66 results about "Functional genomics" patented technology

The invention discloses a panax notoginseng MYB transcription factor gene PnMYB8, the nucleotide sequence of the gene PnMYB8 is as shown in SEQ ID NO: 1, an MYB transcription factor is encoded, molecular biology and functional genomics related technologies prove that the PnMYB8 gene has the capability of improving fungal infection resistance of plants, the PnMYB8 gene is constructed on a plant expression vector and transferred into tobacco for overexpression, and the yield of the panax notoginseng MYB transcription factor gene PnMYB8 is improved. Experimental results show that the resistance of the transgenic tobacco overexpressed with the PnMYB8 to the tryptophan destructor (Cylindrocarpon destructor), the fusarium latericum (Fusarium latericum), the fusarium equiseti (Fusarium equiseti) and the phoma herbarum (Phoma herbarum) is obviously enhanced, and the resistance of the transgenic tobacco overexpressed with the PnMYB8 to the tryptophan destructor (Fusarium latericum) is obviously enhanced.

The invention discloses application of a wheat gene TaGAMYB-like in improvement of plant salt tolerance, and belongs to the technical field of functional genomics. Wherein the nucleotide sequence of the wheat gene TaGAMYB-like is as shown in SEQ ID NO: 1, and the gene can improve the tolerance of plants to salt stress. The method has the beneficial effects that the wheat gene TaGAMYB-like is transformed into the model plant arabidopsis thaliana, the salt tolerance of the arabidopsis thaliana can be obviously improved, if the wheat gene TaGAMYB-like is transformed into plants such as wheat, rice, corn and cauliflower, new germplasm with the salt tolerance characteristic can be possibly obtained, and the new germplasm can be used as a new germplasm of the arabidopsis thaliana. The method is of great significance to cultivation of new varieties of excellent crops and wide application of the new varieties of the excellent crops in production.

The invention discloses a pseudo-ginseng bHLH transcription factor gene PnbHLH2, the nucleotide sequence of the pseudo-ginseng bHLH transcription factor gene PnbHLH2 is as shown in SEQ ID NO: 1, a bHLH transcription factor is encoded, molecular biology and functional genomics related technologies prove that the PnbHLH2 gene has the capability of improving fungal infection resistance of plants, the PnbHLH2 gene is constructed on a plant expression vector and transferred into tobacco for overexpression, and the yield of the pseudo-ginseng bHLH transcription factor gene PnbHLH2 is improved. Experimental results show that the resistance of the transgenic tobacco overexpressed with the PnbHLH2 to fusarium latericum, fusarium moniliforme, humicola fucoatra and cylindrocarpon destructor is obviously enhanced, and the resistance of the transgenic tobacco overexpressed with the PnbHLH2 to the fusarium latericum, the fusarium moniliforme, the humicola fucoatra and the cylindrocarpon destructor is obviously enhanced. The transgenic tobacco overexpressed with the PnbHLH2 has the advantages that the resistance of the transgenic tobacco overexpressed with the PnbHLH2 to the fusarium latericum, the fusarium moniliforme, the fusarium moniliforme and the cylindrocarpon destructor is obviously improved;

The invention relates to a construction method and application of a plant intra-genus generic transcriptome, and the method is realized by the following steps: obtaining second and third generation transcriptome data of different species in a genus and performing quality control, comparing a reference genome by using software such as HISAT2 and the like, and screening effective transcripts through gffcomplex after StringTie splicing; transcripts and genes are classified based on the ORF length (mRNA is greater than or equal to 100 aa, small peptide transcripts are from 10 aa to 99 aa, and ncRNA is smaller than 10 aa); the method comprises the following steps: analyzing sequence conservative properties among species through coding genes and non-coding genes, and dividing the genes into core, optional and specific types; and finally integrating and constructing a genus-level generic transcriptome containing three types of transcriptomes. According to the invention, the system construction of the plant intra-genus cross-species pan transcriptome is realized for the first time, the conservative property and difference of protein coding genes, small peptides and non-coding RNA can be analyzed, and a new tool is provided for the research of plant functional genomes.

The invention relates to an application of a FaPDHE1alpha gene or an encoding protein thereof in prevention and control of strawberry gray mold, and belongs to the field of plant genetic engineering and the field of prevention and control of postharvest diseases of fruits and vegetables. The invention discloses a key positive regulation and control effect of FaPDHE1alpha in regulation and control of strawberry gray mold resistance. By constructing a 35S:: FaPDHE1alpha overexpression vector and a FaPDHE1alpha RNAi interference vector, according to transient gene overexpression and RNA interference silencing tests, it is verified that high expression of the FaPDHE1alpha gene can obviously enhance the resistance of strawberry fruits to botrytis cinerea, and silencing of the gene causes reduction of the disease resistance of the fruits. Mechanism studies show that after the FaPDHE1alpha gene is activated, mitochondrial energy metabolism and controlled ROS signal generation are promoted, antioxidant enzyme activity is enhanced, and defense related gene expression is induced, so that the disease resistance of fruits is improved. By means of functional genomics, the key function of the FaPDHE1alpha gene in prevention and control of gray mold after strawberry harvest is illuminated for the first time, and the FaPDHE1alpha gene can be used for screening disease-resistant breeding materials or developing biological prevention and control preparations for postharvest diseases and has important application value.

The invention discloses application of a wheat gene TaPHR1 in improvement of plant salt tolerance, and belongs to the technical field of functional genomics. Wherein the nucleotide sequence of the wheat gene TaPHR1 is as shown in SEQ ID NO: 2, the tolerance of a plant to salt stress can be improved through overexpression of the gene, and the plant is wheat or arabidopsis thaliana. The wheat gene TaPHR1 has the beneficial effects that the wheat gene TaPHR1 is transformed into a model plant arabidopsis thaliana, so that the salt tolerance of the arabidopsis thaliana can be obviously improved, if the wheat gene TaPHR1 is transformed into plants such as wheat, rice, corn and cauliflower, new germplasm with salt tolerance can be possibly obtained, and the new germplasm can be used as a new germplasm. The method is of great significance to cultivation of new varieties of excellent crops and wide application of the new varieties of the excellent crops in production.

The invention discloses a plant gene function analysis method (FAGEN), and belongs to the technical field of molecular genetics and functional genomics. The method comprises the following steps: constructing a target gene mutant by using a gene editing technology; hybridizing the mutant and the corresponding wild type as a common parent with a plurality of parents with different genetic backgrounds to construct a pair F1 group; an F2 group is obtained through selfing; and determining phenotypic data of target characters of F1 and F2 populations, and comparing phenotypic differences of filial generations of wild types and mutants under different genetic backgrounds to judge the functions of the target genes. The method has the advantages of simplicity in operation, flexibility in design, short construction period and low cost, and gene functions can be efficiently and accurately analyzed under various genetic backgrounds.

This invention discloses the application of the wheat gene TaPSS2 in improving plant drought resistance, belonging to the field of functional genomics. The nucleotide sequence of the wheat gene TaPSS2 is shown in SEQ ID NO: 2. Transforming this gene into the model plant Arabidopsis thaliana can significantly improve the drought resistance of Arabidopsis. If the wheat gene TaPSS2 is transformed into wheat, rice, maize, cauliflower, and other plants, it is possible to obtain new germplasm with drought-resistant characteristics, which is of great significance for the breeding of superior crop varieties and their widespread application in production.

This invention discloses a method for efficient genetic transformation of rice that overcomes genotype dependence and a dedicated culture medium, relating to the field of biotechnology. The dedicated culture medium comprises KCl, KH₂PO₄, MgSO₄·7H₂O, CaCl₂·2H₂O, disodium ethylenediaminetetraacetate, FeSO₄·7H₂O, MnSO₄·H₂O, ZnSO₄·7H₂O, H₃BO₃, KI, CoCl₂·6H₂O, CuSO₄·5H₂O, Na₂MoO₄·2H₂O, glutamine, aspartic acid, arginine, glycine, cyclohexanehexyl alcohol, thiamine hydrochloride, pyridoxine hydrochloride, nicotinic acid, and a carbon source. Using this dedicated culture medium can increase the number of rice cells containing the NiR gene. 375 S 453 The genetic transformation efficiency of haplotype rice varieties is of great significance for overcoming the bottleneck of rice genotype dependence, promoting functional genomics research and molecular breeding.

The invention relates to the technical field of biology, in particular to application of an RhUNE10 gene to regulation and control of root cancer resistance of Chinese roses and a regulation and control method. The nucleotide sequence of the RhUNE10 gene is as shown in SEQ ID NO. 1. The application mode is that the RhUNE10 gene is silenced and knocked out, or the expression of the protein coded by the RhUNE10 gene is inhibited; and the amino acid sequence of the protein coded by the RhUNE10 gene is as shown in SEQ ID NO. 3. After the RhUNE10 gene is silenced, the resistance of the Chinese rose to agrobacterium tumefaciens is remarkably reduced, which indicates that the RhUNE10 gene has important biological functions, is beneficial to promoting Chinese rose functional genomics research, gene editing breeding and transgenic breeding research, excavates and cultivates new varieties of high-resistance Chinese roses, and has wide application prospects. And a certain theoretical basis and key gene resources are provided for comprehensive prevention and treatment of root cancer and cultivation of a new variety of Chinese rose.

The invention relates to a bombyx mori RNA m6A methylation modification system and application thereof, and belongs to the technical field of biology. The invention aims to construct a bombyx mori RNA m6A methylation modification system aiming at the technical bottleneck that the existing CRISPR-dCas9 technology is lack of an insect RNA epigenetic regulation tool, and the system comprises pdCas9-BmMETTL3amp, pdCas9-BmMETTL3amp, pdCas9-BmMETTL3amp, and double plasmids of BmMETTL14-EGFP (Enhanced Green Fluorescent Protein) and pU6-gRNA ( The bombyx mori RNA m6A methylation modification system is fused with two proteins with catalytic enzyme activity, and comprises a BmMETTL3 gene catalytic structural domain sequence and a BmMETTL14 gene catalytic structural domain sequence. The bombyx mori BmPSB1 and BmHSC70 gene RNA is subjected to targeted modification through the system, the RNA m6A methylation modification level of a target gene is changed, the expression level of the target gene is further regulated and controlled, and finally the purpose of functional research on the target gene is achieved. The method is used for bombyx mori gene expression regulation and epigenetic research, and a new strategy is provided for bombyx mori functional genome research.

The present invention generally relates to compositions, methods applications and screens used in functional genomics that focus on gene function in a cell and that may use vector systems and other aspects related to Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas systems and components thereof. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for utilizing the CRISPR-Cas system.

The invention discloses a bombyx mori protein function prediction multi-modal fusion method based on a deep residual network, and the method comprises the steps: collecting the sequences and high-resolution three-dimensional structure data of bombyx mori proteins of different varieties and at different development stages from databases of bombyx mori genomes, protein crystal structures and the like by employing a data crawling and interface calling technology; and constructing a multi-modal data source. The sequence data are cleaned and coded in a one-hot mode, and the structural data are optimized and converted into a graph structure. Sequence and structure features are respectively extracted through a convolutional neural network and a GraphSAGE graph neural network, and the features are dynamically fused through an adaptive weight fusion strategy. And building a deep residual network training model, and realizing accurate prediction of the protein function category and confidence of the bombyx mori with unknown functions. According to the method, the precision and the high robustness of silkworm protein function prediction are improved through full-process technical optimization, and an efficient tool is provided for silkworm molecular breeding and functional genomics research.

The application discloses a chrysanthemum constitutive high-expression promoter and application thereof in gene editing. The nucleotide sequence of the promoter CmUbi is shown as SEQ ID NO. 4. Through double luciferase reporter experiments and stable genetic transformation experiments, it is proved that the expression activity of the CmUbi promoter in chrysanthemum protoplast and callus is significantly higher than that of commonly used CaMV 35S, AtRPS5a and corn ZmUbi promoters. A CRISPR / Cas9 gene editing vector is constructed by using the promoter, and a key gene of branch of hexaploid chrysanthemum is edited BRC1b , and a plurality of allele simultaneous mutation complete editing strains are successfully obtained, and the number of branches of the mutants is significantly increased. The endogenous high-activity promoter of the chrysanthemum provided by the application effectively solves the problems of low expression activity of an existing heterologous promoter in the chrysanthemum and poor gene editing efficiency of a polyploid, and provides an efficient and adaptive expression regulation element for chrysanthemum molecular breeding and functional genomics research.

The invention provides a method and system for gene expression quantitative trait locus analysis, and relates to the technical field of genomics, the method comprises the following steps: carrying out sample and locus level quality control on input genotype data, and generating a standardized genotype matrix; performing standardization processing and low expression gene filtering on the input gene expression data to generate a standardized expression quantity matrix; performing principal component analysis according to the standardized genotype matrix to obtain a group structure covariable; carrying out implicit factor analysis on the basis of the standardized expression quantity matrix to obtain a technical batch effect covariable; quantitative character site correlation analysis is carried out through a standardized genotype matrix, a standardized expression quantity matrix, a population structure covariable and a technical batch effect covariable. The method is suitable for functional genomics research, complex disease genetic mechanism analysis and precision medical related functional genetic variation mining scenes.

The invention discloses a genetic transformation method based on pear somatic embryogenesis, and belongs to the technical field of genetic engineering and molecular breeding. In order to solve the problems that existing pear genetic transformation is low in transformation efficiency, high in chimera rate, long in period, difficult to obtain gene editing regeneration plants and the like, the invention provides two paths: 1, immature zygotic embryos 30-60 days after pear flowering are taken as explants, resistant plants are directly induced through a somatic embryo regeneration path, and the transformation efficiency within 40-60 days reaches 73.91%; secondly, the embryogenic callus with the consistent genetic background is used as an explant for infection, the embryogenic property is maintained and the proliferation efficiency is improved by optimizing a culture medium formula, and a resistant plant with the consistent genetic background can be obtained within 30-50 days. The method overcomes the defect that regeneration plants are difficult to obtain through existing callus transformation, remarkably shortens the breeding period, is high in transformation efficiency, low in chimera rate and controllable in genetic background consistency, and provides technical support for pear functional genomics research and molecular breeding.

The invention relates to the technical field of agriculture, in particular to an efficient ABE base editing tool based on Cas12i3 and application of the efficient ABE base editing tool. The Cas12i3-based efficient ABE base editing tool provided by the invention comprises a protein expression cassette and an RNA (Ribonucleic Acid) expression cassette, the protein expression cassette comprises a promoter, a 2 * BP NLS nuclear localization signal fragment, a 2 * adenine deaminase TadA8e, a connecting peptide, a Cas12i3 notch enzyme fragment and a terminator, the RNA expression cassette comprises a promoter, a crRNA sequence and a terminator; wherein the crRNA sequence is composed of a DR sequence and a target specific spacer sequence. The tool realizes efficient and specific single base substitution of A-to-G in a rice genome by utilizing the targeted binding characteristic of Cas12i3 and the efficient deamination activity of 2 * TadA8e, has the advantages of high editing efficiency, low off-target rate, wide application range and the like, provides an efficient and accurate technical means for plant functional genome research and molecular breeding, and has a wide application prospect. The creation of excellent rice varieties can be accelerated.

Systems, methods, and apparatus for generating a DNA / gene sequence output, given a protein sequence input. In one aspect, the protein-to-DNA mapping system includes a protein language model (embedder) that generates a high-dimensional protein embedding from a low-dimensional protein sequence input; and the system includes a protein-to-DNA translator that processes the protein embedding and generates a DNA sequence output, based on the protein embedding. The protein-to-DNA translator is a neural network (e.g., a Seq2Seq model) and is configured with translation coefficients that may be trained with a training dataset, comprising the training protein and DNA embeddings. Training the translation coefficients can include supervised learning that maps the protein embedding (input) to a DNA sequence (target). The systems, methods, and apparatus may increase protein yield / expression, improve protein functionality, enhance gene therapy efficacy, streamline synthetic biology design, and / or broaden functional genomics studies, all leading to reduced costs, better performance, and increased accessibility.

Aspects of the technology relate to methods and compositions for multiplexed assessment of perturbations with single cell molecular resolution using a regulatable Cas enzyme with intrinsic RNase activity.

The invention relates to a method for rapidly carrying out BSA (Bovine Serum Albumin) gene localization by utilizing a space mutation mutant. The method comprises the following steps: firstly, carrying propagules such as seeds through an aerospace craft, and constructing a broad-spectrum mutant library by utilizing space environment mutagenesis; returning to the ground, culturing and screening M1-generation mutants with target excellent characters, and hybridizing / backcrossing with a wild type to construct a character segregation population; by adopting a group separation analysis (BSA) strategy, selecting phenotype polar differentiation individuals, and respectively mixing the phenotype polar differentiation individuals to form a high-value pool and a low-value pool; and finally, carrying out whole genome high-throughput sequencing on the double pools and the parents, rapidly locking a genome region linked with a target character by combining bioinformatics analysis such as SNP-index and the like, and verifying candidate genes through gene annotation, molecular marking and gene editing. According to the invention, the broad spectrum of space mutagenesis and the high efficiency of the BSA-seq technology are integrated, the period from mutation creation to gene identification is remarkably shortened, and an innovative technical scheme is provided for crop genetic improvement and functional genomics research.

The present invention provides high-content and high-resolution in vivo screens for analyzing functions of a plurality of genes. In the functional screens of the invention, genetic perturbations are delivered to a CRISPR-expressing transgenic system by specific AAV vectors that are fully compatible with Perturb-seq platforms. The screens enable functional genomics analyses across diverse tissues, cell types, and model organisms in vivo, with high-throughput single-cell readout.

The application discloses a panax notoginseng transcription factor gene PnHY5 and application thereof in improving total saponin content and monomer saponin content of panax notoginseng cells, wherein the nucleotide sequence of the PnHY5 gene is shown as SEQ ID NO:1; the application proves that the panax notoginseng PnHY5 transcription factor has a function of positively regulating panax notoginseng saponin biosynthesis by using functional genomics and metabolic engineering related technologies; the panax notoginseng PnHY5 transcription factor gene is constructed on a plant expression vector and is transferred into panax notoginseng cells to make the panax notoginseng PnHY5 transcription factor gene overexpress, so that the expression amount of a key enzyme gene of a panax notoginseng saponin synthesis pathway is improved, and the biosynthesis of panax notoginseng total saponins is promoted.

The invention discloses a CYP2C9 enzyme drug metabolism function prediction method based on transfer learning and application, and belongs to the field of functional genomics, the method comprises the following steps: firstly, generating a source domain data set and a target domain data set containing CYP2C9 gene variation information; then constructing a convolutional neural network model, and inputting the source domain data set into the model for training; utilizing a transfer learning algorithm to transfer the trained model weight to a convolutional neural network model for the target domain data set for further training, and obtaining model parameters of training optimization; and finally, inputting CYP2C9 gene variation information into the trained model, and predicting the CYP2C9 enzyme drug metabolism function. According to the method, data enhancement, a residual network and a channel attention mechanism are combined, the limitation that manual interpretation of the drug metabolism type is carried out only according to known single or double-site mutation of the CYP2C9 gene in a traditional method is broken through, artificial intelligent interpretation and prediction of the drug metabolism type are carried out on mutation of a plurality of sites and even whole-gene sequences of the CYP2C9 gene, and the drug metabolism type of the CYP2C9 gene is determined. And clinical precise medication is guided.

The invention discloses application of a kelp endogenous promoter in kelp breeding and cultivation and a method, and relates to the technical field of biology. The invention provides a kelp endogenous promoter. The sequence of the kelp endogenous promoter is selected from one of the following sequences: (1) an amino acid sequence as shown in any one of SEQ ID NO: 1-3; (2) a sequence obtained by substituting, deleting or adding one or more nucleotides to the sequence shown in any one of SEQ ID NO: 1 to SEQ ID NO: 3; and (3) a sequence having 80% homology with the sequence as shown in SEQ ID NO: 1-3. The promoter can drive gene specific expression or main expression in a kelp gametophyte, can realize effective expression of a GUS reporter gene in transgenic kelp, and promotes development of kelp genetic engineering and functional genomics research.

The invention belongs to the technical field of forest tree gene engineering, and particularly relates to a construction method of an agate red cherry seedling PDS gene virus-induced gene silencing (VIGS) system based on agrobacterium tumefaciens mediation. According to the method, a recombinant virus vector containing a PDS gene specific fragment as shown in SEQ ID NO.1 is constructed, the recombinant virus vector is introduced into an agate red cherry leaf tissue by utilizing an agrobacterium infection technology, and efficient silencing of a target gene is successfully realized. As a first VIGS technical platform established in the woody fruit tree agate red cherry, the system can visually verify the gene function by inducing the typical albino phenotype of the plant leaf of the agate red seedling, and breaks through the technical bottlenecks of long period and low efficiency of the traditional woody plant gene function research. The achievement fills the blank of a woody fruit tree VIGS technical system, provides a traceable research tool for analyzing a molecular mechanism formed by key traits of the agate red cherries, and has milestone significance for promoting functional genomics research of rosaceae fruit trees.

This invention discloses a Panax notoginseng MYB transcription factor gene. PnMYB34 Its nucleotide sequence is as described in SEQ ID NO:1, encoding the MYB transcription factor. This invention confirms through molecular biology and functional genomics related technologies. PnMYB34 The gene has the ability to enhance the plant's resistance to viral infection, and the present invention will... PnMYB34 Genes were constructed into plant expression vectors and overexpressed in Panax notoginseng and tobacco, respectively. Experimental results showed that overexpression... PnMYB34 Genetically modified Panax notoginseng against Panax notoginseng A virus (GMO) Panax notoginseng virus A The resistance to ) was significantly enhanced, and overexpression PnMYB34 Genetically modified tobacco is susceptible to tobacco mosaic virus (BMP). Tobacco mosaic virus Its resistance was also significantly enhanced.

This invention belongs to the fields of microbiology and molecular biology, specifically relating to a homologous recombinase combination in myxobacteria and its application in gene editing. Specifically, this invention provides four pairs of homologous recombinase systems capable of efficiently mediating in vivo recombination in myxobacteria. Each pair includes a protein YqaJ with exonuclease function and a protein RecT with single-strand annealing function. This invention provides a method for myxobacterial gene editing: under the action of homologous recombinase pairs, mutant strains are obtained through positive screening using resistance tags. The resistance tags are then successfully removed through the combined action of the Cre / loxP system and the reverse screening gene galK. This method achieves a gene editing efficiency of up to 100%, has a short cycle time, requires no purification, and can be used for iterative deletion of multiple genes to achieve genome simplification in myxobacteria, or for inserting functional promoters and other elements to activate silent gene clusters. This method is of great significance for the bioexploration and functional genomics research of myxobacteria.

The application discloses application of a wheat gene TaSNAC11 in improving plant salt tolerance, and belongs to the technical field of functional genomics. The nucleotide sequence of the wheat gene TaSNAC11 is shown in SEQ ID NO:2, and the gene can improve the salt stress tolerance of plants. The application has the advantages that the wheat gene TaSNAC11 is transformed into a model plant Arabidopsis thaliana, and the salt tolerance of the Arabidopsis thaliana can be obviously improved. If the wheat gene TaSNAC11 is transformed into plants such as wheat, rice, corn and cauliflower, new germplasm with salt tolerance characteristics can be obtained, and the application has important significance for cultivation of excellent crop new varieties and wide application of the excellent crop new varieties in production.

A species feature descriptor construction method based on functional genomics is beneficial to providing a new method for toxicity prediction and risk assessment modeling of chemicals to multiple species, and is characterized by comprising the following steps: step 1, collecting proteome data of a target species; 2, deploying a software tool for extracting the functional gene information of the species on a cloud server, and developing a command line tool for the software tool to realize gene annotation of multiple species and uploading and downloading of data; 3, importing the proteome data into the tool software for query, matching and annotation to obtain functional genome information of the target species; step 4, preprocessing and visualizing the annotated functional genome information; and step 5, constructing species feature descriptors of multiple species based on the functional genome information.

The present invention discloses a Panax notoginseng sterol C-22 desaturase gene PnCYP710A and its applications, PnCYP710A The nucleotide sequence of the gene is shown in SEQ ID NO: 1, encoding a sterol C-22 desaturase of the plant cytochrome P450 monooxygenase family. The invention has been confirmed by functional genomics related technology research. PnCYP710A The gene has the function of improving the resistance of plants to fungal infection. PnCYP710A The gene was constructed into a plant expression vector and transferred into tobacco for expression. PnCYP710A The resistance of transgenic tobacco to Fusarium solani and Curvularia solani was significantly improved.