argyi and lays a foundation for further research on molecular mechanism of quality formation of Artemisia Argyi Folium.

Selection and validation of reference genes for quantitative Real-time PCR analysis in Amana edulis / 中国中药杂志

Amana edulis is a traditional Chinese medicinal plant with low propagation coefficient. In recent years, the increasing demands of A. edulis lead to a shortage of its wild resources. In order to analyze the expression of related functional genes in A. edulis, the selection of suitable internal reference genes is crucial to improve the accuracy of experimental results. Eight genes(ACT, TUA, CYP, GAPDH, UBQ, UBI, EF1a, UBC)were chosen as candidate reference genes based on the RNA-Seq. Real-time fluorescence quantitative technique was used to detect the expression level of candidate internal reference genes in different organs(bulb, leaf, flo-wer) and stolons at different development stages of A. edulis. Then GeNorm, NormFinder, BestKeeper softwares and RefFinder website were used for a comprehensive analysis of the expression stability of the candidate genes.The results showed that among the 8 candidate reference genes, the variation range of Ct value of UBC was the smallest, and the expression level was stable, which was suitable for an reference gene. GeNorm and NormFinder software analysis showed that UBC and UBI were the optimal reference genes. BestKeeper analysis showed that CYP and UBC expression were relatively stable. Comprehensive evaluation of RefFinder website showed that UBC and UBI were the most stable genes, and ACT displayed the lowest stability in all software evaluation, indicating UBC and UBI were suitable for reference genes. Additionally, the most stable UBC, UBI and the most unstable ACT were used as internal reference genes to detect the expression of GBSS gene in A. edulis, and expression pattern of GBSS gene was the same under the calibration of UBC and UBI. The expression data of GBSS gene confirmed that UBC and UBI genes were reliable for A. edulis qRT-PCR as internal reference genes. The results would benefit future studies on related gene expression of A. edulis.

Reference gene screening for Real-time quantitative PCR in Polygonum multiflorum / 中国中药杂志

To select suitable references gene of Polygonum multiflorum for gene expression analysis in different tissues, five candidate reference genes like Actin,GAPDH,SAND,PP2A,TIP41 were selected from the transcriptome data of P. multiflorum, then the specific primers were designed. The expression stability of the five reference genes in different tissues of P. multiflorum was analyzed by Real-time quantitative PCR through avilable analysis methods such as geNorm, NormFinder, BestKeeper, Delta CT and RefFinder, to ensure the reliability of the analysis results. The results showed that there were significant differences in the expression levels and stability of candidate genes in different tissues of P. multiflorum. Ct distribution analysis of the expression levels of candidate genes showed that the expression levels of Actin and GAPDH genes were relatively high in different tissues, while the expression levels of SAND, PP2A and TIP41 were lower. The stability of each candidate gene was analyzed by different methods. The results of geNorm analysis showed that the expression of PP2A and GAPDH was the most stable, the expression stability of SAND was the worst, the stability of PP2A was the highest in both NormFinder and Delta CT, the stability of SAND was the lowest, and the stability of Actin was the most stable in BestKeeper analysis. Through the comprehensive evaluation and analysis of the stability of candidate genes by RefFinder, it is concluded that the stability of PP2A gene is the highest, followed by GAPDH, Actin, TIP41, SAND, and SAND gene is the worst. Therefore, the PP2A gene is an ideal reference gene for the analysis of gene expression in different tissues of P. multiflorum.

Selection of optimal qRT-PCR reference genes for Aconitum vilmorinianum / 中国中药杂志

Screening suitable reference genes is the premise of quantitative Real-time PCR(qRT-PCR)for gene expression analysis. To provide stable reference genes for expression analysis of genes in Aconitum vilmorinianum, this study selected 19 candidate re-ference genes(ACT1, ACT2, ACT3, aTUB1, aTUB2, bTUB, 18S rRNA, UBQ, eIF2, eIF3, eIF4, eIF5, CYP, GAPDH1, GAPDH2, PP2A1, PP2A2, ACP, and EF1α) based on the transcriptome data of A. vilmorinianum. qRT-PCR was conducted to profile the expression of these genes in the root, stem, leaf, and flower of A. vilmorinianum. The Ct values showed that 18S rRNA with high expression level and GAPDH2 with large expression difference among organs were not suitable as the reference genes. NormFinder and geNorm showed similar results of the expression stability of the other candidate reference genes and demonstrated PP2A1, EF1α, and CYP as the highly stable ones. However, BestKeeper suggested EF1α, ACT3, and PP2A1 as the top stable genes. In view of the different results from different softwares, the geometric mean method was employed to analyze the expression stability of the candidate re-ference genes, the results of which indicated that PP2A1, EF1α, and ACT3 were the most stable. Based on the comprehensive analysis results of geNorm, NormFinder, BestKeeper, and geometric mean method, PP2A1 and EF1α presented the most stable expression in different organs of A. vilmorinianum. PP2A1 and EF1α were the superior reference genes for gene expression profiling in different organs of A. vilmorinianum.

Research progress in biosynthesis of podophyllotoxin and its derivatives / 生物工程学报

Podophyllotoxin (PTOX) is an aryl-tetralin lignan of plant origin found in some species of Podophyllum such as Dysosma versipellis, Diphylleia sinensis, and Sinopodophyllum hexandrum. Etoposide and teniposide are produced semisynthetically from PTOX and used clinically to treat several forms of cancer. As a typical representative of new drug discovery from natural products, the production of PTOX solely depends on extraction from plants, resulting in severe contradiction between supply and demand. With the advantages of unconstrained resources and eco-friendly reaction conditions, biosynthesis method has become a trend in the production of PTOX and its derivatives. In this review, we summarize the research progress of PTOX biosynthesis in plants and expound the functions of the key enzymes as well as their subcellular location. The synthetic biology for production of PTOX intermediates in a tobacco chassis is also introduced. Finally, the heterologous expression and biotransformation of PTOX in microorganisms is summarized, which sets the foundation for the efficient microbial production of PTOX using cell factories.

Disruption of OsRhoGDI2 by CRISPR/Cas9 technology leads to semi-dwarf in rice / 生物工程学报

OsRhoGDI2 was isolated as a putative partner of Rho protein family member OsRacD from rice panicles by yeast two-hybrid, but its function remains unknown. In order to identify the function of OsRhoGDI2, OsRhoGDI2 knockout mutants were created by CRISPR/Cas9 technology. The results showed that two different homozygous mutants were obtained in T0 generation, and eight kinds homozygous mutants were identified in T1 generation. Sequence analysis revealed that the base substitution or base deletion occurred near the editing targets of the gene in knockout rice, and it could be expected that the truncated OsRhoGDI2 proteins lacking the RhoGDI conserved domain would be generated. Phenotype analysis showed that the OsRhoGDI2 knockout rice plants were significantly lower than the control plants. Statistical analysis confirmed that the significant decrease of plant height was due to the shortening of the second and third internodes, suggesting that OsRhoGDI2 gene may be related with rice height control.

Identificación de marcadores moleculares (SNP) y genes candidatos asociados a la tolerancia genética al complejo mancha de asfalto en variedades nativas de maíz (Zea mays L) / Identification of molecular markers (SNP) and candidate genes associated to genetic tolerance to tar spot complex disease in maize (Zeamays L) landraces

El complejo mancha de asfalto (CMA) en maíz (ZeamaysL.), causado por los hongos Phyllachora maydis Maubl. Y Monographella maydis Müller & Samuels, es una enfermedad de importancia económica en Guatemala, que ha causado pérdida en el rendimiento entre 30 a 50%, inclusive del 100% si las condiciones son favorables. El objetivo de esta investigación fue identificar marcadores de un solo nucleótido o SNP (Single Nucleotide Polymorphism, por sus siglas en inglés) y genes candidatos asociados a la tolerancia genética al CMA. Para ello se analizaron 463 poblaciones nativas y 329,692 SNP, y se compararon dos modelos genómicos, single markery BayesB, para la identificación de regiones asociadas a la tolerancia genética al CMA. Se identificaron 40 marcadores SNP asociados significativamente a la tolerancia genética al CMA con ambos modelos. La proporción de variación fenotípica total explicada (PVE) por los 40 SNPs fue de 56%, atribuida a efectos genéticos aditivos. Múltiples genes de resistencia a enfermedades fueron identificados en las regiones señaladas por los marcadores SNP. Sus funciones principales son receptores y transductores de señal, factores de transcripción que regulan positivamente la expresión de genes de tolerancia y genes de la familia kinasa, por lo que potencialmente están involucrados en el mecanismo de defensa al CMA.

The tar spot complex (TSC) diseasein maize (ZeamaysL.), caused by the fungi Phyllachora maydis Maubl. And Monographella maydis Müller & Samuels, is an economic important disease in Guatemala, producing yield losses between 30 to 50%, inclusive of 100% if the conditionsare favorable. The objective of this researchwasto identify single nucleoti depolymorphism markers (SNP) and candidate genes associated withgenetictoleranceto TSC. Asetof 463 native populations and 329,692 SNP were analyzed with two genomic models, single marker and BayesB, for the identification of regions associated with genetic tolerance to TSC. Forty SNP markers were significantly associated with the genetic tolerance to TSC with both models. The proportion of total phenotypic variation explained (PVE) by the 40 SNPs was 56%, attributed to additive genetice ffects. Multiple candidate genes for disease resistance were identified in the región sindicated by the SNP markers. Their main functionsare signal transducersand receptors, transcription factors that positively regulatethe expression of tolerance genes and family kinase genes, there fore, they are potentially involved in the defense mechanism to TSC.

Cloning and molecular characterization of a putative habanero pepper SERK1 cDNA expressed during somatic and zygotic embryogenesis

Background: Plant gene homologs that control cell differentiation can be used as biotechnological tools to study the in vitro cell proliferation competence of tissue culture-recalcitrant species such as peppers. It has been demonstrated that SERK1 homologs enhance embryogenic competence when overexpressed in transformed tissues; therefore, cloning of a pepper SERK1 homolog was performed to further evaluate its biotechnological potential. Results: A Capsicum chinense SERK full-length cDNA (CchSERK1) was cloned and characterized at the molecular level. Its deduced amino acid sequence exhibits high identity with sequences annotated as SERK1 and predicted-SERK2 homologs in the genomes of the Capsicum annuum CM-334 and Zunla-1 varieties, respectively, and with SERK1 homologs from members of the Solanaceae family. Transcription of CchSERK1 in plant tissues, measured by quantitative RT-PCR, was higher in stems, flowers, and roots but lower in leaves and floral primordia. During seed development, CchSERK1 was transcribed in all zygotic stages, with higher expression at 14 days post anthesis. During somatic embryogenesis, CchSERK1 was transcribed at all differentiation stages, with a high increment in the heart stage and lower levels at the torpedo/cotyledonal stages. Conclusion: DNA sequence alignments and gene expression patterns suggest that CchSERK1 is the C. chinense SERK1 homolog. Significant levels of CchSERK1 transcripts were found in tissues with cell differentiation activities such as vascular axes and during the development of zygotic and somatic embryos. These results suggest that CchSERK1 might have regulatory functions in cell differentiation and could be used as a biotechnological tool to study the recalcitrance of peppers to proliferate in vitro.

Screening and analysis on the differentially expression genes between diploid and autotetraploid watermelon by using of digital gene expression profile / Triagem e análise da expressão diferencial dos genes entre melancia diplóide e autotetraplóide através do perfil de expressão gênica digital

Abstract Synthetic polyploids are key breeding materials for watermelon. Compared with diploid watermelon, the tetraploid watermelon often exhibit wide phenotypic differences and differential gene expression. Digital gene expression (DGE) profile technique was performed in this study to present gene expression patterns in an autotetraploid and its progenitor diploid watermelon, and deferentially expressed genes (DEGs) related to the abiotic and biotic stress were also addressed. Altogether, 4,985 DEGs were obtained in the autotetraploid against its progenitor diploid, and 66.02% DEGs is up-regulated. GO analysis shows that these DEGs mainly distributed in 'metabolic process', 'cell' and 'catalytic activity'. KEGG analysis revealed that these DEGs mainly cover 'metabolic pathways', 'secondary metabolites' and 'ribosome'. Moreover, 134 tolerance related DEGs were identified which cover osmotic adjustment substance, protective enzymes/protein, signaling proteins and pathogenesis-related proteins. This study present the differential expression of stress related genes and global gene expression patterns at background level in autotetraploid watermelons. These new evidences could supplement the molecular theoretical basis for the better resistance after the genome doubling in the gourd family.

Resumo Poliploides sintéticos são materias fundamentais para melhoramento genético da melancia. Comparativamente ao seu homólogo diploide, a melancia tetraploide apresenta amplas diferenças genotípica e fenotípica e diferença de expressão gênica. A expressão gênica digital ou DGE (digital gene expression) foi utilizada neste estudo para representar o perfil de expressão gênica da melancia autotetraploide e seu progenitor diploide e a expressão diferencial de genes relacionados ao estresse biótico e abiótico. Os resultados mostraram que 4.985 DEGs foram observados no organismo autotetraploide, sendo que, deste total, 66.02%foram supra-regulados. A análise de ontologia gênica (GO) mostrou que estes DEGs estão relacionados principalmente com processos metabólicas, célula e atividade catalítica, abrangendo de acordo com a análise de genes e genoma (KEGG) rotas metabólicas, metabolismo secundário e ribossomos. Além disso, 134 genes de defesa foram identificados, abrangendo substâncias de ajuste osmótico, enzimas/proteínas de proteção, proteínas sinalizadoras e proteínas relacionadas à patogênese. Este estudo mostrou a expressão diferencial de genes relacionados ao estresse e o perfil global de expressão gênica de melancia autotetraploide, estes resultados podem complementar, a nível molecular, o entendimento do fator resistência após a duplicação do genoma em cucurbitáceas.

Origination and selection of ABCDE and AGL6 subfamily MADS-box genes in gymnosperms and angiosperms

BACKGROUND: The morphological diversity of flower organs is closely related to functional divergence within the MADS-box gene family. Bryophytes and seedless vascular plants have MADS-box genes but do not have ABCDE or AGAMOUS-LIKE6 (AGL6) genes. ABCDE and AGL6 genes belong to the subgroup of MADS-box genes. Previous works suggest that the B gene was the first ABCDE and AGL6 genes to emerge in plant but there are no mentions about the probable origin time of ACDE and AGL6 genes. Here, we collected ABCDE and AGL6 gene 381 protein sequences and 361 coding sequences from gymnosperms and angiosperms and reconstructed a complete Bayesian phylogeny of these genes. In this study, we want to clarify the probable origin time of ABCDE and AGL6 genes is a great help for understanding the role of the formation of the flower, which can decipher the forming order of MADS-box genes in the future. RESULTS: These genes appeared to have been under purifying selection and their evolutionary rates are not significantly different from each other. Using the Bayesian evolutionary analysis by sampling trees (BEAST) tool, we estimated that: the mutation rate of the ABCDE and AGL6 genes was 2.617 × 10-3 substitutions/site/million years, and that B genes originated 339 million years ago (MYA), CD genes originated 322 MYA, and A genes shared the most recent common ancestor with E/AGL6 296 MYA, respectively. CONCLUSIONS: The phylogeny of ABCDE and AGL6 genes subfamilies differed. The APETALA1 (AP1 or A gene) subfamily clustered into one group. The APETALA3/PISTILLATA (AP3/PI or B genes) subfamily clustered into two groups: the AP3 and PI clades. The AGAMOUS/SHATTERPROOF/SEEDSTICK (AG/SHP/STK or CD genes) subfamily clustered into a single group. The SEPALLATA (SEP or E gene) subfamily in angiosperms clustered into two groups: the SEP1/2/4 and SEP3 clades. The AGL6 subfamily clustered into a single group. Moreover, ABCDE and AGL6 genes appeared in the following order: AP3/PI → AG/SHP/STK → AGL6/SEP/AP1. In this study, we collected candidate sequences from gymnosperms and angiosperms. This study highlights important events in the evolutionary history of the ABCDE and AGL6 gene families and clarifies their evolutionary path.

PDIL1-2 can indirectly and negatively regulate expression of the AGPL1 gene in bread wheat

BACKGROUND: ADP-glucose pyrophosphorylase (AGPase), the key enzyme in plant starch biosynthesis, is a heterotetramer composed of two identical large subunits and two identical small subunits. AGPase has plastidial and cytosolic isoforms in higher plants, whereas it is mainly detected in the cytosol of grain endosperms in cereal crops. Our previous results have shown that the expression of the TaAGPL1 gene, encoding the cytosolic large subunit of wheat AGPase, temporally coincides with the rate of starch accumulation and that its overexpression dramatically increases wheat AGPase activity and the rate of starch accumulation, suggesting an important role. METHODS: In this study, we performed yeast one-hybrid screening using the promoter of the TaAGPL1 gene as bait and a wheat grain cDNA library as prey to screen out the upstream regulators of TaAGPL1 gene. And the barley stripe mosaic virus-induced gene-silencing (BSMV-VIGS) method was used to verify the functional characterization of the identified regulators in starch biosynthesis. RESULTS: Disulfide isomerase 1-2 protein (TaPDIL1-2) was screened out, and its binding to the TaAGPL1-1D promoter was further verified using another yeast one-hybrid screen. Transiently silenced wheat plants of the TaPDIL1-2 gene were obtained by using BSMV-VIGS method under field conditions. In grains of BSMV-VIGS-TaPDIL1-2-silenced wheat plants, the TaAGPL1 gene transcription levels, grain starch contents, and 1000-kernel weight also significantly increased. CONCLUSIONS: As important chaperones involved in oxidative protein folding, PDIL proteins have been reported to form hetero-dimers with some transcription factors, and thus, our results suggested that TaPDIL1-2 protein could indirectly and negatively regulate the expression of the TaAGPL1 gene and function in starch biosynthesis.

Global Quantitative Mapping of Enhancers in Rice by STARR-seq / 基因组蛋白质组与生物信息学报·英文版

Enhancers activate transcription in a distance-, orientation-, and position-independent manner, which makes them difficult to be identified. Self-transcribing active regulatory region sequencing (STARR-seq) measures the enhancer activity of millions of DNA fragments in parallel. Here we used STARR-seq to generate a quantitative global map of rice enhancers. Most enhancers were mapped within genes, especially at the 5' untranslated regions (5'UTR) and in coding sequences. Enhancers were also frequently mapped proximal to silent and lowly-expressed genes in transposable element (TE)-rich regions. Analysis of the epigenetic features of enhancers at their endogenous loci revealed that most enhancers do not co-localize with DNase I hypersensitive sites (DHSs) and lack the enhancer mark of histone modification H3K4me1. Clustering analysis of enhancers according to their epigenetic marks revealed that about 40% of identified enhancers carried one or more epigenetic marks. Repressive H3K27me3 was frequently enriched with positive marks, H3K4me3 and/or H3K27ac, which together label enhancers. Intergenic enhancers were also predicted based on the location of DHS regions relative to genes, which overlap poorly with STARR-seq enhancers. In summary, we quantitatively identified enhancers by functional analysis in the genome of rice, an important model plant. This work provides a valuable resource for further mechanistic studies in different biological contexts.

Pyramiding of 3-resistant-gene to improve rice blast resistance of a restorer line, Fuhui 673 / 生物工程学报

To improve the blast resistance of elite rice restorer line Fuhui 673, 3 blast resistance genes Pi-1, Pi-9 and Pi-kh were introduced into Fuhui 673 from a good-quality restorer line Jinhui 1059 through 3 successive backcrosses followed by one selfing using the technique of marker-assisted selection. Ten near-isogenic lines (NILs) of Fuhui 673 carrying the 3 introduced resistance genes were created. Genotype analysis using 68 SSR markers evenly distributed in the genome indicated that 92.96%-98.59% of the NILs' genetic background had been recovered to Fuhui 673. Both indoor and field resistance tests indicated that the NILs and their hybrids with sterile line Yixiang A were all resistant to rice blast, with resistance levels significantly higher than those of controls Fuhui 673 and hybrid Yiyou 673 (Yixiang A  Fuhui 673). In addition, among the 10 hybrids between the NILs and Yixiang A, 2 showed significantly higher yield than and 4 displayed similar yield to that of control Yiyou 673, suggesting that most of the NILs retained the elite characteristics of Fuhui 673. Two new hybrid rice cultivars Liangyou 7283 and Jintaiyou 683 from NIL Line 9 showed high yield, good resistance to blast and moderate growth period in regional trial, suggesting that the NIL Line 9 has a good prospect for application.

Functional characterization of SsNES responsible for nerolidol biosynthesis in Senecio scandens / 中国中药杂志

A short terpene synthase gene was obtained by screening the transcriptome data of Senecio scandens. The phylogenetic tree and sequence alignment putatively identified this gene as a nerolidol synthase gene, named SsNES(GenBank MH518312). Protein homology modeling indicated that SsNES contained a complete conserved domain and folded correctly. SsNES was cloned and successfully expressed in Escherichia coli as soluble protein. The biochemical function of SsNES was characterized by E. coli metabolic engineering, which showed that SsNES catalyzed formation of trans-nerolidol with(E, E)-farnesyl diphosphate as the substrate. Nerolidol was also detected in stems and leaves of S. scandens, indicating that SsNES might act as the nerolidol synthase in plant. RT-PCR analysis indicated that SsNES was mainly expressed in stem, flowers and leaves, and no expression was observed in roots. After the treatment of SA, MeJA or Ala, SsNES was induced significantly at 6 h, indicating involvement in the defense response of S. scandens. The identification of SsNES not only clarified biosynthesis of nerolidol in S. scandens, but also provided diversity of sesquiterpene synthase, as well as theoretical basis for disease and pest defense mediated by the terpene metabolites.

Identification of Corydalis yanhusuo,C. turtschaninovii,C. decumbens by allele-specific PCR / 中国中药杂志

To establish a DNA molecular markers method for identification of Corydalis yanhusuo,C. turtschaninovii and C. decumbens,the mat K,trn G and psb A-trn H sequences of 56 samples from 14 species of C. yanhusuo,C. turtschaninovii,C. decumbens and their related species were obtained by sequencing. The SNP loci were obtained by Bio Edit 7. 2. 2 software. The primers for AS-PCR identification were designed based on the mutation sites,and the conditions of PCR were optimized to identify C. yanhusuo,C. turtschaninovii,and C. decumbens according to the specific bands. The results showed that the amount of template( 0. 6-1 200 ng)and annealing temperature( 42-60 ℃) had little influence on the amplification results,and the number of cycles had much influence on the amplification results. When the number of cycles was 20,the specific bands of 297 bp( mat K),353 bp( trn G) and 544 bp( mat K) were amplified from C. yanhusuo,C. turtschaninovii and C. decumbens,respectively. The method established in this study had a minimum detection limit of 6 ng for C. yanhusuo,60 ng for C. decumbens and less than 0. 6 ng for C. turtschaninovii. Thus,the allelespecific PCR method established in the research can specifically identify C. yanhusuo,C. turtschaninovii,and C. decumbens.

Cloning and expression analysis of calmodulin gene from Pinellia ternate / 中国中药杂志

According to the data of Pinellia ternate transcriptome,two calmodulin genes were cloned and named as Pt Ca M1 and PtCa M2 respectively. The results of bioinformatics analysis showed that Pt Ca Ms genes contained a 450 bp open reading frame,encoding149 amino acids.The identity of the coding sequences was 80%,and the identity of amino acids sequence was 91%. Pt Ca Ms genes contained EF-hand structure domain,belonging to the Ca M families. The Real-time PCR analysed the expression patterns of Pt Ca Ms in different tissues and different treatments. RESULTS:: showed that Pt Ca M1 and Pt Ca M2 gene were the highest expression level in tuber. Under Ca Cl2 treatment,the expressions of Pt Ca Ms were significantly higher than the control. Under EGTA,La Cl3 and TFP treatments,the expression level of Pt Ca Ms decreased gradually. In this study,the Pt Ca Ms gene were successfully cloned from P. ternate,which laid a foundation for the functional characteristic of Pt Ca Ms gene and the synthesis of alkaloids from P. ternata for further study.

Molecular cloning and expression analysis of iridoid synthase genes from Rehmannia glutinosa / 中国中药杂志

Iridoid synthase( IS),the key enzyme in the natural biosynthesis of vegetal iridoids,catalyzes the irreversible cyclization of 10-oxogeranial to epi-iridodial. In this study,we screened the Rehmannia glutinosa transcriptome data by BLASTn with Catharanthus roseus CrIS cDNA,and found four c DNA fragments with length of 1 527,1 743,1 425,1 718 bp,named RgIS1,RgIS2,RgIS3 and RgIS4,respectively. Bioinformatics analysis revealed that the four iridoid synthase genes encoding proteins with 389-392 amino acid residues,protein molecular weights were between 44. 30-44. 74 k Da,and theoretical isoelectric points were between 5. 30 and 5. 87. Subcellular localization predictions showed that the four iridoid synthase were distributed in the cytoplasm. Structure analysis revealed that R. glutinosa iridoid synthases contain six conserved short-chain dehydrogenase/reductase( SDR) motifs,and their 3 D models were composed typical dinucleotide-binding " Rossmann" folds covered by helical C-terminal extensions. Using the amino acid sequences of four R. glutinosa iridoid synthases,phylogenetic analysis was performed,the result indicated that RgIS3,CrIS and Olea europaea OeIS were grouped together,the other R. glutinosa iridoid synthases and fifteen proteins in other plants had close relationship. Real-time fluorescent quantitative PCR revealed that RgIS1 and RgIS3 highly expressed in unfold leaves,however,RgIS2 and RgIS4 highly expressed in stems and tuberous roots,respectively. RgIS3 showed higher expression levels in non-radial striations( nRS) of the two cultivars,and RgIS1 and RgIS2 had higher expression levels in nRS of QH,while RgIS4 had less expression levels in nRS of QH1. RgIS1,RgIS2 and RgIS3 were up-regulated by Me JA treatment,although the time and degree of response differed. Our findings are helpful to reveal molecular function of R. glutinosa iridoid synthases and provide a clue for studing the molecular mechanism of iridoid biosynthesis.